{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Multi-stage\" and technology = \"bulk\"", "rows": [[25182, "SRR25670729", "SRX21396042", "SRS18636200", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA germ ring PAL seq v4", "GSM7716871", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA germ ring PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716871", "GSM7716871: Fish embryo mRNA germ ring PAL seq v4; Danio rerio; OTHER", "GSM7716871 r1", "GSM7716871", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep1_raw_read2.fastq.gz Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep1_raw_read1.fastq.gz", "fastq fastq", 2834842912.0, 9234016.0, "GSM7716871 r1", "0:52 1:255", "A:725811118;C:702410592;G:747583409;T:651018348;N:8019445", 52, 255, null, null, 725811118, 702410592, 747583409, 651018348, 8019445, "SRX21396042", "SRS18636200", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00023, 0.30494, 8e-05, 0.01793, 0.99967, 0.99971, 0.5, 1.0, 52, 255, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25183, "SRR25670730", "SRX21396042", "SRS18636200", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA germ ring PAL seq v4", "GSM7716871", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA germ ring PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716871", "GSM7716871: Fish embryo mRNA germ ring PAL seq v4; Danio rerio; OTHER", "GSM7716871 r1", "GSM7716871", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep2_raw_read2.fastq.gz", "fastq fastq", 3473033898.0, 11312814.0, "GSM7716871 r2", "0:52 1:255", "A:853178471;C:899976159;G:962100712;T:750811461;N:6967095", 52, 255, null, null, 853178471, 899976159, 962100712, 750811461, 6967095, "SRX21396042", "SRS18636200", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00049, 0.0, 0.00012, 0.0, 0.99941, 1.0, 0.64864, null, 52, 255, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25184, "SRR25670731", "SRX21396041", "SRS18636199", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA zfs:0000015 PAL seq v4", "GSM7716870", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA zfs:0000015 PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716870", "GSM7716870: Fish embryo mRNA zfs:0000015 PAL seq v4; Danio rerio; OTHER", "GSM7716870 r1", "GSM7716870", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep1_raw_read2.fastq.gz", "fastq fastq", 2695203962.0, 8779166.0, "GSM7716870 r1", "0:52 1:255", "A:684535386;C:669852151;G:719008886;T:614209811;N:7597728", 52, 255, null, null, 684535386, 669852151, 719008886, 614209811, 7597728, "SRX21396041", "SRS18636199", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00117, 0.35837, 0.00017, 0.00682, 0.99859, 0.99963, 0.69473, 1.0, 52, 255, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25185, "SRR25670732", "SRX21396041", "SRS18636199", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA zfs:0000015 PAL seq v4", "GSM7716870", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA zfs:0000015 PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716870", "GSM7716870: Fish embryo mRNA zfs:0000015 PAL seq v4; Danio rerio; OTHER", "GSM7716870 r1", "GSM7716870", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep2_raw_read2.fastq.gz Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep2_raw_read1.fastq.gz", "fastq fastq", 3476338446.0, 11323578.0, "GSM7716870 r2", "0:52 1:255", "A:841832234;C:898325199;G:968774318;T:760398070;N:7008625", 52, 255, null, null, 841832234, 898325199, 968774318, 760398070, 7008625, "SRX21396041", "SRS18636199", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00245, 0.0, 0.00047, 0.0, 0.99803, 1.0, 0.58536, null, 52, 255, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25186, "SRR25670733", "SRX21396040", "SRS18636198", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA sphere PAL seq v4", "GSM7716869", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA sphere PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716869", "GSM7716869: Fish embryo mRNA sphere PAL seq v4; Danio rerio; OTHER", "GSM7716869 r1", "GSM7716869", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_sphere_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_sphere_PAL_seq_v4_rep1_raw_read2.fastq.gz", "fastq fastq", 3211687254.0, 10461522.0, "GSM7716869 r1", "0:52 1:255", "A:813560400;C:775326762;G:854563477;T:759161458;N:9075157", 52, 255, null, null, 813560400, 775326762, 854563477, 759161458, 9075157, "SRX21396040", "SRS18636198", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00088, 0.43191, 0.0004, 0.01556, 0.99916, 0.99961, 0.55769, 1.0, 52, 255, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25187, "SRR25670734", "SRX21396040", "SRS18636198", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA sphere PAL seq v4", "GSM7716869", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA sphere PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716869", "GSM7716869: Fish embryo mRNA sphere PAL seq v4; Danio rerio; OTHER", "GSM7716869 r1", "GSM7716869", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_sphere_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_sphere_PAL_seq_v4_rep2_raw_read2.fastq.gz", "fastq fastq", 3179916131.0, 10358033.0, "GSM7716869 r2", "0:52 1:255", "A:771755667;C:804256300;G:883166175;T:714242073;N:6495916", 52, 255, null, null, 771755667, 804256300, 883166175, 714242073, 6495916, "SRX21396040", "SRS18636198", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00186, 0.0, 0.00088, 0.0, 0.99862, 1.0, 0.64705, null, 52, 255, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25190, "SRR25670737", "SRX21396038", "SRS18636196", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA 128cell PAL seq v4", "GSM7716867", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA 128cell PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716867", "GSM7716867: Fish embryo mRNA 128cell PAL seq v4; Danio rerio; OTHER", "GSM7716867 r1", "GSM7716867", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_128cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_128cell_PAL_seq_v4_rep1_raw_read2.fastq.gz", "fastq fastq", 2104868443.0, 6856249.0, "GSM7716867 r1", "0:52 1:255", "A:539122676;C:505234642;G:558793048;T:495876292;N:5841785", 52, 255, null, null, 539122676, 505234642, 558793048, 495876292, 5841785, "SRX21396038", "SRS18636196", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00035, 0.29379, 7e-05, 0.01129, 0.99949, 0.99971, 0.55882, 0.79591, 52, 255, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25191, "SRR25670738", "SRX21396038", "SRS18636196", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA 128cell PAL seq v4", "GSM7716867", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA 128cell PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716867", "GSM7716867: Fish embryo mRNA 128cell PAL seq v4; Danio rerio; OTHER", "GSM7716867 r1", "GSM7716867", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_128cell_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_128cell_PAL_seq_v4_rep2_raw_read2.fastq.gz", "fastq fastq", 3135806371.0, 10214353.0, "GSM7716867 r2", "0:52 1:255", "A:776612486;C:774126305;G:853951502;T:724788612;N:6327466", 52, 255, null, null, 776612486, 774126305, 853951502, 724788612, 6327466, "SRX21396038", "SRS18636196", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00066, 0.0, 0.00011, 0.0, 0.99939, 1.0, 0.55737, null, 52, 255, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25192, "SRR25670739", "SRX21396037", "SRS18636195", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA 8cell PAL seq v4", "GSM7716866", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA 8cell PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716866", "GSM7716866: Fish embryo mRNA 8cell PAL seq v4; Danio rerio; OTHER", "GSM7716866 r1", "GSM7716866", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_8cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_8cell_PAL_seq_v4_rep1_raw_read2.fastq.gz", "fastq fastq", 2618998887.0, 8530941.0, "GSM7716866 r1", "0:52 1:255", "A:673066508;C:641446717;G:706546263;T:590452494;N:7486905", 52, 255, null, null, 673066508, 641446717, 706546263, 590452494, 7486905, "SRX21396037", "SRS18636195", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.0009, 0.43244, 0.00014, 0.0054, 0.99902, 0.99967, 0.54901, 1.0, 52, 255, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25193, "SRR25670740", "SRX21396037", "SRS18636195", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA 8cell PAL seq v4", "GSM7716866", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA 8cell PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716866", "GSM7716866: Fish embryo mRNA 8cell PAL seq v4; Danio rerio; OTHER", "GSM7716866 r1", "GSM7716866", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_8cell_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_8cell_PAL_seq_v4_rep2_raw_read2.fastq.gz", "fastq fastq", 3028839589.0, 9865927.0, "GSM7716866 r2", "0:52 1:255", "A:756368817;C:758868409;G:836949742;T:670545278;N:6107343", 52, 255, null, null, 756368817, 758868409, 836949742, 670545278, 6107343, "SRX21396037", "SRS18636195", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00156, 0.0, 0.00026, 0.0, 0.99835, 1.0, 0.44791, null, 52, 255, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30755, "SRR28348921", "SRX23954975", "SRS20755396", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage IV  rep2", "GSM8147872", null, "source name:Oocyte|tissue:Oocyte|developmental stage:Stage IV|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Oocyte  Stage IV  rep2", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Oocyte", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Oocyte|developmental stage:Stage IV|genotype:AB  TF and TLF", "GSM8147872", "GSM8147872: Zebrafish Oocyte  Stage IV  rep2; Danio rerio; RNA Seq", "GSM8147872 r1", "GSM8147872", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "Z_oocyte_stage_4_2_Pa.fastq", "fastq", 2456514332.0, 32322557.0, "GSM8147872 r1", "0:76", "A:588246161;C:609187233;G:593122683;T:665837765;N:120490", 76, null, null, null, 588246161, 609187233, 593122683, 665837765, 120490, "SRX23954975", "SRS20755396", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [30756, "SRR28348922", "SRX23954974", "SRS20755395", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage IV  rep1", "GSM8147871", null, "source name:Oocyte|tissue:Oocyte|developmental stage:Stage IV|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Oocyte  Stage IV  rep1", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Oocyte", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Oocyte|developmental stage:Stage IV|genotype:AB  TF and TLF", "GSM8147871", "GSM8147871: Zebrafish Oocyte  Stage IV  rep1; Danio rerio; RNA Seq", "GSM8147871 r1", "GSM8147871", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "Z_oocyte_stage_4_1_Pa.fastq", "fastq", 2650784696.0, 34878746.0, "GSM8147871 r1", "0:76", "A:649971632;C:640667370;G:632570967;T:727447552;N:127175", 76, null, null, null, 649971632, 640667370, 632570967, 727447552, 127175, "SRX23954974", "SRS20755395", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [30757, "SRR28348923", "SRX23954973", "SRS20755394", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage III  rep2", "GSM8147870", null, "source name:Oocyte|tissue:Oocyte|developmental stage:Stage III|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Oocyte  Stage III  rep2", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Oocyte", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Oocyte|developmental stage:Stage III|genotype:AB  TF and TLF", "GSM8147870", "GSM8147870: Zebrafish Oocyte  Stage III  rep2; Danio rerio; RNA Seq", "GSM8147870 r1", "GSM8147870", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "Z_oocyte_stage_3_2_Pa.fastq", "fastq", 2809957956.0, 36973131.0, "GSM8147870 r1", "0:76", "A:679041537;C:690924547;G:702857353;T:736996218;N:138301", 76, null, null, null, 679041537, 690924547, 702857353, 736996218, 138301, "SRX23954973", "SRS20755394", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [30758, "SRR28348924", "SRX23954972", "SRS20755393", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage III  rep1", "GSM8147869", null, "source name:Oocyte|tissue:Oocyte|developmental stage:Stage III|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Oocyte  Stage III  rep1", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Oocyte", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Oocyte|developmental stage:Stage III|genotype:AB  TF and TLF", "GSM8147869", "GSM8147869: Zebrafish Oocyte  Stage III  rep1; Danio rerio; RNA Seq", "GSM8147869 r1", "GSM8147869", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "Z_oocyte_stage_3_1_Pa.fastq", "fastq", 2828372376.0, 37215426.0, "GSM8147869 r1", "0:76", "A:701751055;C:680571938;G:664212213;T:781698241;N:138929", 76, null, null, null, 701751055, 680571938, 664212213, 781698241, 138929, "SRX23954972", "SRS20755393", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [30759, "SRR28348925", "SRX23954971", "SRS20755392", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage II  rep2", "GSM8147868", null, "source name:Oocyte|tissue:Oocyte|developmental stage:Stage II|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Oocyte  Stage II  rep2", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Oocyte", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Oocyte|developmental stage:Stage II|genotype:AB  TF and TLF", "GSM8147868", "GSM8147868: Zebrafish Oocyte  Stage II  rep2; Danio rerio; RNA Seq", "GSM8147868 r1", "GSM8147868", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "Z_oocyte_stage_2_2_Pa.fastq", "fastq", 2837652432.0, 37337532.0, "GSM8147868 r1", "0:76", "A:698931608;C:681467909;G:683751172;T:773364392;N:137351", 76, null, null, null, 698931608, 681467909, 683751172, 773364392, 137351, "SRX23954971", "SRS20755392", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [30760, "SRR28348926", "SRX23954970", "SRS20755391", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage II  rep1", "GSM8147867", null, "source name:Oocyte|tissue:Oocyte|developmental stage:Stage II|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Oocyte  Stage II  rep1", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Oocyte", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Oocyte|developmental stage:Stage II|genotype:AB  TF and TLF", "GSM8147867", "GSM8147867: Zebrafish Oocyte  Stage II  rep1; Danio rerio; RNA Seq", "GSM8147867 r1", "GSM8147867", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "Z_oocyte_stage_2_1_Pa.fastq", "fastq", 3360126820.0, 44212195.0, "GSM8147867 r1", "0:76", "A:829333798;C:802089215;G:804982077;T:923557236;N:164494", 76, null, null, null, 829333798, 802089215, 804982077, 923557236, 164494, "SRX23954970", "SRS20755391", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [30761, "SRR28348927", "SRX23954969", "SRS20755390", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage I  rep2", "GSM8147866", null, "source name:Oocyte|tissue:Oocyte|developmental stage:Stage I|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Oocyte  Stage I  rep2", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Oocyte", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Oocyte|developmental