{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"other\", experiment.library_source = \"TRANSCRIPTOMIC\" 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"], [25188, "SRR25670735", "SRX21396039", "SRS18636197", "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 1024cell PAL seq v4", "GSM7716868", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA 1024cell 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", "GSM7716868", "GSM7716868: Fish embryo mRNA 1024cell PAL seq v4; Danio rerio; OTHER", "GSM7716868 r1", "GSM7716868", "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_1024cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_1024cell_PAL_seq_v4_rep1_raw_read2.fastq.gz", "fastq fastq", 2191900794.0, 7139742.0, "GSM7716868 r1", "0:52 1:255", "A:571954354;C:551162617;G:572445400;T:490238669;N:6099754", 52, 255, null, null, 571954354, 551162617, 572445400, 490238669, 6099754, "SRX21396039", "SRS18636197", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.0011, 0.43387, 6e-05, 0.01058, 0.99864, 0.99971, 0.74576, 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", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25189, "SRR25670736", "SRX21396039", "SRS18636197", "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 1024cell PAL seq v4", "GSM7716868", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA 1024cell 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", "GSM7716868", "GSM7716868: Fish embryo mRNA 1024cell PAL seq v4; Danio rerio; OTHER", "GSM7716868 r1", "GSM7716868", "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_1024cell_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_1024cell_PAL_seq_v4_rep2_raw_read2.fastq.gz", "fastq fastq", 3840723193.0, 12510499.0, "GSM7716868 r2", "0:52 1:255", "A:985340216;C:991311706;G:1034487140;T:821820974;N:7763157", 52, 255, null, null, 985340216, 991311706, 1034487140, 821820974, 7763157, "SRX21396039", "SRS18636197", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.0021, 0.0, 0.00026, 0.0, 0.99859, 1.0, 0.71022, 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", "Zygote", "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"], [25194, "SRR25670741", "SRX21396036", "SRS18636194", "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 1cell PAL seq v4", "GSM7716865", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA 1cell 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", "GSM7716865", "GSM7716865: Fish embryo mRNA 1cell PAL seq v4; Danio rerio; OTHER", "GSM7716865 r1", "GSM7716865", "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_1cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_1cell_PAL_seq_v4_rep1_raw_read2.fastq.gz", "fastq fastq", 2050143851.0, 6677993.0, "GSM7716865 r1", "0:52 1:255", "A:536391564;C:527126186;G:557802929;T:422990166;N:5833006", 52, 255, null, null, 536391564, 527126186, 557802929, 422990166, 5833006, "SRX21396036", "SRS18636194", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00016, 0.46479, 4e-05, 0.01408, 0.99979, 0.99969, 0.54545, 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", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25195, "SRR25670742", "SRX21396036", "SRS18636194", "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 1cell PAL seq v4", "GSM7716865", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA 1cell 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", "GSM7716865", "GSM7716865: Fish embryo mRNA 1cell PAL seq v4; Danio rerio; OTHER", "GSM7716865 r1", "GSM7716865", "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_1cell_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_1cell_PAL_seq_v4_rep2_raw_read2.fastq.gz", "fastq fastq", 3406093776.0, 11094768.0, "GSM7716865 r2", "0:52 1:255", "A:868054279;C:890446070;G:945289336;T:695324057;N:6980034", 52, 255, null, null, 868054279, 890446070, 945289336, 695324057, 6980034, "SRX21396036", "SRS18636194", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00049, 0.0, 0.00014, 0.0, 0.99939, 1.0, 0.58974, 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", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [32033, "SRR28976522", "SRX24505963", "SRS21254128", "SRP506702", "PRJNA1109723", "rbm24a is an organizer component of germ plasm to determine germ cell fate", "GSE267086", "Other", "The  formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants  but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs  which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows  where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs  resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm  highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish  we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.", null, null, null, "Zebrafish  RIP seq  Rbm24a Knock in IP", "GSM8259538", null, "source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:GFP|geo loc name:missing|collection date:missing", "Zebrafish  RIP seq  Rbm24a Knock in IP", "Each library was amplified by a 15 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample", "whole embryo", null, "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer\u2019s instructions.", "Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C", "tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:GFP", "GSM8259538", "GSM8259538: Zebrafish  RIP seq  Rbm24a Knock in IP; Danio rerio; RIP Seq", "GSM8259538 r1", "GSM8259538", "1", "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer's instructions.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP506702", null, null, "RIP_KI_IP_R2.fq.gz RIP_KI_IP_R1.fq.gz", "fastq fastq", 6457893104.0, 21383752.0, "GSM8259538 r1", "0:151 1:151", "A:975588225;C:2019180290;G:2469634919;T:992947702;N:541968", 151, 151, null, null, 975588225, 2019180290, 2469634919, 992947702, 541968, "SRX24505963", "SRS21254128", "SRA1863578", "Ang Li, College of Life Sciences, shandong university", "Ang Li, College of Life Sciences, shandong university", 2, 0.90304, 0.86018, 0.20083, 0.20471, 0.96382, 0.96743, 0.96102, 0.98876, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "China", "2024-05-09", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [32034, "SRR28976523", "SRX24505962", "SRS21254127", "SRP506702", "PRJNA1109723", "rbm24a is an organizer component of germ plasm to determine germ cell fate", "GSE267086", "Other", "The  formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants  but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs  which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows  where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs  resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm  highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish  we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.", null, null, null, "Zebrafish  RIP seq  wild type IP", "GSM8259537", null, "source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:GFP|geo loc name:missing|collection date:missing", "Zebrafish  RIP seq  wild type IP", "Each library was amplified by a 15 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample", "whole embryo", null, "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer\u2019s instructions.", "Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C", "tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:GFP", "GSM8259537", "GSM8259537: Zebrafish  RIP seq  wild type IP; Danio rerio; RIP Seq", "GSM8259537 r1", "GSM8259537", "1", "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer's instructions.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP506702", null, null, "RIP_WT_IP_R2.fq.gz RIP_WT_IP_R1.fq.gz", "fastq fastq", 4501412680.0, 14905340.0, "GSM8259537 r1", "0:151 1:151", "A:651609366;C:1285679784;G:1901211768;T:662533141;N:378621", 151, 151, null, null, 651609366, 1285679784, 1901211768, 662533141, 378621, "SRX24505962", "SRS21254127", "SRA1863578", "Ang Li, College of Life Sciences, shandong university", "Ang Li, College of Life Sciences, shandong university", 2, 0.96426, 0.81361, 0.26579, 0.2253, 0.97784, 0.97806, 0.8699, 0.93379, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "China", "2024-05-09", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [32035, "SRR28976524", "SRX24505961", "SRS21254126", "SRP506702", "PRJNA1109723", "rbm24a is an organizer component of germ plasm to determine germ cell fate", "GSE267086", "Other", "The  formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants  but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs  which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows  where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs  resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm  highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish  we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.", null, null, null, "Zebrafish  RIP seq  Rbm24a Knock in input", "GSM8259536", null, "source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:input|geo loc name:missing|collection date:missing", "Zebrafish  RIP seq  Rbm24a Knock in input", "Each library was amplified by a 15 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample", "whole embryo", null, "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer\u2019s instructions.", "Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C", "tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:input", "GSM8259536", "GSM8259536: Zebrafish  RIP seq  Rbm24a Knock in input; Danio rerio; RIP Seq", "GSM8259536 r1", "GSM8259536", "1", "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer's instructions.