stage:Stage I|genotype:AB  TF and TLF", "GSM8147866", "GSM8147866: Zebrafish Oocyte  Stage I  rep2; Danio rerio; RNA Seq", "GSM8147866 r1", "GSM8147866", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "Z_oocyte_stage_1_2_Pa.fastq", "fastq", 2739674220.0, 36048345.0, "GSM8147866 r1", "0:76", "A:653441701;C:681445567;G:663740568;T:740918288;N:128096", 76, null, null, null, 653441701, 681445567, 663740568, 740918288, 128096, "SRX23954969", "SRS20755390", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [30762, "SRR28348928", "SRX23954968", "SRS20755389", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage I  rep1", "GSM8147865", null, "source name:Oocyte|tissue:Oocyte|developmental stage:Stage I|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Oocyte  Stage I  rep1", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Oocyte", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Oocyte|developmental stage:Stage I|genotype:AB  TF and TLF", "GSM8147865", "GSM8147865: Zebrafish Oocyte  Stage I  rep1; Danio rerio; RNA Seq", "GSM8147865 r1", "GSM8147865", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "Z_oocyte_stage_1_1_Pa.fastq", "fastq", 3348831852.0, 44063577.0, "GSM8147865 r1", "0:76", "A:815134657;C:817210346;G:809175239;T:907149915;N:161695", 76, null, null, null, 815134657, 817210346, 809175239, 907149915, 161695, "SRX23954968", "SRS20755389", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [34206, "SRR31539731", "SRX26906755", "SRS23386341", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 7 dpf sox10 mutant embryos   biol rep 3", "GSM8655460", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:7 dpf|geo loc name:missing|collection date:missing", "Whole body 7 dpf sox10 mutant embryos   biol rep 3", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:7 dpf", "GSM8655460", "GSM8655460: Whole body 7 dpf sox10 mutant embryos   biol rep 3; Danio rerio; RNA Seq", "GSM8655460 r1", "GSM8655460", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "7 dpf_mut 3_R1.fastq.gz 7 dpf_mut 3_R2.fastq.gz", "fastq fastq", 14265929756.0, 47238178.0, "GSM8655460 r1", "0:151 1:151", "A:3890017873;C:3282588566;G:3079614796;T:4012518928;N:1189593", 151, 151, null, null, 3890017873, 3282588566, 3079614796, 4012518928, 1189593, "SRX26906755", "SRS23386341", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34207, "SRR31539732", "SRX26906754", "SRS23386340", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 7 dpf sox10 mutant embryos   biol rep 2", "GSM8655459", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:7 dpf|geo loc name:missing|collection date:missing", "Whole body 7 dpf sox10 mutant embryos   biol rep 2", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:7 dpf", "GSM8655459", "GSM8655459: Whole body 7 dpf sox10 mutant embryos   biol rep 2; Danio rerio; RNA Seq", "GSM8655459 r1", "GSM8655459", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "7 dpf_mut 2_R1.fastq.gz 7 dpf_mut 2_R2.fastq.gz", "fastq fastq", 16096968138.0, 53301219.0, "GSM8655459 r1", "0:151 1:151", "A:4158085994;C:3672102993;G:3915623401;T:4349806816;N:1348934", 151, 151, null, null, 4158085994, 3672102993, 3915623401, 4349806816, 1348934, "SRX26906754", "SRS23386340", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34208, "SRR31539733", "SRX26906753", "SRS23386339", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 7 dpf sox10 mutant embryos   biol rep 1", "GSM8655458", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:7 dpf|geo loc name:missing|collection date:missing", "Whole body 7 dpf sox10 mutant embryos   biol rep 1", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:7 dpf", "GSM8655458", "GSM8655458: Whole body 7 dpf sox10 mutant embryos   biol rep 1; Danio rerio; RNA Seq", "GSM8655458 r1", "GSM8655458", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "7 dpf_mut 1_R1.fastq.gz 7 dpf_mut 1_R2.fastq.gz", "fastq fastq", 15919165034.0, 52712467.0, "GSM8655458 r1", "0:151 1:151", "A:4153549187;C:3626188288;G:3782139805;T:4355972996;N:1314758", 151, 151, null, null, 4153549187, 3626188288, 3782139805, 4355972996, 1314758, "SRX26906753", "SRS23386339", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34209, "SRR31539734", "SRX26906752", "SRS23386338", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 7 dpf wild type embryos   biol rep 3", "GSM8655457", null, "source name:whole body|tissue:whole body|genotype:WT|time:7 dpf|geo loc name:missing|collection date:missing", "Whole body 7 dpf wild type embryos   biol rep 3", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:7 dpf", "GSM8655457", "GSM8655457: Whole body 7 dpf wild type embryos   biol rep 3; Danio rerio; RNA Seq", "GSM8655457 r1", "GSM8655457", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "7 dpf_WT 3_R1.fastq.gz 7 dpf_WT 3_R2.fastq.gz", "fastq fastq", 15543953590.0, 51470045.0, "GSM8655457 r1", "0:151 1:151", "A:4031818994;C:3704599213;G:3577251498;T:4228986622;N:1297263", 151, 151, null, null, 4031818994, 3704599213, 3577251498, 4228986622, 1297263, "SRX26906752", "SRS23386338", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34210, "SRR31539735", "SRX26906751", "SRS23386337", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 7 dpf wild type embryos   biol rep 2", "GSM8655456", null, "source name:whole body|tissue:whole body|genotype:WT|time:7 dpf|geo loc name:missing|collection date:missing", "Whole body 7 dpf wild type embryos   biol rep 2", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:7 dpf", "GSM8655456", "GSM8655456: Whole body 7 dpf wild type embryos   biol rep 2; Danio rerio; RNA Seq", "GSM8655456 r1", "GSM8655456", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "7 dpf_WT 2_R1.fastq.gz 7 dpf_WT 2_R2.fastq.gz", "fastq fastq", 14325089744.0, 47434072.0, "GSM8655456 r1", "0:151 1:151", "A:3806636861;C:3343198938;G:3185927363;T:3988104951;N:1221631", 151, 151, null, null, 3806636861, 3343198938, 3185927363, 3988104951, 1221631, "SRX26906751", "SRS23386337", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34211, "SRR31539736", "SRX26906750", "SRS23386333", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 7 dpf wild type embryos   biol rep 1", "GSM8655455", null, "source name:whole body|tissue:whole body|genotype:WT|time:7 dpf|geo loc name:missing|collection date:missing", "Whole body 7 dpf wild type embryos   biol rep 1", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:7 dpf", "GSM8655455", "GSM8655455: Whole body 7 dpf wild type embryos   biol rep 1; Danio rerio; RNA Seq", "GSM8655455 r1", "GSM8655455", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "7 dpf_WT 1_R1.fastq.gz 7 dpf_WT 1_R2.fastq.gz", "fastq fastq", 16398118008.0, 54298404.0, "GSM8655455 r1", "0:151 1:151", "A:4341778579;C:3858758690;G:3657590940;T:4538608543;N:1381256", 151, 151, null, null, 4341778579, 3858758690, 3657590940, 4538608543, 1381256, "SRX26906750", "SRS23386333", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34212, "SRR31539737", "SRX26906749", "SRS23386334", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 4 dpf sox10 mutant embryos   biol rep 3", "GSM8655454", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:4 dpf|geo loc name:missing|collection date:missing", "Whole body 4 dpf sox10 mutant embryos    biol rep 3", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:4 dpf", "GSM8655454", "GSM8655454: Whole body 4 dpf sox10 mutant embryos    biol rep 3; Danio rerio; RNA Seq", "GSM8655454 r1", "GSM8655454", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "4 dpf_mut 3_R1.fastq.gz 4 dpf_mut 3_R2.fastq.gz", "fastq fastq", 15071278894.0, 49904897.0, "GSM8655454 r1", "0:151 1:151", "A:3996223512;C:3537174277;G:3398338576;T:4138304072;N:1238457", 151, 151, null, null, 3996223512, 3537174277, 3398338576, 4138304072, 1238457, "SRX26906749", "SRS23386334", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34213, "SRR31539738", "SRX26906748", "SRS23386336", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 4 dpf sox10 mutant embryos   biol rep 2", "GSM8655453", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:4 dpf|geo loc name:missing|collection date:missing", "Whole body 4 dpf sox10 mutant embryos    biol rep 2", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:4 dpf", "GSM8655453", "GSM8655453: Whole body 4 dpf sox10 mutant embryos    biol rep 2; Danio rerio; RNA Seq", "GSM8655453 r1", "GSM8655453", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "4 dpf_mut 2_R1.fastq.gz 4 dpf_mut 2_R2.fastq.gz", "fastq fastq", 14918687958.0, 49399629.0, "GSM8655453 r1", "0:151 1:151", "A:3994132161;C:3464356999;G:3293001897;T:4165943265;N:1253636", 151, 151, null, null, 3994132161, 3464356999, 3293001897, 4165943265, 1253636, "SRX26906748", "SRS23386336", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34214, "SRR31539739", "SRX26906747", "SRS23386332", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 4 dpf sox10 mutant embryos   biol rep 1", "GSM8655452", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:4 dpf|geo loc name:missing|collection date:missing", "Whole body 4 dpf sox10 mutant embryos    biol rep 1", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:4 dpf", "GSM8655452", "GSM8655452: Whole body 4 dpf sox10 mutant embryos    biol rep 1; Danio rerio; RNA Seq", "GSM8655452 r1", "GSM8655452", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "4 dpf_mut 1_R1.fastq.gz 4 dpf_mut 1_R2.fastq.gz", "fastq fastq", 14573247372.0, 48255786.0, "GSM8655452 r1", "0:151 1:151", "A:3964700989;C:3340575136;G:3128233836;T:4138502375;N:1235036", 151, 151, null, null, 3964700989, 3340575136, 3128233836, 4138502375, 1235036, "SRX26906747", "SRS23386332", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34215, "SRR31539740", "SRX26906746", "SRS23386331", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 4 dpf wild type embryos   biol rep 3", "GSM8655451", null, "source name:whole body|tissue:whole body|genotype:WT|time:4 dpf|geo loc name:missing|collection date:missing", "Whole body 4 dpf wild type embryos   biol rep 3", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:4 dpf", "GSM8655451", "GSM8655451: Whole body 4 dpf wild type embryos   biol rep 3; Danio rerio; RNA Seq", "GSM8655451 r1", "GSM8655451", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "4 dpf_WT 3_R1.fastq.gz 4 dpf_WT 3_R2.fastq.gz", "fastq fastq", 15132219172.0, 50106686.0, "GSM8655451 r1", "0:151 1:151", "A:4030654907;C:3519071260;G:3404455031;T:4176756699;N:1281275", 151, 151, null, null, 4030654907, 3519071260, 3404455031, 4176756699, 1281275, "SRX26906746", "SRS23386331", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34216, "SRR31539741", "SRX26906745", "SRS23386335", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 4 dpf wild type embryos   biol rep 2", "GSM8655450", null, "source name:whole body|tissue:whole body|genotype:WT|time:4 dpf|geo loc name:missing|collection date:missing", "Whole body 4 dpf wild type embryos   biol rep 2", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:4 dpf", "GSM8655450", "GSM8655450: Whole body 4 dpf wild type embryos   biol rep 2; Danio rerio; RNA Seq", "GSM8655450 r1", "GSM8655450", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "4 dpf_WT 2_R1.fastq.gz 4 dpf_WT 2_R2.fastq.gz", "fastq fastq", 15546478914.0, 51478407.0, "GSM8655450 r1", "0:151 1:151", "A:4105803894;C:3606318412;G:3589944905;T:4243130619;N:1281084", 151, 151, null, null, 4105803894, 3606318412, 3589944905, 4243130619, 1281084, "SRX26906745", "SRS23386335", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34217, "SRR31539742", "SRX26906744", "SRS23386330", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 4 dpf wild type embryos   biol rep 1", "GSM8655449", null, "source name:whole body|tissue:whole body|genotype:WT|time:4 dpf|geo loc name:missing|collection date:missing", "Whole body 4 dpf wild type embryos   biol rep 1", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:4 dpf", "GSM8655449", "GSM8655449: Whole body 4 dpf wild type embryos   biol rep 1; Danio rerio; RNA Seq", "GSM8655449 r1", "GSM8655449", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "4 dpf_WT 1_R1.fastq.gz 4 dpf_WT 1_R2.fastq.gz", "fastq fastq", 15246602880.0, 50485440.0, "GSM8655449 r1", "0:151 1:151", "A:4017771448;C:3536729749;G:3495956173;T:4194910365;N:1235145", 151, 151, null, null, 4017771448, 3536729749, 3495956173, 4194910365, 1235145, "SRX26906744", "SRS23386330", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34218, "SRR31539743", "SRX26906743", "SRS23386329", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 45 hpf sox10 mutant embryos   biol rep 3", "GSM8655448", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:45 hpf|geo loc name:missing|collection date:missing", "Whole body 45 hpf sox10 mutant embryos   biol rep 3", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:45 hpf", "GSM8655448", "GSM8655448: Whole body 45 hpf sox10 mutant embryos   biol rep 3; Danio rerio; RNA Seq", "GSM8655448 r1", "GSM8655448", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "45 hpf_mut 3_R1.fastq.gz 45 hpf_mut 3_R2.fastq.gz", "fastq fastq", 14338321572.0, 47477886.0, "GSM8655448 r1", "0:151 1:151", "A:3808719246;C:3382555065;G:3212075099;T:3933758367;N:1213795", 151, 151, null, null, 3808719246, 3382555065, 3212075099, 3933758367, 1213795, "SRX26906743", "SRS23386329", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34219, "SRR31539744", "SRX26906742", "SRS23386326", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 45 hpf sox10 mutant embryos   biol rep 2", "GSM8655447", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:45 hpf|geo loc name:missing|collection date:missing", "Whole body 45 hpf sox10 mutant embryos   biol rep 2", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:45 hpf", "GSM8655447", "GSM8655447: Whole body 45 hpf sox10 mutant embryos   biol rep 2; Danio rerio; RNA Seq", "GSM8655447 r1", "GSM8655447", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "45 hpf_mut 2_R1.fastq.gz 45 hpf_mut 2_R2.fastq.gz", "fastq fastq", 15462167158.0, 51199229.0, "GSM8655447 r1", "0:151 1:151", "A:4089691508;C:3622289242;G:3495097207;T:4253826187;N:1263014", 151, 151, null, null, 4089691508, 3622289242, 3495097207, 4253826187, 1263014, "SRX26906742", "SRS23386326", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34220, "SRR31539745", "SRX26906741", "SRS23386327", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 45 hpf sox10 mutant embryos   biol rep 1", "GSM8655446", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:45 hpf|geo loc name:missing|collection date:missing", "Whole body 45 hpf sox10 mutant embryos   biol rep 1", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:45 hpf", "GSM8655446", "GSM8655446: Whole body 45 hpf sox10 mutant embryos   biol rep 1; Danio rerio; RNA Seq", "GSM8655446 r1", "GSM8655446", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "45 hpf_mut 1_R1.fastq.gz 45 hpf_mut 1_R2.fastq.gz", "fastq fastq", 15655817712.0, 51840456.0, "GSM8655446 r1", "0:151 1:151", "A:4157360171;C:3674570903;G:3484564544;T:4338002005;N:1320089", 151, 151, null, null, 4157360171, 3674570903, 3484564544, 4338002005, 1320089, "SRX26906741", "SRS23386327", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34221, "SRR31539746", "SRX26906740", "SRS23386328", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 