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP506702", null, null, "RIP_KI_Input_R2.fq.gz RIP_KI_Input_R1.fq.gz", "fastq fastq", 9539398726.0, 31587413.0, "GSM8259536 r1", "0:151 1:151", "A:2233069830;C:2078359171;G:3009942870;T:2217201959;N:824896", 151, 151, null, null, 2233069830, 2078359171, 3009942870, 2217201959, 824896, "SRX24505961", "SRS21254126", "SRA1863578", "Ang Li, College of Life Sciences, shandong university", "Ang Li, College of Life Sciences, shandong university", 2, 0.90112, 0.81448, 0.02415, 0.01993, 0.79287, 0.79807, 0.47884, 0.48186, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "China", "2024-05-09", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [32036, "SRR28976525", "SRX24505960", "SRS21254125", "SRP506702", "PRJNA1109723", "rbm24a is an organizer component of germ plasm to determine germ cell fate", "GSE267086", "Other", "The  formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants  but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs  which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows  where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs  resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm  highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish  we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.", null, null, null, "Zebrafish  RIP seq  wild type input", "GSM8259535", null, "source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:input|geo loc name:missing|collection date:missing", "Zebrafish  RIP seq  wild type input", "Each library was amplified by a 15 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample", "whole embryo", null, "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer\u2019s instructions.", "Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C", "tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:input", "GSM8259535", "GSM8259535: Zebrafish  RIP seq  wild type input; Danio rerio; RIP Seq", "GSM8259535 r1", "GSM8259535", "1", "Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 \u00b5g/each sample. 1 \u03bcg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer's instructions.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP506702", null, null, "RIP_WT_Input_R2.fq.gz RIP_WT_Input_R1.fq.gz", "fastq fastq", 14180410302.0, 46955001.0, "GSM8259535 r1", "0:151 1:151", "A:3380011534;C:2883841476;G:4593876270;T:3321465622;N:1215400", 151, 151, null, null, 3380011534, 2883841476, 4593876270, 3321465622, 1215400, "SRX24505960", "SRS21254125", "SRA1863578", "Ang Li, College of Life Sciences, shandong university", "Ang Li, College of Life Sciences, shandong university", 2, 0.86497, 0.64685, 0.04432, 0.02854, 0.79324, 0.8031, 0.52927, 0.53304, 151, 151, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "China", "2024-05-09", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [36373, "SRR499871", "SRX148961", "SRS334490", "SRP013309", "PRJNA167302", "Transcriptomic profiles of zebrafish embryos exposed to silver nanoparticles  bulk and ions using HT SuperSAGE in a Illumina GA2 platform", "GSE38125", "Other", "Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.", null, "pubmed:23758687", null, "Dre 48h silver ions", "GSM935123", null, "source name:Dre 48h silver ions|strain:wild type WIK strain|tissue:whole embryos|developmental stage:48 hpf|treatment:silver ions 0.25 \u00b5g/L of silver nitrate|barcode:GCGA", "Dre 48h silver ions", "FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. FASTQ to FASTA from the FASTX Toolkit was used to convert the fastq files to fasta files. FASTQ/A trimmer from the FASTX Toolkit was used to remove the barcodes the first 4 bases from the sequence. A Perl script was used to remove all bases post the last occurence of CATG NlaIII restriction site  used for sequence tag preparation in each of the sequences FASTX collapser was used to collapse the sequences and calculate the frequency of unique sequence tags unitags in each library Supplementary files format and content: tabulated text files include frequency of all unitags in the treatment library", "Dre 48h silver ions", "Stock solutions for Ag NP  Ag Bulk and silver nitrate were made up in ultrapure water  and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers  at 28+/  1\u00b0C with a 12h light: dark photoperiod. Immediately prior to the start of the exposures  glass chambers received 400 mL of ISO water  prepared according to OECD guidelines for zebrafish embryo experiments http://www.oecd.org/  containing 5 \u00b5g/L of 10nm Ag NP  5  \u00b5g/L of Ag Bulk or 0.25  \u00b5g/L of silver nitrate. A control chamber was set up containing water alone.  