45 hpf wild type embryos   biol rep 3", "GSM8655445", null, "source name:whole body|tissue:whole body|genotype:WT|time:45 hpf|geo loc name:missing|collection date:missing", "Whole body 45 hpf wild type embryos   biol rep 3", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:45 hpf", "GSM8655445", "GSM8655445: Whole body 45 hpf wild type embryos   biol rep 3; Danio rerio; RNA Seq", "GSM8655445 r1", "GSM8655445", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "45 hpf_WT 3_R1.fastq.gz 45 hpf_WT 3_R2.fastq.gz", "fastq fastq", 14580346184.0, 48279292.0, "GSM8655445 r1", "0:151 1:151", "A:3858927638;C:3450290173;G:3271701209;T:3998202503;N:1224661", 151, 151, null, null, 3858927638, 3450290173, 3271701209, 3998202503, 1224661, "SRX26906740", "SRS23386328", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34222, "SRR31539747", "SRX26906739", "SRS23386325", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 45 hpf wild type embryos   biol rep 2", "GSM8655444", null, "source name:whole body|tissue:whole body|genotype:WT|time:45 hpf|geo loc name:missing|collection date:missing", "Whole body 45 hpf wild type embryos   biol rep 2", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:45 hpf", "GSM8655444", "GSM8655444: Whole body 45 hpf wild type embryos   biol rep 2; Danio rerio; RNA Seq", "GSM8655444 r1", "GSM8655444", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "45 hpf_WT 2_R1.fastq.gz 45 hpf_WT_2_R2.fastq.gz", "fastq fastq", 15005198878.0, 49686089.0, "GSM8655444 r1", "0:151 1:151", "A:3950487195;C:3509517845;G:3418800225;T:4125159820;N:1233793", 151, 151, null, null, 3950487195, 3509517845, 3418800225, 4125159820, 1233793, "SRX26906739", "SRS23386325", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34223, "SRR31539748", "SRX26906738", "SRS23386324", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 45 hpf wild type embryos   biol rep 1", "GSM8655443", null, "source name:whole body|tissue:whole body|genotype:WT|time:45 hpf|geo loc name:missing|collection date:missing", "Whole body 45 hpf wild type embryos   biol rep 1", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:45 hpf", "GSM8655443", "GSM8655443: Whole body 45 hpf wild type embryos   biol rep 1; Danio rerio; RNA Seq", "GSM8655443 r1", "GSM8655443", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "45 hpf_WT 1_R1.fastq.gz 45 hpf_WT 1_R2.fastq.gz", "fastq fastq", 14884992912.0, 49288056.0, "GSM8655443 r1", "0:151 1:151", "A:3878762924;C:3475070121;G:3485186845;T:4044768200;N:1204822", 151, 151, null, null, 3878762924, 3475070121, 3485186845, 4044768200, 1204822, "SRX26906738", "SRS23386324", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [35389, "SRR32737834", "SRX28024098", "SRS24385653", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 5 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf", "GSM8851836", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:35.14ng/mL oxycod1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 5 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:35.14ng/mL oxycod1|batch:3/25/2024", "GSM8851836", "GSM8851836: replicate 5 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf; Danio rerio; RNA Seq", "GSM8851836 r1", "GSM8851836", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R7OT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R7OT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 18969663600.0, 63232212.0, "GSM8851836 r1", "0:150 1:150", "A:5368170604;C:4078596357;G:4113230716;T:5408149968;N:1515955", 150, 150, null, null, 5368170604, 4078596357, 4113230716, 5408149968, 1515955, "SRX28024098", "SRS24385653", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35390, "SRR32737835", "SRX28024097", "SRS24385650", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 4 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf", "GSM8851835", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:35.14ng/mL oxycod1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 4 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:35.14ng/mL oxycod1|batch:3/25/2024", "GSM8851835", "GSM8851835: replicate 4 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf; Danio rerio; RNA Seq", "GSM8851835 r1", "GSM8851835", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R5OT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R5OT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 19589608200.0, 65298694.0, "GSM8851835 r1", "0:150 1:150", "A:5414548081;C:4374558112;G:4362382403;T:5436601325;N:1518279", 150, 150, null, null, 5414548081, 4374558112, 4362382403, 5436601325, 1518279, "SRX28024097", "SRS24385650", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35391, "SRR32737836", "SRX28024096", "SRS24385649", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 3 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf", "GSM8851834", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:35.14ng/mL oxycod1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 3 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:35.14ng/mL oxycod1|batch:3/25/2024", "GSM8851834", "GSM8851834: replicate 3 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf; Danio rerio; RNA Seq", "GSM8851834 r1", "GSM8851834", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R4OT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R4OT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 19946087100.0, 66486957.0, "GSM8851834 r1", "0:150 1:150", "A:5380413495;C:4584083127;G:4577230707;T:5402765142;N:1594629", 150, 150, null, null, 5380413495, 4584083127, 4577230707, 5402765142, 1594629, "SRX28024096", "SRS24385649", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35392, "SRR32737837", "SRX28024095", "SRS24385647", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 2 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf", "GSM8851833", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:35.14ng/mL oxycod1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 2 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:35.14ng/mL oxycod1|batch:3/25/2024", "GSM8851833", "GSM8851833: replicate 2 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf; Danio rerio; RNA Seq", "GSM8851833 r1", "GSM8851833", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R2OT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R2OT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 12448266300.0, 41494221.0, "GSM8851833 r1", "0:150 1:150", "A:3395623757;C:2824144586;G:2822937408;T:3404571425;N:989124", 150, 150, null, null, 3395623757, 2824144586, 2822937408, 3404571425, 989124, "SRX28024095", "SRS24385647", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35393, "SRR32737838", "SRX28024094", "SRS24385648", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 1 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf", "GSM8851832", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:35.14ng/mL oxycod1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 1 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:35.14ng/mL oxycod1|batch:3/25/2024", "GSM8851832", "GSM8851832: replicate 1 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf; Danio rerio; RNA Seq", "GSM8851832 r1", "GSM8851832", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R1OT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R1OT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 19798955700.0, 65996519.0, "GSM8851832 r1", "0:150 1:150", "A:5229008693;C:4668558136;G:4674407786;T:5225398568;N:1582517", 150, 150, null, null, 5229008693, 4668558136, 4674407786, 5225398568, 1582517, "SRX28024094", "SRS24385648", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35394, "SRR32737842", "SRX28024093", "SRS24385646", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 5 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf", "GSM8851831", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:10.6pg/mL oxycod1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 5 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:10.6pg/mL oxycod1|batch:3/25/2024", "GSM8851831", "GSM8851831: replicate 5 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851831 r1", "GSM8851831", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R6OE_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R6OE_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 18130666800.0, 60435556.0, "GSM8851831 r1", "0:150 1:150", "A:4966144411;C:4092769735;G:4085294185;T:4985017148;N:1441321", 150, 150, null, null, 4966144411, 4092769735, 4085294185, 4985017148, 1441321, "SRX28024093", "SRS24385646", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35395, "SRR32737839", "SRX28024092", "SRS24385645", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 4 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf", "GSM8851830", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:10.6pg/mL oxycod1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 4 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:10.6pg/mL oxycod1|batch:3/25/2024", "GSM8851830", "GSM8851830: replicate 4 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851830 r1", "GSM8851830", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R4OE_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R4OE_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 19991640600.0, 66638802.0, "GSM8851830 r1", "0:150 1:150", "A:5447335535;C:4526376231;G:4535727704;T:5480632098;N:1569032", 150, 150, null, null, 5447335535, 4526376231, 4535727704, 5480632098, 1569032, "SRX28024092", "SRS24385645", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35396, "SRR32737840", "SRX28024091", "SRS24385644", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 3 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf", "GSM8851829", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:10.6pg/mL oxycod1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 3 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:10.6pg/mL oxycod1|batch:3/25/2024", "GSM8851829", "GSM8851829: replicate 3 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851829 r1", "GSM8851829", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R3OE_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R3OE_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 22065261900.0, 73550873.0, "GSM8851829 r1", "0:150 1:150", "A:5991325177;C:5034454094;G:5016024645;T:6021738394;N:1719590", 150, 150, null, null, 5991325177, 5034454094, 5016024645, 6021738394, 1719590, "SRX28024091", "SRS24385644", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35397, "SRR32737841", "SRX28024090", "SRS24385643", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 2 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf", "GSM8851828", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:10.6pg/mL oxycod1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 2 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:10.6pg/mL oxycod1|batch:3/25/2024", "GSM8851828", "GSM8851828: replicate 2 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851828 r1", "GSM8851828", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R2OE_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R2OE_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 14038941600.0, 46796472.0, "GSM8851828 r1", "0:150 1:150", "A:3916268130;C:3079070561;G:3101493441;T:3941005195;N:1104273", 150, 150, null, null, 3916268130, 3079070561, 3101493441, 3941005195, 1104273, "SRX28024090", "SRS24385643", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35398, "SRR32737843", "SRX28024089", "SRS24385641", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 1 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf", "GSM8851827", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:10.6pg/mL oxycod1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 1 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:10.6pg/mL oxycod1|batch:3/25/2024", "GSM8851827", "GSM8851827: replicate 1 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851827 r1", "GSM8851827", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R1OE_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R1OE_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 13386761100.0, 44622537.0, "GSM8851827 r1", "0:150 1:150", "A:3794190335;C:2871376272;G:2905470401;T:3814688762;N:1035330", 150, 150, null, null, 3794190335, 2871376272, 2905470401, 3814688762, 1035330, "SRX28024089", "SRS24385641", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35399, "SRR32737844", "SRX28024088", "SRS24385642", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 5 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf", "GSM8851826", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:3.14 ng/mL fentanyl|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 5 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:3.14 ng/mL fentanyl|batch:3/25/2024", "GSM8851826", "GSM8851826: replicate 5 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851826 r1", "GSM8851826", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R6FT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R6FT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 21105961200.0, 70353204.0, "GSM8851826 r1", "0:150 1:150", "A:5809999918;C:4738287088;G:4727306148;T:5828688062;N:1679984", 150, 150, null, null, 5809999918, 4738287088, 4727306148, 5828688062, 1679984, "SRX28024088", "SRS24385642", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35400, "SRR32737845", "SRX28024087", "SRS24385640", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 4 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf", "GSM8851825", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:3.14 ng/mL fentanyl|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 4 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:3.14 ng/mL fentanyl|batch:3/25/2024", "GSM8851825", "GSM8851825: replicate 4 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851825 r1", "GSM8851825", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R5FT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R5FT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 23123472900.0, 77078243.0, "GSM8851825 r1", "0:150 1:150", "A:6076414910;C:5484056288;G:5478904909;T:6082279094;N:1817699", 150, 150, null, null, 6076414910, 5484056288, 5478904909, 6082279094, 1817699, "SRX28024087", "SRS24385640", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35401, "SRR32737846", "SRX28024086", "SRS24385638", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 3 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf", "GSM8851824", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:3.14 ng/mL fentanyl|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 3 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:3.14 ng/mL fentanyl|batch:3/25/2024", "GSM8851824", "GSM8851824: replicate 3 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851824 r1", "GSM8851824", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R4FT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R4FT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 21177911700.0, 70593039.0, "GSM8851824 r1", "0:150 1:150", "A:5565860585;C:5018913046;G:5013238014;T:5578213850;N:1686205", 150, 150, null, null, 