Solutions were replaced every 12h during the exposure period  and dead embryos were removed at the times of replacement of the exposure water. At 24h and 48h  3 pools of 50 embryos were removed from each exposure tank  immediately frozen in liquid nitrogen and stored at  80\u00b0C for analysis of gene expression. The experiment was terminated at 48 hpf.", "High throughput HT SuperSAGE libraries were prepared as described in Matsumura et al 2010  PLoS ONE 58:e12010. Samples were multiplexed on each lane of the Illumina flow cell.", "Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al.  2008 Aquat Toxicol. 872:115 26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers  approximately 1 hpf. Eggs were then cleaned and unfertilised embryos were removed prior to the exposures.", "strain:wild type WIK strain|tissue:whole embryos|developmental stage:48 hpf|treatment:silver ions 0.25 \u00b5g/L of silver nitrate|barcode:GCGA", "GSM935123", "GSM935123: Dre 48h silver ions; Danio rerio; OTHER", "GSM935123 1", "GSM935123: Dre 48h silver ions", "1", null, "GEO Accession:GSM935123", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013309", null, null, "Dre_48h_ag.gz", "fastq", 85514364.0, 2375399.0, "GSM935123 r1", "0:36", "A:18075876;C:24481350;G:23393114;T:19494907;N:69117", 36, null, null, null, 18075876, 24481350, 23393114, 19494907, 69117, "SRX148961", "SRS334490", "SRA053074", "GEO", "van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter", 1, 0.11101, null, 0.00946, null, 0.96224, null, 0.6991, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "other", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2012-05-22", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [36374, "SRR499870", "SRX148960", "SRS334489", "SRP013309", "PRJNA167302", "Transcriptomic profiles of zebrafish embryos exposed to silver nanoparticles  bulk and ions using HT SuperSAGE in a Illumina GA2 platform", "GSE38125", "Other", "Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.", null, "pubmed:23758687", null, "Dre 48h silver bulk", "GSM935122", null, "source name:Dre 48h silver bulk|strain:wild type WIK strain|tissue:whole embryos|developmental stage:48 hpf|treatment:silver bulk 0.6 1.6\u00b5m; 5 \u00b5g/L|barcode:GCGC", "Dre 48h silver bulk", "FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. FASTQ to FASTA from the FASTX Toolkit was used to convert the fastq files to fasta files. FASTQ/A trimmer from the FASTX Toolkit was used to remove the barcodes the first 4 bases from the sequence. A Perl script was used to remove all bases post the last occurence of CATG NlaIII restriction site  used for sequence tag preparation in each of the sequences FASTX collapser was used to collapse the sequences and calculate the frequency of unique sequence tags unitags in each library Supplementary files format and content: tabulated text files include frequency of all unitags in the treatment library", "Dre 48h silver bulk", "Stock solutions for Ag NP  Ag Bulk and silver nitrate were made up in ultrapure water  and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers  at 28+/  1\u00b0C with a 12h light: dark photoperiod. Immediately prior to the start of the exposures  glass chambers received 400 mL of ISO water  prepared according to OECD guidelines for zebrafish embryo experiments http://www.oecd.org/  containing 5 \u00b5g/L of 10nm Ag NP  5  \u00b5g/L of Ag Bulk or 0.25  \u00b5g/L of silver nitrate. A control chamber was set up containing water alone.  Solutions were replaced every 12h during the exposure period  and dead embryos were removed at the times of replacement of the exposure water. At 24h and 48h  3 pools of 50 embryos were removed from each exposure tank  immediately frozen in liquid nitrogen and stored at  80\u00b0C for analysis of gene expression. The experiment was terminated at 48 hpf.", "High throughput HT SuperSAGE libraries were prepared as described in Matsumura et al 2010  PLoS ONE 58:e12010. Samples were multiplexed on each lane of the Illumina flow cell.", "Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al.  2008 Aquat Toxicol. 872:115 26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers  approximately 1 hpf. Eggs were then cleaned and unfertilised embryos were removed prior to the exposures.", "strain:wild type WIK strain|tissue:whole embryos|developmental stage:48 hpf|treatment:silver bulk 0.6 1.6\u00b5m; 5 \u00b5g/L|barcode:GCGC", "GSM935122", "GSM935122: Dre 48h silver bulk; Danio rerio; OTHER", "GSM935122 1", "GSM935122: Dre 48h silver bulk", "1", null, "GEO Accession:GSM935122", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013309", null, null, "Dre_48h_bulk.gz", "fastq", 95750712.0, 2659742.0, "GSM935122 r1", "0:36", "A:17624901;C:29735122;G:26376026;T:21938121;N:76542", 36, null, null, null, 17624901, 29735122, 26376026, 21938121, 76542, "SRX148960", "SRS334489", "SRA053074", "GEO", "van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter", 1, 0.18319, null, 0.01693, null, 0.94391, null, 0.57004, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "other", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2012-05-22", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [36375, "SRR499869", "SRX148959", "SRS334488", "SRP013309", "PRJNA167302", "Transcriptomic profiles of zebrafish embryos exposed to silver nanoparticles  bulk and ions using HT SuperSAGE in a Illumina GA2 platform", "GSE38125", "Other", "Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.", null, "pubmed:23758687", null, "Dre 48h silver NP", "GSM935121", null, "source name:Dre 48h silver NP|strain:wild type WIK strain|tissue:whole embryos|developmental stage:48 hpf|treatment:silver nanoparticles 10nm; 5\u00b5g/L|barcode:GCTG", "Dre 48h silver NP", "FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. FASTQ to FASTA from the FASTX Toolkit was used to convert the fastq files to fasta files. FASTQ/A trimmer from the FASTX Toolkit was used to remove the barcodes the first 4 bases from the sequence. A Perl script was used to remove all bases post the last occurence of CATG NlaIII restriction site  used for sequence tag preparation in each of the sequences FASTX collapser was used to collapse the sequences and calculate the frequency of unique sequence tags unitags in each library Supplementary files format and content: tabulated text files include frequency of all unitags in the treatment library", "Dre 48h silver NP", "Stock solutions for Ag NP  Ag Bulk and silver nitrate were made up in ultrapure water  and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers  at 28+/  1\u00b0C with a 12h light: dark photoperiod. Immediately prior to the start of the exposures  glass chambers received 400 mL of ISO water  prepared according to OECD guidelines for zebrafish embryo experiments http://www.oecd.org/  containing 5 \u00b5g/L of 10nm Ag NP  5  \u00b5g/L of Ag Bulk or 0.25  \u00b5g/L of silver nitrate. A control chamber was set up containing water alone.  Solutions were replaced every 12h during the exposure period  and dead embryos were removed at the times of replacement of the exposure water. At 24h and 48h  3 pools of 50 embryos were removed from each exposure tank  immediately frozen in liquid nitrogen and stored at  80\u00b0C for analysis of gene expression. The experiment was terminated at 48 hpf.", "High throughput HT SuperSAGE libraries were prepared as described in Matsumura et al 2010  PLoS ONE 58:e12010. Samples were multiplexed on each lane of the Illumina flow cell.", "Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al.  2008 Aquat Toxicol. 872:115 26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers  approximately 1 hpf. Eggs were then cleaned and unfertilised embryos were removed prior to the exposures.", "strain:wild type WIK strain|tissue:whole embryos|developmental stage:48 hpf|treatment:silver nanoparticles 10nm; 5\u00b5g/L|barcode:GCTG", "GSM935121", "GSM935121: Dre 48h silver NP; Danio rerio; OTHER", "GSM935121 1", "GSM935121: Dre 48h silver NP", "1", null, "GEO Accession:GSM935121", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013309", null, null, "Dre_48h_NP.gz", "fastq", 52931304.0, 1470314.0, "GSM935121 r1", "0:36", "A:10003539;C:15279729;G:14487570;T:13116768;N:43698", 36, null, null, null, 10003539, 15279729, 14487570, 13116768, 43698, "SRX148959", "SRS334488", "SRA053074", "GEO", "van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter", 1, 0.14206, null, 0.01226, null, 0.95477, null, 0.58652, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "other", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2012-05-22", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [36376, "SRR499868", "SRX148958", "SRS334487", "SRP013309", "PRJNA167302", "Transcriptomic