5565860585, 5018913046, 5013238014, 5578213850, 1686205, "SRX28024086", "SRS24385638", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35402, "SRR32737850", "SRX28024085", "SRS24385639", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 2 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf", "GSM8851823", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:3.14 ng/mL fentanyl|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 2 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:3.14 ng/mL fentanyl|batch:3/25/2024", "GSM8851823", "GSM8851823: replicate 2 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851823 r1", "GSM8851823", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R2FT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R2FT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 23561164500.0, 78537215.0, "GSM8851823 r1", "0:150 1:150", "A:7284568054;C:4438434312;G:4560720005;T:7275566382;N:1875747", 150, 150, null, null, 7284568054, 4438434312, 4560720005, 7275566382, 1875747, "SRX28024085", "SRS24385639", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35403, "SRR32737847", "SRX28024084", "SRS24385637", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 1 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf", "GSM8851822", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:3.14 ng/mL fentanyl|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 1 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:3.14 ng/mL fentanyl|batch:3/25/2024", "GSM8851822", "GSM8851822: replicate 1 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851822 r1", "GSM8851822", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R1FT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R1FT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 11262181200.0, 37540604.0, "GSM8851822 r1", "0:150 1:150", "A:3084661516;C:2546033080;G:2544910194;T:3085685271;N:891139", 150, 150, null, null, 3084661516, 2546033080, 2544910194, 3085685271, 891139, "SRX28024084", "SRS24385637", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35404, "SRR32737848", "SRX28024083", "SRS24385636", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 5 fentanyl effluent exposed 0 24hpf total RNA at xxxhpf", "GSM8851821", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:0.629pg/mL fentanyl|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 5 fentanyl effluent exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:0.629pg/mL fentanyl|batch:3/25/2024", "GSM8851821", "GSM8851821: replicate 5 fentanyl effluent exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851821 r1", "GSM8851821", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R7FE_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R7FE_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 15368398200.0, 51227994.0, "GSM8851821 r1", "0:150 1:150", "A:4439560630;C:3205670434;G:3245419161;T:4476535407;N:1212568", 150, 150, null, null, 4439560630, 3205670434, 3245419161, 4476535407, 1212568, "SRX28024083", "SRS24385636", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35405, "SRR32737849", "SRX28024082", "SRS24385635", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 4 fentanyl effluent exposed 0 24hpf total RNA at xxxhpf", "GSM8851820", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:0.629pg/mL fentanyl|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 4 fentanyl effluent exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:0.629pg/mL fentanyl|batch:3/25/2024", "GSM8851820", "GSM8851820: replicate 4 fentanyl effluent exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851820 r1", "GSM8851820", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R6FE_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R6FE_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 18515267400.0, 61717558.0, "GSM8851820 r1", "0:150 1:150", "A:5143084505;C:4097554946;G:4102756202;T:5170389972;N:1481775", 150, 150, null, null, 5143084505, 4097554946, 4102756202, 5170389972, 1481775, "SRX28024082", "SRS24385635", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35406, "SRR32737851", "SRX28024081", "SRS24385634", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 3 fentanyl effluent exposed 0 24hpf total RNA at xxxhpf", "GSM8851819", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:0.629pg/mL fentanyl|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 3 fentanyl effluent exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:0.629pg/mL fentanyl|batch:3/25/2024", "GSM8851819", "GSM8851819: replicate 3 fentanyl effluent exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851819 r1", "GSM8851819", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R4FE_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R4FE_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 22025174100.0, 73417247.0, "GSM8851819 r1", "0:150 1:150", "A:6102961818;C:4890276079;G:4886456272;T:6143741983;N:1737948", 150, 150, null, null, 6102961818, 4890276079, 4886456272, 6143741983, 1737948, "SRX28024081", "SRS24385634", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35407, "SRR32737852", "SRX28024080", "SRS24385632", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 2 fentanyl effluent exposed 0 24hpf total RNA at xxxhpf", "GSM8851818", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:0.629pg/mL fentanyl|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 2 fentanyl effluent exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:0.629pg/mL fentanyl|batch:3/25/2024", "GSM8851818", "GSM8851818: replicate 2 fentanyl effluent exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851818 r1", "GSM8851818", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R2FE_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R2FE_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 10834750500.0, 36115835.0, "GSM8851818 r1", "0:150 1:150", "A:3041146508;C:2356912296;G:2379606625;T:3056251263;N:833808", 150, 150, null, null, 3041146508, 2356912296, 2379606625, 3056251263, 833808, "SRX28024080", "SRS24385632", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35408, "SRR32737853", "SRX28024079", "SRS24385633", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 1 fentanyl effluent exposed 0 24hpf total RNA at xxxhpf", "GSM8851817", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:0.629pg/mL fentanyl|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 1 fentanyl effluent exposed 0 24hpf total RNA at xxxhpf", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:0.629pg/mL fentanyl|batch:3/25/2024", "GSM8851817", "GSM8851817: replicate 1 fentanyl effluent exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq", "GSM8851817 r1", "GSM8851817", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R1FE_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R1FE_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 12001746900.0, 40005823.0, "GSM8851817 r1", "0:150 1:150", "A:3575866939;C:2389704942;G:2473378269;T:3561826526;N:970224", 150, 150, null, null, 3575866939, 2389704942, 2473378269, 3561826526, 970224, "SRX28024079", "SRS24385633", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35409, "SRR32737854", "SRX28024078", "SRS24385631", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 9 control WT zebrafish 48hpf total RNA", "GSM8851816", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:N1|batch:8/25/2024|geo loc name:missing|collection date:missing", "replicate 9 control WT zebrafish 48hpf total RNA", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:N1|batch:8/25/2024", "GSM8851816", "GSM8851816: replicate 9 control WT zebrafish 48hpf total RNA; Danio rerio; RNA Seq", "GSM8851816 r1", "GSM8851816", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R5Control_CKDL240028231-1A_22NFN3LT3_L7_1.fq.gz R5Control_CKDL240028231-1A_22NFN3LT3_L7_2.fq.gz", "fastq fastq", 15135158100.0, 50450527.0, "GSM8851816 r1", "0:150 1:150", "A:4016578965;C:3529417594;G:3534266238;T:4054131464;N:763839", 150, 150, null, null, 4016578965, 3529417594, 3534266238, 4054131464, 763839, "SRX28024078", "SRS24385631", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35410, "SRR32737858", "SRX28024077", "SRS24385629", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 8 control WT zebrafish 48hpf total RNA", "GSM8851815", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:N1|batch:8/24/2024|geo loc name:missing|collection date:missing", "replicate 8 control WT zebrafish 48hpf total RNA", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:N1|batch:8/24/2024", "GSM8851815", "GSM8851815: replicate 8 control WT zebrafish 48hpf total RNA; Danio rerio; RNA Seq", "GSM8851815 r1", "GSM8851815", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R4Control_CKDL240028231-1A_22NFN3LT3_L7_1.fq.gz R4Control_CKDL240028231-1A_22NFN3LT3_L7_2.fq.gz", "fastq fastq", 21418548600.0, 71395162.0, "GSM8851815 r1", "0:150 1:150", "A:5819254122;C:4852193197;G:4858910685;T:5887118494;N:1072102", 150, 150, null, null, 5819254122, 4852193197, 4858910685, 5887118494, 1072102, "SRX28024077", "SRS24385629", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35411, "SRR32737855", "SRX28024076", "SRS24385630", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 7 control WT zebrafish 48hpf total RNA", "GSM8851814", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:N1|batch:8/23/2024|geo loc name:missing|collection date:missing", "replicate 7 control WT zebrafish 48hpf total RNA", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:N1|batch:8/23/2024", "GSM8851814", "GSM8851814: replicate 7 control WT zebrafish 48hpf total RNA; Danio rerio; RNA Seq", "GSM8851814 r1", "GSM8851814", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R3Control_CKDL240028231-1A_22NFN3LT3_L7_1.fq.gz R3Control_CKDL240028231-1A_22NFN3LT3_L7_2.fq.gz", "fastq fastq", 16495878600.0, 54986262.0, "GSM8851814 r1", "0:150 1:150", "A:4377581963;C:3838726683;G:3859250667;T:4419488236;N:831051", 150, 150, null, null, 4377581963, 3838726683, 3859250667, 4419488236, 831051, "SRX28024076", "SRS24385630", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35412, "SRR32737856", "SRX28024075", "SRS24385628", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 6 control WT zebrafish 48hpf total RNA", "GSM8851813", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:N1|batch:8/22/2024|geo loc name:missing|collection date:missing", "replicate 6 control WT zebrafish 48hpf total RNA", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:N1|batch:8/22/2024", "GSM8851813", "GSM8851813: replicate 6 control WT zebrafish 48hpf total RNA; Danio rerio; RNA Seq", "GSM8851813 r1", "GSM8851813", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R2Control_CKDL240028231-1A_22NFN3LT3_L7_1.fq.gz R2Control_CKDL240028231-1A_22NFN3LT3_L7_2.fq.gz", "fastq fastq", 14617714200.0, 48725714.0, "GSM8851813 r1", "0:150 1:150", "A:3998241249;C:3282188059;G:3287516949;T:4049030965;N:736978", 150, 150, null, null, 3998241249, 3282188059, 3287516949, 4049030965, 736978, "SRX28024075", "SRS24385628", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35413, "SRR32737857", "SRX28024074", "SRS24385626", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 5 control WT zebrafish 48hpf total RNA", "GSM8851812", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:N1|batch:8/21/2024|geo loc name:missing|collection date:missing", "replicate 5 control WT zebrafish 48hpf total RNA", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:N1|batch:8/21/2024", "GSM8851812", "GSM8851812: replicate 5 control WT zebrafish 48hpf total RNA; Danio rerio; RNA Seq", "GSM8851812 r1", "GSM8851812", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R1Control_CKDL240028231-1A_22NFN3LT3_L7_1.fq.gz R1Control_CKDL240028231-1A_22NFN3LT3_L7_2.fq.gz", "fastq fastq", 12865270800.0, 42884236.0, "GSM8851812 r1", "0:150 1:150", "A:3532327000;C:2875146764;G:2882267112;T:3574883553;N:646371", 150, 150, null, null, 3532327000, 2875146764, 2882267112, 3574883553, 646371, "SRX28024074", "SRS24385626", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35414, "SRR32737859", "SRX28024073", "SRS24385627", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 4 control WT zebrafish 48hpf total RNA", "GSM8851811", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:N1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 4 control WT zebrafish 48hpf total RNA", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:N1|batch:3/25/2024", "GSM8851811", "GSM8851811: replicate 4 control WT zebrafish 48hpf total RNA; Danio rerio; RNA Seq", "GSM8851811 r1", "GSM8851811", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R8Control_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R8Control_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 22801688400.0, 76005628.0, "GSM8851811 r1", "0:150 1:150", "A:6271418792;C:5111375560;G:5125950914;T:6291143738;N:1799396", 150, 150, null, null, 6271418792, 5111375560, 5125950914, 6291143738, 1799396, "SRX28024073", "SRS24385627", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35415, "SRR32737860", "SRX28024072", "SRS24385625", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 3 control WT zebrafish 48hpf total RNA", "GSM8851810", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:N1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 3 control WT zebrafish 48hpf total RNA", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:N1|batch:3/25/2024", "GSM8851810", "GSM8851810: replicate 3 control WT zebrafish 48hpf total RNA; Danio rerio; RNA Seq", "GSM8851810 r1", "GSM8851810", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R5Control_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R5Control_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 20790977400.0, 69303258.0, "GSM8851810 r1", "0:150 1:150", "A:5566891894;C:4832327067;G:4813178723;T:5576916246;N:1663470", 150, 150, null, null, 5566891894, 4832327067, 4813178723, 5576916246, 1663470, "SRX28024072", "SRS24385625", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35416, "SRR32737861", "SRX28024071", "SRS24385623", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 2 control WT zebrafish 48hpf total RNA", "GSM8851809", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:N1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 2 control WT zebrafish 48hpf total RNA", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:N1|batch:3/25/2024", "GSM8851809", "GSM8851809: replicate 2 control WT zebrafish 48hpf total RNA; Danio rerio; RNA Seq", "GSM8851809 r1", "GSM8851809", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R4Control_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R4Control_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 26635769700.0, 88785899.0, "GSM8851809 r1", "0:150 1:150", "A:7025914832;C:6292580960;G:6279849099;T:7035294349;N:2130460", 150, 150, null, null, 7025914832, 6292580960, 6279849099, 7035294349, 2130460, "SRX28024071", "SRS24385623", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35417, "SRR32737862", "SRX28024070", "SRS24385624", "SRP570947", "PRJNA1237347", "Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos", "GSE292183", "Transcriptome Analysis", "The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented  early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf  followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses  potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total  892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization  cell adhesion  and visual and nervous system formation. Key pathways include axon guidance  synapse formation  and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems  providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos  embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf  50 embryos were sample were harvested for total RNA  cDNA library prep  and RNAseq.", null, "pubmed:40429979", null, "replicate 1 control WT zebrafish 48hpf total RNA", "GSM8851808", null, "source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:N1|batch:3/25/2024|geo loc name:missing|collection date:missing", "replicate 1 control WT zebrafish 48hpf total RNA", "Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic  and ran through rCorrector  then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes  see above Supplementary files format and content: the counts derived from Salmon", "Total embryo 50 embryo homogenate", "one of the following conditions: fentanyl effluent FE; 0.629 pg/mL  fentanyl therapeutic FT; 3.14 ng/mL  oxycodone effluent OE; 10.6 pg/mL  oxycodone therapeutic OT; 35.14 ng/mL  Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", "zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C", "tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:N1|batch:3/25/2024", "GSM8851808", "GSM8851808: replicate 1 control WT zebrafish 48hpf total RNA; Danio rerio; RNA Seq", "GSM8851808 r1", "GSM8851808", "1", "Trizol Chloroform extraction of total RNA followed by Dnase I treatment  and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP570947", null, null, "R2Control_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R2Control_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz", "fastq fastq", 14366496900.0, 47888323.0, "GSM8851808 r1", "0:150 1:150", "A:4012213164;C:3167946102;G:3163546704;T:4021691335;N:1099595", 150, 150, null, null, 4012213164, 3167946102, 3163546704, 4021691335, 1099595, "SRX28024070", "SRS24385624", "SRA2094947", "Merzdorf, MCB, Montana State University", "Merzdorf, MCB, Montana State University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-03-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35871, "SRR33167498", "SRX28428354", "SRS24751227", "SRP579141", "PRJNA1251588", "Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish", "GSE294778", "Transcriptome Analysis", "Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.", null, null, null, "MB125 2B L6.D708", "GSM8919410", null, "source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1|geo loc name:missing|collection date:missing", "MB125 2B L6.D708", "For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3\u2019 Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples", "pooled heads collected anterior to swim bladder of larval zebrafish", null, "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1", "GSM8919410", "GSM8919410: MB125 2B L6.D708; Danio rerio; RNA Seq", "GSM8919410 r1", "GSM8919410", "1", "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP579141", null, null, "MB125_2B_L6.D708_1.fastq.gz MB125_2B_L6.D708_2.fastq.gz", "fastq fastq", 2319886164.0, 22743982.0, "GSM8919410 r1", "0:51 1:51", "A:553297266;C:587452449;G:584241025;T:594875512;N:19912", 51, 51, null, null, 553297266, 587452449, 584241025, 594875512, 19912, "SRX28428354", "SRS24751227", "SRA2113523", "US EPA", "US EPA", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2025-04-16", "Multi-stage", "Multi-stage", "Multi-tissue", "Multi-system"], [35892, "SRR33167519", "SRX28428333", "SRS24751206", "SRP579141", "PRJNA1251588", "Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish", "GSE294778", "Transcriptome Analysis", "Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.", null, null, null, "GRC355 AC7 S7", "GSM8919392", null, "source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing", "GRC355 AC7 S7", "For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3\u2019 Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples", "pooled heads collected anterior to swim bladder of larval zebrafish", null, "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2", "GSM8919392", "GSM8919392: GRC355 AC7 S7; Danio rerio; RNA Seq", "GSM8919392 r1", "GSM8919392", "1", "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP579141", null, null, "GRC355_AC7_S7_R1_001.fastq.gz", "fastq", 2227335150.0, 29697802.0, "GSM8919392 r1", "0:75", "A:600851630;C:506204586;G:559397063;T:560849750;N:32121", 75, null, null, null, 600851630, 506204586, 559397063, 560849750, 32121, "SRX28428333", "SRS24751206", "SRA2113523", "US EPA", "US EPA", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2025-04-16", "Multi-stage", "Multi-stage", "Multi-tissue", "Multi-system"], [35893, "SRR33167520", "SRX28428332", "SRS24751204", "SRP579141", "PRJNA1251588", "Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish", "GSE294778", "Transcriptome Analysis", "Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.", null, null, null, "GRC355 AC6 S11", "GSM8919391", null, "source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing", "GRC355 AC6 S11", "For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3\u2019 Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples", "pooled heads collected anterior to swim bladder of larval zebrafish", null, "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2", "GSM8919391", "GSM8919391: GRC355 AC6 S11; Danio rerio; RNA Seq", "GSM8919391 r1", "GSM8919391", "1", "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP579141", null, null, "GRC355_AC6_S11_R1_001.fastq.gz", "fastq", 2585681925.0, 34475759.0, "GSM8919391 r1", "0:75", "A:689801171;C:608098568;G:666027069;T:621732490;N:22627", 75, null, null, null, 689801171, 608098568, 666027069, 621732490, 22627, "SRX28428332", "SRS24751204", "SRA2113523", "US EPA", "US EPA", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2025-04-16", "Multi-stage", "Multi-stage", "Multi-tissue", "Multi-system"], [35894, "SRR33167521", "SRX28428331", "SRS24751205", "SRP579141", "PRJNA1251588", "Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish", "GSE294778", "Transcriptome Analysis", "Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.", null, null, null, "GRC355 AC5 S14", "GSM8919390", null, "source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing", "GRC355 AC5 S14", "For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3\u2019 Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples", "pooled heads collected anterior to swim bladder of larval zebrafish", null, "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2", "GSM8919390", "GSM8919390: GRC355 AC5 S14; Danio rerio; RNA Seq", "GSM8919390 r1", "GSM8919390", "1", "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP579141", null, null, "GRC355_AC5_S14_R1_001.fastq.gz", "fastq", 2494451250.0, 33259350.0, "GSM8919390 r1", "0:75", "A:663836714;C:570411156;G:619148577;T:641019188;N:35615", 75, null, null, null, 663836714, 570411156, 619148577, 641019188, 35615, "SRX28428331", "SRS24751205", "SRA2113523", "US EPA", "US EPA", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2025-04-16", "Multi-stage", "Multi-stage", "Multi-tissue", "Multi-system"], [35895, "SRR33167522", "SRX28428330", "SRS24751203", "SRP579141", "PRJNA1251588", "Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish", "GSE294778", "Transcriptome Analysis", "Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.", null, null, null, "GRC355 AC4 S16", "GSM8919389", null, "source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing", "GRC355 AC4 S16", "For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3\u2019 Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples", "pooled heads collected anterior to swim bladder of larval zebrafish", null, "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2", "GSM8919389", "GSM8919389: GRC355 AC4 S16; Danio rerio; RNA Seq", "GSM8919389 r1", "GSM8919389", "1", "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP579141", null, null, "GRC355_AC4_S16_R1_001.fastq.gz", "fastq", 2318944500.0, 30919260.0, "GSM8919389 r1", "0:75", "A:622730628;C:558676778;G:600421168;T:537095873;N:20053", 75, null, null, null, 622730628, 558676778, 600421168, 537095873, 20053, "SRX28428330", "SRS24751203", "SRA2113523", "US EPA", "US EPA", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2025-04-16", "Multi-stage", "Multi-stage", "Multi-tissue", "Multi-system"], [35896, "SRR33167523", "SRX28428329", "SRS24751201", "SRP579141", "PRJNA1251588", "Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish", "GSE294778", "Transcriptome Analysis", "Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.", null, null, null, "GRC355 AC3 S10", "GSM8919388", null, "source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing", "GRC355 AC3 S10", "For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3\u2019 Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples", "pooled heads collected anterior to swim bladder of larval zebrafish", null, "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2", "GSM8919388", "GSM8919388: GRC355 AC3 S10; Danio rerio; RNA Seq", "GSM8919388 r1", "GSM8919388", "1", "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP579141", null, null, "GRC355_AC3_S10_R1_001.fastq.gz", "fastq", 2294756475.0, 30596753.0, "GSM8919388 r1", "0:75", "A:602530943;C:536584842;G:585162453;T:570445286;N:32951", 75, null, null, null, 602530943, 536584842, 585162453, 570445286, 32951, "SRX28428329", "SRS24751201", "SRA2113523", "US EPA", "US EPA", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2025-04-16", "Multi-stage", "Multi-stage", "Multi-tissue", "Multi-system"], [35897, "SRR33167524", "SRX28428328", "SRS24751202", "SRP579141", "PRJNA1251588", "Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish", "GSE294778", "Transcriptome Analysis", "Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.", null, null, null, "GRC355 AC2 S1", "GSM8919387", null, "source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing", "GRC355 AC2 S1", "For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3\u2019 Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples", "pooled heads collected anterior to swim bladder of larval zebrafish", null, "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2", "GSM8919387", "GSM8919387: GRC355 AC2 S1; Danio rerio; RNA Seq", "GSM8919387 r1", "GSM8919387", "1", "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP579141", null, null, "GRC355_AC2_S1_R1_001.fastq.gz", "fastq", 2339756250.0, 31196750.0, "GSM8919387 r1", "0:75", "A:612473749;C:554816637;G:611772519;T:560660557;N:32788", 75, null, null, null, 612473749, 554816637, 611772519, 560660557, 32788, "SRX28428328", "SRS24751202", "SRA2113523", "US EPA", "US EPA", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2025-04-16", "Multi-stage", "Multi-stage", "Multi-tissue", "Multi-system"], [35901, "SRR33167528", "SRX28428324", "SRS24751197", "SRP579141", "PRJNA1251588", "Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish", "GSE294778", "Transcriptome Analysis", "Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.", null, null, null, "MB125 2H L6.D701", "GSM8919415", null, "source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1|geo loc name:missing|collection date:missing", "MB125 2H L6.D701", "For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3\u2019 Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples", "pooled heads collected anterior to swim bladder of larval zebrafish", null, "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1", "GSM8919415", "GSM8919415: MB125 2H L6.D701; Danio rerio; RNA Seq", "GSM8919415 r1", "GSM8919415", "1", "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP579141", null, null, "MB125_2H_L6.D701_1.fastq.gz MB125_2H_L6.D701_2.fastq.gz", "fastq fastq", 2248766358.0, 22046729.0, "GSM8919415 r1", "0:51 1:51", "A:535472034;C:572268414;G:569258495;T:571751143;N:16272", 51, 51, null, null, 535472034, 572268414, 569258495, 571751143, 16272, "SRX28428324", "SRS24751197", "SRA2113523", "US EPA", "US EPA", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2025-04-16", "Multi-stage", "Multi-stage", "Multi-tissue", "Multi-system"], [35902, "SRR33167529", "SRX28428323", "SRS24751196", "SRP579141", "PRJNA1251588", "Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish", "GSE294778", "Transcriptome Analysis", "Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.", null, null, null, "MB125 2G L6.D711", "GSM8919414", null, "source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1|geo loc name:missing|collection date:missing", "MB125 2G L6.D711", "For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3\u2019 Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples", "pooled heads collected anterior to swim bladder of larval zebrafish", null, "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1", "GSM8919414", "GSM8919414: MB125 2G L6.D711; Danio rerio; RNA Seq", "GSM8919414 r1", "GSM8919414", "1", "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP579141", null, null, "MB125_2G_L6.D711_1.fastq.gz MB125_2G_L6.D711_2.fastq.gz", "fastq fastq", 2198049510.0, 21549505.0, "GSM8919414 r1", "0:51 1:51", "A:535878049;C:547290891;G:544359481;T:570502976;N:18113", 51, 51, null, null, 535878049, 547290891, 544359481, 570502976, 18113, "SRX28428323", "SRS24751196", "SRA2113523", "US EPA", "US EPA", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2025-04-16", "Multi-stage", "Multi-stage", "Multi-tissue", "Multi-system"], [35903, "SRR33167530", "SRX28428322", "SRS24751195", "SRP579141", "PRJNA1251588", "Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish", "GSE294778", "Transcriptome Analysis", "Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.", null, null, null, "MB125 2F L6.D712", "GSM8919413", null, "source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1|geo loc name:missing|collection date:missing", "MB125 2F L6.D712", "For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3\u2019 Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples", "pooled heads collected anterior to swim bladder of larval zebrafish", null, "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1", "GSM8919413", "GSM8919413: MB125 2F L6.D712; Danio rerio; RNA Seq", "GSM8919413 r1", "GSM8919413", "1", "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP579141", null, null, "MB125_2F_L6.D712_1.fastq.gz MB125_2F_L6.D712_2.fastq.gz", "fastq fastq", 2601840378.0, 25508239.0, "GSM8919413 r1", "0:51 1:51", "A:584354104;C:693159013;G:696042575;T:628262140;N:22546", 51, 51, null, null, 584354104, 693159013, 696042575, 628262140, 22546, "SRX28428322", "SRS24751195", "SRA2113523", "US EPA", "US EPA", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2025-04-16", "Multi-stage", "Multi-stage", "Multi-tissue", "Multi-system"], [35904, "SRR33167531", "SRX28428321", "SRS24751194", "SRP579141", "PRJNA1251588", "Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish", "GSE294778", "Transcriptome Analysis", "Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.", null, null, null, "MB125 