profiles of zebrafish embryos exposed to silver nanoparticles  bulk and ions using HT SuperSAGE in a Illumina GA2 platform", "GSE38125", "Other", "Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.", null, "pubmed:23758687", null, "Dre 48h control", "GSM935120", null, "source name:Dre 48h control|strain:wild type WIK strain|tissue:whole embryos|developmental stage:48 hpf|treatment:control|barcode:GCTT", "Dre 48h control", "FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. FASTQ to FASTA from the FASTX Toolkit was used to convert the fastq files to fasta files. FASTQ/A trimmer from the FASTX Toolkit was used to remove the barcodes the first 4 bases from the sequence. A Perl script was used to remove all bases post the last occurence of CATG NlaIII restriction site  used for sequence tag preparation in each of the sequences FASTX collapser was used to collapse the sequences and calculate the frequency of unique sequence tags unitags in each library Supplementary files format and content: tabulated text files include frequency of all unitags in the treatment library", "Dre 48h control", "Stock solutions for Ag NP  Ag Bulk and silver nitrate were made up in ultrapure water  and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers  at 28+/  1\u00b0C with a 12h light: dark photoperiod. Immediately prior to the start of the exposures  glass chambers received 400 mL of ISO water  prepared according to OECD guidelines for zebrafish embryo experiments http://www.oecd.org/  containing 5 \u00b5g/L of 10nm Ag NP  5  \u00b5g/L of Ag Bulk or 0.25  \u00b5g/L of silver nitrate. A control chamber was set up containing water alone.  Solutions were replaced every 12h during the exposure period  and dead embryos were removed at the times of replacement of the exposure water. At 24h and 48h  3 pools of 50 embryos were removed from each exposure tank  immediately frozen in liquid nitrogen and stored at  80\u00b0C for analysis of gene expression. The experiment was terminated at 48 hpf.", "High throughput HT SuperSAGE libraries were prepared as described in Matsumura et al 2010  PLoS ONE 58:e12010. Samples were multiplexed on each lane of the Illumina flow cell.", "Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al.  2008 Aquat Toxicol. 872:115 26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers  approximately 1 hpf. Eggs were then cleaned and unfertilised embryos were removed prior to the exposures.", "strain:wild type WIK strain|tissue:whole embryos|developmental stage:48 hpf|treatment:control|barcode:GCTT", "GSM935120", "GSM935120: Dre 48h control; Danio rerio; OTHER", "GSM935120 1", "GSM935120: Dre 48h control", "1", null, "GEO Accession:GSM935120", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013309", null, null, "Dre_48h_control.gz", "fastq", 75389652.0, 2094157.0, "GSM935120 r1", "0:36", "A:13252992;C:21927091;G:18790968;T:21232585;N:186016", 36, null, null, null, 13252992, 21927091, 18790968, 21232585, 186016, "SRX148958", "SRS334487", "SRA053074", "GEO", "van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter", 1, 0.12359, null, 0.01182, null, 0.95929, null, 0.56028, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "other", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2012-05-22", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [36377, "SRR499867", "SRX148957", "SRS334486", "SRP013309", "PRJNA167302", "Transcriptomic profiles of zebrafish embryos exposed to silver nanoparticles  bulk and ions using HT SuperSAGE in a Illumina GA2 platform", "GSE38125", "Other", "Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.", null, "pubmed:23758687", null, "Dre 24h silver ions", "GSM935119", null, "source name:Dre 24h silver ions|strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:silver ions 0.25 \u00b5g/L of silver nitrate|barcode:GCTA", "Dre 24h silver ions", "FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. FASTQ to FASTA from the FASTX Toolkit was used to convert the fastq files to fasta files. FASTQ/A trimmer from the FASTX Toolkit was used to remove the barcodes the first 4 bases from the sequence. A Perl script was used to remove all bases post the last occurence of CATG NlaIII restriction site  used for sequence tag preparation in each of the sequences FASTX collapser was used to collapse the sequences and calculate the frequency of unique sequence tags unitags in each library Supplementary files format and content: tabulated text files include frequency of all unitags in the treatment library", "Dre 24h silver ions", "Stock solutions for Ag NP  Ag Bulk and silver nitrate were made up in ultrapure water  and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers  at 28+/  1\u00b0C with a 12h light: dark photoperiod. Immediately prior to the start of the exposures  glass chambers received 400 mL of ISO water  prepared according to OECD guidelines for zebrafish embryo experiments http://www.oecd.org/  containing 5 \u00b5g/L of 10nm Ag NP  5  \u00b5g/L of Ag Bulk or 0.25  \u00b5g/L of silver nitrate. A control chamber was set up containing water alone.  