2E L6.D709", "GSM8919412", null, "source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1|geo loc name:missing|collection date:missing", "MB125 2E L6.D709", "For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3\u2019 Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples", "pooled heads collected anterior to swim bladder of larval zebrafish", null, "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1", "GSM8919412", "GSM8919412: MB125 2E L6.D709; Danio rerio; RNA Seq", "GSM8919412 r1", "GSM8919412", "1", "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP579141", null, null, "MB125_2E_L6.D709_1.fastq.gz MB125_2E_L6.D709_2.fastq.gz", "fastq fastq", 2393568822.0, 23466361.0, "GSM8919412 r1", "0:51 1:51", "A:573394367;C:604936257;G:602232683;T:612984188;N:21327", 51, 51, null, null, 573394367, 604936257, 602232683, 612984188, 21327, "SRX28428321", "SRS24751194", "SRA2113523", "US EPA", "US EPA", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2025-04-16", "Multi-stage", "Multi-stage", "Multi-tissue", "Multi-system"], [35905, "SRR33167532", "SRX28428320", "SRS24751192", "SRP579141", "PRJNA1251588", "Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish", "GSE294778", "Transcriptome Analysis", "Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.", null, null, null, "MB125 2D L6.D710", "GSM8919411", null, "source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1|geo loc name:missing|collection date:missing", "MB125 2D L6.D710", "For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3\u2019 Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples", "pooled heads collected anterior to swim bladder of larval zebrafish", null, "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1", "GSM8919411", "GSM8919411: MB125 2D L6.D710; Danio rerio; RNA Seq", "GSM8919411 r1", "GSM8919411", "1", "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP579141", null, null, "MB125_2D_L6.D710_1.fastq.gz MB125_2D_L6.D710_2.fastq.gz", "fastq fastq", 2322596610.0, 22770555.0, "GSM8919411 r1", "0:51 1:51", "A:563147167;C:580081508;G:578201930;T:601145790;N:20215", 51, 51, null, null, 563147167, 580081508, 578201930, 601145790, 20215, "SRX28428320", "SRS24751192", "SRA2113523", "US EPA", "US EPA", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2025-04-16", "Multi-stage", "Multi-stage", "Multi-tissue", "Multi-system"], [35906, "SRR33167533", "SRX28428319", "SRS24751193", "SRP579141", "PRJNA1251588", "Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish", "GSE294778", "Transcriptome Analysis", "Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.", null, null, null, "GRC355 AC1 S4", "GSM8919386", null, "source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing", "GRC355 AC1 S4", "For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3\u2019 Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples", "pooled heads collected anterior to swim bladder of larval zebrafish", null, "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product\u2019s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2", "GSM8919386", "GSM8919386: GRC355 AC1 S4; Danio rerio; RNA Seq", "GSM8919386 r1", "GSM8919386", "1", "Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol\u2122 RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 \u03bcl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library \u03bcl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP579141", null, null, "GRC355_AC1_S4_R1_001.fastq.gz", "fastq", 2063624400.0, 27514992.0, "GSM8919386 r1", "0:75", "A:560729563;C:466634352;G:528754548;T:507475626;N:30311", 75, null, null, null, 560729563, 466634352, 528754548, 507475626, 30311, "SRX28428319", "SRS24751193", "SRA2113523", "US EPA", "US EPA", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2025-04-16", "Multi-stage", "Multi-stage", "Multi-tissue", "Multi-system"], [47641, "SRR6798780", "SRX3757617", "SRS3013125", "SRP133827", "PRJNA436713", "Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish", "GSE111359", "Transcriptome Analysis", "Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development  which is closely involved in adaptation and evolution. In this study  we showed that inhibition of embryonic HSP90 function  either by a chemical inhibitor radicicol or low conductivity stress  induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.", null, "pubmed:33343615", null, "RLT rep3", "GSM3029086", null, "source name:muscle tissues|tissue:muscle|treatment:radicicol", "RLT rep3", "Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene", "muscle tissues", "Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf  followed by the removal of the drug using three rinses  the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO.", "Total RNA was extracted using TRIZOL Reagent 15596 018  Life technologies following the manufacturer\u2019s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies  Santa Clara  CA  US. Qualified total RNA was further purified by RNAClean XP Kit A63987  Beckman Coulterand RNase Free DNase Set 79254  QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02  Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged.", "tissue:muscle|treatment:radicicol", "GSM3029086", "GSM3029086: RLT rep3; Danio rerio; RNA Seq", "GSM3029086", null, "1", "Total RNA was extracted using TRIZOL Reagent 15596 018  Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies  Santa Clara  CA  US. Qualified total RNA was further purified by RNAClean XP Kit A63987  Beckman Coulterand RNase Free DNase Set 79254  QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02  Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029086", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "WT3_1.fq.gz WT3_2.fq.gz", "fastq fastq", 8153906700.0, 27179689.0, "GSM3029086 r1", "0:150 1:150", "A:1876474081;C:2211352217;G:2118339495;T:1947510591;N:230316", 150, 150, null, null, 1876474081, 2211352217, 2118339495, 1947510591, 230316, "SRX3757617", "SRS3013125", "SRA663830", "GEO", "School of basic medicine science, Zhejiang University", 2, 0.93476, 0.93504, 0.13893, 0.13499, 0.82913, 0.83487, 0.53361, 0.54372, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [47642, "SRR6798779", "SRX3757616", "SRS3013124", "SRP133827", "PRJNA436713", "Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish", "GSE111359", "Transcriptome Analysis", "Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development  which is closely involved in adaptation and evolution. In this study  we showed that inhibition of embryonic HSP90 function  either by a chemical inhibitor radicicol or low conductivity stress  induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.", null, "pubmed:33343615", null, "RLT rep2", "GSM3029085", null, "source name:muscle tissues|tissue:muscle|treatment:radicicol", "RLT rep2", "Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene", "muscle tissues", "Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf  followed by the removal of the drug using three rinses  the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO.", "Total RNA was extracted using TRIZOL Reagent 15596 018  Life technologies following the manufacturer\u2019s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies  Santa Clara  CA  US. Qualified total RNA was further purified by RNAClean XP Kit A63987  Beckman Coulterand RNase Free DNase Set 79254  QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02  Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged.", "tissue:muscle|treatment:radicicol", "GSM3029085", "GSM3029085: RLT rep2; Danio rerio; RNA Seq", "GSM3029085", null, "1", "Total RNA was extracted using TRIZOL Reagent 15596 018  Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies  Santa Clara  CA  US. Qualified total RNA was further purified by RNAClean XP Kit A63987  Beckman Coulterand RNase Free DNase Set 79254  QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02  Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029085", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "WT2_1.fq.gz WT2_2.fq.gz", "fastq fastq", 7278822000.0, 24262740.0, "GSM3029085 r1", "0:150 1:150", "A:1623249687;C:2023479004;G:1940623122;T:1691262512;N:207675", 150, 150, null, null, 1623249687, 2023479004, 1940623122, 1691262512, 207675, "SRX3757616", "SRS3013124", "SRA663830", "GEO", "School of basic medicine science, Zhejiang University", 2, 0.94445, 0.94327, 0.112, 0.10647, 0.83591, 0.84226, 0.5112, 0.52155, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [47643, "SRR6798778", "SRX3757615", "SRS3013123", "SRP133827", "PRJNA436713", "Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish", "GSE111359", "Transcriptome Analysis", "Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development  which is closely involved in adaptation and evolution. In this study  we showed that inhibition of embryonic HSP90 function  either by a chemical inhibitor radicicol or low conductivity stress  induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.", null, "pubmed:33343615", null, "RLT rep1", "GSM3029084", null, "source name:muscle tissues|tissue:muscle|treatment:radicicol", "RLT rep1", "Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene", "muscle tissues", "Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf  followed by the removal of the drug using three rinses  the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO.", "Total RNA was extracted using TRIZOL Reagent 15596 018  Life technologies following the manufacturer\u2019s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies  Santa Clara  CA  US. Qualified total RNA was further purified by RNAClean XP Kit A63987  Beckman Coulterand RNase Free DNase Set 79254  QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02  Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged.", "tissue:muscle|treatment:radicicol", "GSM3029084", "GSM3029084: RLT rep1; Danio rerio; RNA Seq", "GSM3029084", null, "1", "Total RNA was extracted using TRIZOL Reagent 15596 018  Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies  Santa Clara  CA  US. Qualified total RNA was further purified by RNAClean XP Kit A63987  Beckman Coulterand RNase Free DNase Set 79254  QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02  Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029084", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "WT1_1.fq.gz WT1_2.fq.gz", "fastq fastq", 8127579000.0, 27091930.0, "GSM3029084 r1", "0:150 1:150", "A:1936609330;C:2121138923;G:2083423270;T:1986178311;N:229166", 150, 150, null, null, 1936609330, 2121138923, 2083423270, 1986178311, 229166, "SRX3757615", "SRS3013123", "SRA663830", "GEO", "School of basic medicine science, Zhejiang University", 2, 0.66403, 0.66289, 0.14695, 0.14227, 0.82503, 0.82958, 0.54774, 0.55661, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [47644, "SRR6798777", "SRX3757614", "SRS3013122", "SRP133827", "PRJNA436713", "Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish", "GSE111359", "Transcriptome Analysis", "Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development  which is closely involved in adaptation and evolution. In this study  we showed that inhibition of embryonic HSP90 function  either by a chemical inhibitor radicicol or low conductivity stress  induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.", null, "pubmed:33343615", null, "WT rep3", "GSM3029083", null, "source name:muscle tissues|tissue:muscle|treatment:DMSO", "WT rep3", "Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene", "muscle tissues", "Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf  followed by the removal of the drug using three rinses  the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO.", "Total RNA was extracted using TRIZOL Reagent 15596 018  Life technologies following the manufacturer\u2019s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies  Santa Clara  CA  US. Qualified total RNA was further purified by RNAClean XP Kit A63987  Beckman Coulterand RNase Free DNase Set 79254  QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02  Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged.", "tissue:muscle|treatment:DMSO", "GSM3029083", "GSM3029083: WT rep3; Danio rerio; RNA Seq", "GSM3029083", null, "1", "Total RNA was extracted using TRIZOL Reagent 15596 018  Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies  Santa Clara  CA  US. Qualified total RNA was further purified by RNAClean XP Kit A63987  Beckman Coulterand RNase Free DNase Set 79254  QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02  Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029083", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "RLT3_1.fq.gz RLT3_2.fq.gz", "fastq fastq", 7458295500.0, 24860985.0, "GSM3029083 r1", "0:150 1:150", "A:1875422371;C:1858400851;G:1819493497;T:1904874518;N:104263", 150, 150, null, null, 1875422371, 1858400851, 1819493497, 1904874518, 104263, "SRX3757614", "SRS3013122", "SRA663830", "GEO", "School of basic medicine science, Zhejiang University", 2, 0.88642, 0.88696, 0.1881, 0.18533, 0.79537, 0.80073, 0.50351, 0.48568, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [47645, "SRR6798776", "SRX3757613", "SRS3013120", "SRP133827", "PRJNA436713", "Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish", "GSE111359", "Transcriptome Analysis", "Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development  which is closely involved in adaptation and evolution. In this study  we showed that inhibition of embryonic HSP90 function  either by a chemical inhibitor radicicol or low conductivity stress  induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.", null, "pubmed:33343615", null, "WT rep2", "GSM3029082", null, "source name:muscle tissues|tissue:muscle|treatment:DMSO", "WT rep2", "Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene", "muscle tissues", "Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf  followed by the removal of the drug using three rinses  the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO.", "Total RNA was extracted using TRIZOL Reagent 15596 018  Life technologies following the manufacturer\u2019s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies  Santa Clara  CA  US. Qualified total RNA was further purified by RNAClean XP Kit A63987  Beckman Coulterand RNase Free DNase Set 79254  QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02  Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged.", "tissue:muscle|treatment:DMSO", "GSM3029082", "GSM3029082: WT rep2; Danio rerio; RNA Seq", "GSM3029082", null, "1", "Total RNA was extracted using TRIZOL Reagent 15596 018  Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies  Santa Clara  CA  US. Qualified total RNA was further purified by RNAClean XP Kit A63987  Beckman Coulterand RNase Free DNase Set 79254  QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02  Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029082", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "RLT2_2.fq.gz RLT2_1.fq.gz", "fastq fastq", 9462767100.0, 31542557.0, "GSM3029082 r1", "0:150 1:150", "A:2301678607;C:2445064584;G:2361534540;T:2354357373;N:131996", 150, 150, null, null, 2301678607, 2445064584, 2361534540, 2354357373, 131996, "SRX3757613", "SRS3013120", "SRA663830", "GEO", "School of basic medicine science, Zhejiang University", 2, 0.91337, 0.91337, 0.17924, 0.17526, 0.78317, 0.79011, 0.50203, 0.51647, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [47646, "SRR6798775", "SRX3757612", "SRS3013121", "SRP133827", "PRJNA436713", "Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish", "GSE111359", "Transcriptome Analysis", "Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development  which is closely involved in adaptation and evolution. In this study  we showed that inhibition of embryonic HSP90 function  either by a chemical inhibitor radicicol or low conductivity stress  induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.", null, "pubmed:33343615", null, "WT rep1", "GSM3029081", null, "source name:muscle tissues|tissue:muscle|treatment:DMSO", "WT rep1", "Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene", "muscle tissues", "Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf  followed by the removal of the drug using three rinses  the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO.", "Total RNA was extracted using TRIZOL Reagent 15596 018  Life technologies following the manufacturer\u2019s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies  Santa Clara  CA  US. Qualified total RNA was further purified by RNAClean XP Kit A63987  Beckman Coulterand RNase Free DNase Set 79254  QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02  Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged.", "tissue:muscle|treatment:DMSO", "GSM3029081", "GSM3029081: WT rep1; Danio rerio; RNA Seq", "GSM3029081", null, "1", "Total RNA was extracted using TRIZOL Reagent 15596 018  Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies  Santa Clara  CA  US. Qualified total RNA was further purified by RNAClean XP Kit A63987  Beckman Coulterand RNase Free DNase Set 79254  QIAGEN. Libraries were constructed using VAHTS Total RNA Seq\uff08H/M/R Library PrepKit for Illumina NR603 02  Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029081", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "RLT1_1.fq.gz RLT1_2.fq.gz", "fastq fastq", 7599797400.0, 25332658.0, "GSM3029081 r1", "0:150 1:150", "A:1883972109;C:1921348946;G:1869717767;T:1924652451;N:106127", 150, 150, null, null, 1883972109, 1921348946, 1869717767, 1924652451, 106127, "SRX3757612", "SRS3013121", "SRA663830", "GEO", "School of basic medicine science, Zhejiang University", 2, 0.88692, 0.88623, 0.18432, 0.18166, 0.79928, 0.80693, 0.50362, 0.5124, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2018-03-02", "Multi-stage", "Embryo", "Muscle", "Muscular System"], [52139, "SRR8945527", "SRX5725657", "SRS4663725", "SRP193485", "PRJNA534270", "Genome wide strategies reveal downstream target genes of Npas4l associated with cardiovascular development in zebrafish [RNA Seq 2]", "GSE130200", "Transcriptome Analysis", "The development of a vascular network is essential to nourish tissues and sustain organ function throughout life.  Endothelial cells ECs are the building blocks of blood vessels  yet our understanding of EC specification in vertebrates remains incomplete.  cloche/npas4l mutants have broadly been used as an avascular model in zebrafish  but little is known about the molecular mechanism of action of Npas4l.  Here  to identify the direct and indirect target genes of this transcription factor  we combined complementary genome wide approaches  including transcriptome analyses and chromatin immunoprecipitation ChIP.  The cross analysis of these datasets indicate that Npas4l functions as a master regulator by directly inducing a wave of transcription factor genes crucial for hematoendothelial specification in vertebrates  including etv2  tal1  and lmo2.  We identified additional target genes acting downstream of npas4l and investigated the function of a subset of them using CRISPR/Cas9 technology.  Phenotypic characterization of tspan18b mutants reveals a novel role for tspan18b in developmental angiogenesis  confirming the reliability of the datasets generated.  Collectively  these data represent a useful resource for future studies aimed to investigate novel genes with a potential role in vascular development and EC fate determination in vertebrates. Overall design: RNA seq examination of Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 zebrafish embryos at 6 somite stage  in duplicates.", "parent bioproject:PRJNA534269", "pubmed:31097478", null, "Cre Injected 2", "GSM3733699", null, "tissue:Embryo|genotype:Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 injected with Cre to induce recombinase", "Cre Injected 2", "The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC 0.11.8 Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Trimmomatic version 0.36 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Only reads longer than 15 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11 using STAR 2.6.0c with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.6.0 from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.14.1 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. The Ensemble annotation was enriched with UniProt data release 12.04.2018 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: danrer11 / GRCz11 Supplementary files format and content: The tab delimited matrix with DESeq normalized counts.", "Embryo", "Fish embryos raised at 28 \u030aC were subject to a 37 \u030aC heat shock for 1 hr by replacing the egg water with pre warmed 37 \u030aC egg water starting at different time points  and then keeping them in a 37 \u030aC incubator.", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 injected with cre at the one cell stage and uninjected  were grown in E3 medium at xxx\u00b0C until tailbud stage.", "genotype:Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 injected with Cre to induce recombinase", "GSM3733699", "GSM3733699: Cre Injected 2; Danio rerio; RNA Seq", "GSM3733699", null, "1", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3733699", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP193485", null, null, "Marass_RNA_lib_inj_2.fastq.gz", "fastq", 1318624367.0, 17749685.0, "GSM3733699 r1", "0:74.29 1:0", "A:320435609;C:333825364;G:380093353;T:284207932;N:62109", 74, 0, null, null, 320435609, 333825364, 380093353, 284207932, 62109, "SRX5725657", "SRS4663725", "SRA878585", "GEO", "Bioinformatics, Max Planck Institute for Heart and Lung Research", 1, 0.93022, null, 0.12203, null, 0.75935, null, 0.65366, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "Germany", "2019-04-23", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [52140, "SRR8945526", "SRX5725656", "SRS4663727", "SRP193485", "PRJNA534270", "Genome wide strategies reveal downstream target genes of Npas4l associated with cardiovascular development in zebrafish [RNA Seq 2]", "GSE130200", "Transcriptome Analysis", "The development of a vascular network is essential to nourish tissues and sustain organ function throughout life.  Endothelial cells ECs are the building blocks of blood vessels  yet our understanding of EC specification in vertebrates remains incomplete.  cloche/npas4l mutants have broadly been used as an avascular model in zebrafish  but little is known about the molecular mechanism of action of Npas4l.  Here  to identify the direct and indirect target genes of this transcription factor  we combined complementary genome wide approaches  including transcriptome analyses and chromatin immunoprecipitation ChIP.  The cross analysis of these datasets indicate that Npas4l functions as a master regulator by directly inducing a wave of transcription factor genes crucial for hematoendothelial specification in vertebrates  including etv2  tal1  and lmo2.  We identified additional target genes acting downstream of npas4l and investigated the function of a subset of them using CRISPR/Cas9 technology.  Phenotypic characterization of tspan18b mutants reveals a novel role for tspan18b in developmental angiogenesis  confirming the reliability of the datasets generated.  Collectively  these data represent a useful resource for future studies aimed to investigate novel genes with a potential role in vascular development and EC fate determination in vertebrates. Overall design: RNA seq examination of Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 zebrafish embryos at 6 somite stage  in duplicates.", "parent bioproject:PRJNA534269", "pubmed:31097478", null, "Cre Injected 1", "GSM3733698", null, "tissue:Embryo|genotype:Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 injected with Cre to induce recombinase", "Cre Injected 1", "The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC 0.11.8 Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Trimmomatic version 0.36 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Only reads longer than 15 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11 using STAR 2.6.0c with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.6.0 from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.14.1 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. The Ensemble annotation was enriched with UniProt data release 12.04.2018 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: danrer11 / GRCz11 Supplementary files format and content: The tab delimited matrix with DESeq normalized counts.", "Embryo", "Fish embryos raised at 28 \u030aC were subject to a 37 \u030aC heat shock for 1 hr by replacing the egg water with pre warmed 37 \u030aC egg water starting at different time points  and then keeping them in a 37 \u030aC incubator.", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 injected with cre at the one cell stage and uninjected  were grown in E3 medium at xxx\u00b0C until tailbud stage.", "genotype:Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 injected with Cre to induce recombinase", "GSM3733698", "GSM3733698: Cre Injected 1; Danio rerio; RNA Seq", "GSM3733698", null, "1", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3733698", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP193485", null, null, "Marass_RNA_lib_inj_1.fastq.gz", "fastq", 1238690565.0, 16655617.0, "GSM3733698 r1", "0:74.37 1:0", "A:308225901;C:304528449;G:340420680;T:285472238;N:43297", 74, 0, null, null, 308225901, 304528449, 340420680, 285472238, 43297, "SRX5725656", "SRS4663727", "SRA878585", "GEO", "Bioinformatics, Max Planck Institute for Heart and Lung Research", 1, 0.91996, null, 0.17266, null, 0.75308, null, 0.62697, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "Germany", "2019-04-23", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [52141, "SRR8945525", "SRX5725655", "SRS4663726", "SRP193485", "PRJNA534270", "Genome wide strategies reveal downstream target genes of Npas4l associated with cardiovascular development in zebrafish [RNA Seq 2]", "GSE130200", "Transcriptome Analysis", "The development of a vascular network is essential to nourish tissues and sustain organ function throughout life.  Endothelial cells ECs are the building blocks of blood vessels  yet our understanding of EC specification in vertebrates remains incomplete.  cloche/npas4l mutants have broadly been used as an avascular model in zebrafish  but little is known about the molecular mechanism of action of Npas4l.  Here  to identify the direct and indirect target genes of this transcription factor  we combined complementary genome wide approaches  including transcriptome analyses and chromatin immunoprecipitation ChIP.  The cross analysis of these datasets indicate that Npas4l functions as a master regulator by directly inducing a wave of transcription factor genes crucial for hematoendothelial specification in vertebrates  including etv2  tal1  and lmo2.  We identified additional target genes acting downstream of npas4l and investigated the function of a subset of them using CRISPR/Cas9 technology.  Phenotypic characterization of tspan18b mutants reveals a novel role for tspan18b in developmental angiogenesis  confirming the reliability of the datasets generated.  Collectively  these data represent a useful resource for future studies aimed to investigate novel genes with a potential role in vascular development and EC fate determination in vertebrates. Overall design: RNA seq examination of Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 zebrafish embryos at 6 somite stage  in duplicates.", "parent bioproject:PRJNA534269", "pubmed:31097478", null, "Uninjected 2", "GSM3733697", null, "tissue:Embryo|genotype:Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298", "Uninjected 2", "The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC 0.11.8 Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Trimmomatic version 0.36 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Only reads longer than 15 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11 using STAR 2.6.0c with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.6.0 from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.14.1 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. The Ensemble annotation was enriched with UniProt data release 12.04.2018 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: danrer11 / GRCz11 Supplementary files format and content: The tab delimited matrix with DESeq normalized counts.", "Embryo", "Fish embryos raised at 28 \u030aC were subject to a 37 \u030aC heat shock for 1 hr by replacing the egg water with pre warmed 37 \u030aC egg water starting at different time points  and then keeping them in a 37 \u030aC incubator.", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 injected with cre at the one cell stage and uninjected  were grown in E3 medium at xxx\u00b0C until tailbud stage.", "genotype:Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298", "GSM3733697", "GSM3733697: Uninjected 2; Danio rerio; RNA Seq", "GSM3733697", null, "1", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3733697", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP193485", null, null, "Marass_RNA_lib_Ab_2.fastq.gz", "fastq", 1403915686.0, 18892344.0, "GSM3733697 r1", "0:74.31 1:0", "A:317311926;C:374434129;G:413852871;T:298232684;N:84076", 74, 0, null, null, 317311926, 374434129, 413852871, 298232684, 84076, "SRX5725655", "SRS4663726", "SRA878585", "GEO", "Bioinformatics, Max Planck Institute for Heart and Lung Research", 1, 0.92665, null, 0.1128, null, 0.75929, null, 0.67981, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "Germany", "2019-04-23", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [52142, "SRR8945524", "SRX5725654", "SRS4663724", "SRP193485", "PRJNA534270", "Genome wide strategies reveal downstream target genes of Npas4l associated with cardiovascular development in zebrafish [RNA Seq 2]", "GSE130200", "Transcriptome Analysis", "The development of a vascular network is essential to nourish tissues and sustain organ function throughout life.  Endothelial cells ECs are the building blocks of blood vessels  yet our understanding of EC specification in vertebrates remains incomplete.  cloche/npas4l mutants have broadly been used as an avascular model in zebrafish  but little is known about the molecular mechanism of action of Npas4l.  Here  to identify the direct and indirect target genes of this transcription factor  we combined complementary genome wide approaches  including transcriptome analyses and chromatin immunoprecipitation ChIP.  The cross analysis of these datasets indicate that Npas4l functions as a master regulator by directly inducing a wave of transcription factor genes crucial for hematoendothelial specification in vertebrates  including etv2  tal1  and lmo2.  We identified additional target genes acting downstream of npas4l and investigated the function of a subset of them using CRISPR/Cas9 technology.  Phenotypic characterization of tspan18b mutants reveals a novel role for tspan18b in developmental angiogenesis  confirming the reliability of the datasets generated.  Collectively  these data represent a useful resource for future studies aimed to investigate novel genes with a potential role in vascular development and EC fate determination in vertebrates. Overall design: RNA seq examination of Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 zebrafish embryos at 6 somite stage  in duplicates.", "parent bioproject:PRJNA534269", "pubmed:31097478", null, "Uninjected 1", "GSM3733696", null, "tissue:Embryo|genotype:Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298", "Uninjected 1", "The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC 0.11.8 Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Trimmomatic version 0.36 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Only reads longer than 15 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11 using STAR 2.6.0c with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.6.0 from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.14.1 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. The Ensemble annotation was enriched with UniProt data release 12.04.2018 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: danrer11 / GRCz11 Supplementary files format and content: The tab delimited matrix with DESeq normalized counts.", "Embryo", "Fish embryos raised at 28 \u030aC were subject to a 37 \u030aC heat shock for 1 hr by replacing the egg water with pre warmed 37 \u030aC egg water starting at different time points  and then keeping them in a 37 \u030aC incubator.", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 injected with cre at the one cell stage and uninjected  were grown in E3 medium at xxx\u00b0C until tailbud stage.", "genotype:Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298", "GSM3733696", "GSM3733696: Uninjected 1; Danio rerio; RNA Seq", "GSM3733696", null, "1", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3733696", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP193485", null, null, "Marass_RNA_lib_Ab_1.fastq.gz", "fastq", 1439519955.0, 19389235.0, "GSM3733696 r1", "0:74.24 1:0", "A:306530355;C:398952556;G:440224503;T:293709258;N:103283", 74, 0, null, null, 306530355, 398952556, 440224503, 293709258, 103283, "SRX5725654", "SRS4663724", "SRA878585", "GEO", "Bioinformatics, Max Planck Institute for Heart and Lung Research", 1, 0.93162, null, 0.10646, null, 0.76627, null, 0.68572, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "Germany", "2019-04-23", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [53513, "SRR9906847", "SRX6657804", "SRS5218265", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdahN36R2", "GSM4007833", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 2", "zfRNAnmdahN36R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.", "Retina", "For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 2", "GSM4007833", "GSM4007833: zfRNAnmdahN36R2; Danio rerio; RNA Seq", "GSM4007833", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-TF4N_S8_R1_001.fastq.gz THoa-TF4N_S8_R2_001.fastq.gz", "fastq fastq", 7928700600.0, 52858004.0, "GSM4007833 r1", "0:75 1:75", "A:2214653986;C:1699850211;G:1809132429;T:2204054149;N:1009825", 75, 75, null, null, 2214653986, 1699850211, 1809132429, 2204054149, 1009825, "SRX6657804", "SRS5218265", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.88014, 0.90383, 0.394, 0.41783, 0.76607, 0.77043, 0.5474, 0.55256, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53514, "SRR9906846", "SRX6657803", "SRS5218264", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdahN36R1", "GSM4007832", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 1", "zfRNAnmdahN36R1", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.", "Retina", "For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 1", "GSM4007832", "GSM4007832: zfRNAnmdahN36R1; Danio rerio; RNA Seq", "GSM4007832", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-TF3N_S7_R1_001.fastq.gz THoa-TF3N_S7_R2_001.fastq.gz", "fastq fastq", 7863596250.0, 52423975.0, "GSM4007832 r1", "0:75 1:75", "A:2245214380;C:1641445245;G:1740385747;T:2235554179;N:996699", 75, 75, null, null, 2245214380, 1641445245, 1740385747, 2235554179, 996699, "SRX6657803", "SRS5218264", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.86899, 0.89643, 0.43639, 0.46473, 0.76631, 0.77086, 0.53259, 0.53462, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53515, "SRR9906845", "SRX6657802", "SRS5218263", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdahN20R2", "GSM4007831", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 2", "zfRNAnmdahN20R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.", "Retina", "For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 2", "GSM4007831", "GSM4007831: zfRNAnmdahN20R2; Danio rerio; RNA Seq", "GSM4007831", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-TF2N_S6_R1_001.fastq.gz THoa-TF2N_S6_R2_001.fastq.gz", "fastq fastq", 11221029450.0, 74806863.0, "GSM4007831 r1", "0:75 1:75", "A:3206652122;C:2349148827;G:2475237997;T:3188565893;N:1424611", 75, 75, null, null, 3206652122, 2349148827, 2475237997, 3188565893, 1424611, "SRX6657802", "SRS5218263", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.86571, 0.89458, 0.44089, 0.4703, 0.77163, 0.77573, 0.54887, 0.54576, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53516, "SRR9906844", "SRX6657801", "SRS5218262", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdahN20R1", "GSM4007830", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 1", "zfRNAnmdahN20R1", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.", "Retina", "For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 1", "GSM4007830", "GSM4007830: zfRNAnmdahN20R1; Danio rerio; RNA Seq", "GSM4007830", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-TF1N_S5_R1_001.fastq.gz THoa-TF1N_S5_R2_001.fastq.gz", "fastq fastq", 11263633950.0, 75090893.0, "GSM4007830 r1", "0:75 1:75", "A:3198241763;C:2374935676;G:2514695492;T:3174314457;N:1446562", 75, 75, null, null, 3198241763, 2374935676, 2514695492, 3174314457, 1446562, "SRX6657801", "SRS5218262", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.87624, 0.90304, 0.39909, 0.42417, 0.76984, 0.77376, 0.53406, 0.53718, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53517, "SRR9906843", "SRX6657800", "SRS5218261", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdahP36R2", "GSM4007829", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 2", "zfRNAnmdahP36R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.", "Retina", "For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 2", "GSM4007829", "GSM4007829: zfRNAnmdahP36R2; Danio rerio; RNA Seq", "GSM4007829", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-TF4P_S4_R1_001.fastq.gz THoa-TF4P_S4_R2_001.fastq.gz", "fastq fastq", 10599378900.0, 70662526.0, "GSM4007829 r1", "0:75 1:75", "A:2917939167;C:2338922409;G:2472546084;T:2868616483;N:1354757", 75, 75, null, null, 2917939167, 2338922409, 2472546084, 2868616483, 1354757, "SRX6657800", "SRS5218261", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.89693, 0.9159, 0.31259, 0.33022, 0.7371, 0.74182, 0.56412, 0.56559, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53518, "SRR9906842", "SRX6657799", "SRS5218260", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdahP36R1", "GSM4007828", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 1", "zfRNAnmdahP36R1", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.", "Retina", "For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 1", "GSM4007828", "GSM4007828: zfRNAnmdahP36R1; Danio rerio; RNA Seq", "GSM4007828", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-TF3P_S3_R1_001.fastq.gz THoa-TF3P_S3_R2_001.fastq.gz", "fastq fastq", 11034687150.0, 73564581.0, "GSM4007828 r1", "0:75 1:75", "A:2954740084;C:2509220120;G:2662792371;T:2906521814;N:1412761", 75, 75, null, null, 2954740084, 2509220120, 2662792371, 2906521814, 1412761, "SRX6657799", "SRS5218260", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.90866, 0.9253, 0.29649, 0.3138, 0.7419, 0.74793, 0.57845, 0.59013, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53519, "SRR9906841", "SRX6657798", "SRS5218259", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdahP20R2", "GSM4007827", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 2", "zfRNAnmdahP20R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.", "Retina", "For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 2", "GSM4007827", "GSM4007827: zfRNAnmdahP20R2; Danio rerio; RNA Seq", "GSM4007827", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-TF2P_S2_R1_001.fastq.gz THoa-TF2P_S2_R2_001.fastq.gz", "fastq fastq", 10416796950.0, 69445313.0, "GSM4007827 r1", "0:75 1:75", "A:2846027907;C:2324721617;G:2438862539;T:2805866203;N:1318684", 75, 75, null, null, 2846027907, 2324721617, 2438862539, 2805866203, 1318684, "SRX6657798", "SRS5218259", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.89999, 0.92352, 0.30772, 0.32822, 0.74823, 0.75089, 0.5489, 0.55828, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53520, "SRR9906840", "SRX6657797", "SRS5218258", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdahP20R1", "GSM4007826", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 1", "zfRNAnmdahP20R1", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.", "Retina", "For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 1", "GSM4007826", "GSM4007826: zfRNAnmdahP20R1; Danio rerio; RNA Seq", "GSM4007826", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-TF1P_S1_R1_001.fastq.gz THoa-TF1P_S1_R2_001.fastq.gz", "fastq fastq", 11087990850.0, 73919939.0, "GSM4007826 r1", "0:75 1:75", "A:3086331907;C:2414289581;G:2547013161;T:3038947630;N:1408571", 75, 75, null, null, 3086331907, 2414289581, 2547013161, 3038947630, 1408571, "SRX6657797", "SRS5218258", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.89541, 0.9175, 0.30129, 0.32289, 0.7417, 0.74714, 0.55292, 0.55122, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53521, "SRR9906839", "SRX6657796", "SRS5218257", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdaN36R2", "GSM4007825", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 2", "zfRNAnmdaN36R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.", "Retina", "For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 2", "GSM4007825", "GSM4007825: zfRNAnmdaN36R2; Danio rerio; RNA Seq", "GSM4007825", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF16N_S7_R1_001.fastq.gz THoa-DF16N_S7_R2_001.fastq.gz", "fastq fastq", 7593295650.0, 50621971.0, "GSM4007825 r1", "0:75 1:75", "A:1842742463;C:1931868500;G:2009769570;T:1805690959;N:3224158", 75, 75, null, null, 1842742463, 1931868500, 2009769570, 1805690959, 3224158, "SRX6657796", "SRS5218257", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.93981, 0.95204, 0.24731, 0.26265, 0.81412, 0.81811, 0.67154, 0.67196, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53522, "SRR9906838", "SRX6657795", "SRS5218256", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdaN36R1", "GSM4007824", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 1", "zfRNAnmdaN36R1", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.", "Retina", "For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 1", "GSM4007824", "GSM4007824: zfRNAnmdaN36R1; Danio rerio; RNA Seq", "GSM4007824", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF15N_S6_R1_001.fastq.gz THoa-DF15N_S6_R2_001.fastq.gz", "fastq fastq", 7927875450.0, 52852503.0, "GSM4007824 r1", "0:75 1:75", "A:1938512738;C:1988054202;G:2080463145;T:1917497438;N:3347927", 75, 75, null, null, 1938512738, 1988054202, 2080463145, 1917497438, 3347927, "SRX6657795", "SRS5218256", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.93468, 0.94808, 0.25462, 0.27334, 0.81262, 0.81548, 0.6351, 0.66108, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53523, "SRR9906837", "SRX6657794", "SRS5218255", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdaN20R2", "GSM4007823", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 2", "zfRNAnmdaN20R2", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.", "Retina", "For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 2", "GSM4007823", "GSM4007823: zfRNAnmdaN20R2; Danio rerio; RNA Seq", "GSM4007823", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "DF29N_S7_R1_001.fastq.gz DF29N_S7_R2_001.fastq.gz", "fastq fastq", 7876840694.0, 52829905.0, "GSM4007823 r1", "0:74.55 1:74.55", "A:2010274884;C:1895760244;G:1963812981;T:2004863879;N:2128706", 74, 74, null, null, 2010274884, 1895760244, 1963812981, 2004863879, 2128706, "SRX6657794", "SRS5218255", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.90858, 0.91979, 0.28522, 0.29978, 0.81742, 0.82104, 0.6582, 0.65941, 74, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [53524, "SRR9906836", "SRX6657793", "SRS5218254", "SRP217505", "PRJNA558770", "Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia", "GSE135406", "Other", "Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.", null, "pubmed:33004674;pubmed:35259089;pubmed:38123561", null, "zfRNAnmdaN20R1", "GSM4007822", null, "source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 1", "zfRNAnmdaN20R1", "Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.", "Retina", "For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32\u00b0C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 \u03bcl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32\u00b0C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", "To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on \u2013 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5\u00b0C.", "tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 1", "GSM4007822", "GSM4007822: zfRNAnmdaN20R1; Danio rerio; RNA Seq", "GSM4007822", null, "1", "RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37\u00b0C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP217505", null, null, "THoa-DF13N_S5_R1_001.fastq.gz THoa-DF13N_S5_R2_001.fastq.gz", "fastq fastq", 8003905950.0, 53359373.0, "GSM4007822 r1", "0:75 1:75", "A:1925414212;C:2030985118;G:2137411382;T:1906727349;N:3367889", 75, 75, null, null, 1925414212, 2030985118, 2137411382, 1906727349, 3367889, "SRX6657793", "SRS5218254", "SRA934563", "GEO", "Ophthalmology, Johns Hopkins University", 2, 0.94476, 0.95272, 0.22584, 0.24304, 0.81404, 0.8186, 0.68349, 0.6811, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "trueseq", "sc_generic", "bulk", "bulk", null, "United States", "2019-08-05", "Multi-stage", "Multi-stage", "Eye", "Sensory System"]], "truncated": false, 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