Solutions were replaced every 12h during the exposure period  and dead embryos were removed at the times of replacement of the exposure water. At 24h and 48h  3 pools of 50 embryos were removed from each exposure tank  immediately frozen in liquid nitrogen and stored at  80\u00b0C for analysis of gene expression. The experiment was terminated at 48 hpf.", "High throughput HT SuperSAGE libraries were prepared as described in Matsumura et al 2010  PLoS ONE 58:e12010. Samples were multiplexed on each lane of the Illumina flow cell.", "Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al.  2008 Aquat Toxicol. 872:115 26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers  approximately 1 hpf. Eggs were then cleaned and unfertilised embryos were removed prior to the exposures.", "strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:silver ions 0.25 \u00b5g/L of silver nitrate|barcode:GCTA", "GSM935119", "GSM935119: Dre 24h silver ions; Danio rerio; OTHER", "GSM935119 1", "GSM935119: Dre 24h silver ions", "1", null, "GEO Accession:GSM935119", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013309", null, null, "Dre_24h_ag.gz", "fastq", 57745404.0, 1604039.0, "GSM935119 r1", "0:36", "A:11280863;C:17795869;G:15444087;T:13175334;N:49251", 36, null, null, null, 11280863, 17795869, 15444087, 13175334, 49251, "SRX148957", "SRS334486", "SRA053074", "GEO", "van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter", 1, 0.10143, null, 0.00773, null, 0.96435, null, 0.60432, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "other", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2012-05-22", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [36378, "SRR499866", "SRX148956", "SRS334485", "SRP013309", "PRJNA167302", "Transcriptomic profiles of zebrafish embryos exposed to silver nanoparticles  bulk and ions using HT SuperSAGE in a Illumina GA2 platform", "GSE38125", "Other", "Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.", null, "pubmed:23758687", null, "Dre 24h silver bulk", "GSM935118", null, "source name:Dre 24h silver bulk|strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:silver bulk 0.6 1.6\u00b5m; 5 \u00b5g/L|barcode:GCTC", "Dre 24h silver bulk", "FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. FASTQ to FASTA from the FASTX Toolkit was used to convert the fastq files to fasta files. FASTQ/A trimmer from the FASTX Toolkit was used to remove the barcodes the first 4 bases from the sequence. A Perl script was used to remove all bases post the last occurence of CATG NlaIII restriction site  used for sequence tag preparation in each of the sequences FASTX collapser was used to collapse the sequences and calculate the frequency of unique sequence tags unitags in each library Supplementary files format and content: tabulated text files include frequency of all unitags in the treatment library", "Dre 24h silver bulk", "Stock solutions for Ag NP  Ag Bulk and silver nitrate were made up in ultrapure water  and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers  at 28+/  1\u00b0C with a 12h light: dark photoperiod. Immediately prior to the start of the exposures  glass chambers received 400 mL of ISO water  prepared according to OECD guidelines for zebrafish embryo experiments http://www.oecd.org/  containing 5 \u00b5g/L of 10nm Ag NP  5  \u00b5g/L of Ag Bulk or 0.25  \u00b5g/L of silver nitrate. A control chamber was set up containing water alone.  Solutions were replaced every 12h during the exposure period  and dead embryos were removed at the times of replacement of the exposure water. At 24h and 48h  3 pools of 50 embryos were removed from each exposure tank  immediately frozen in liquid nitrogen and stored at  80\u00b0C for analysis of gene expression. The experiment was terminated at 48 hpf.", "High throughput HT SuperSAGE libraries were prepared as described in Matsumura et al 2010  PLoS ONE 58:e12010. Samples were multiplexed on each lane of the Illumina flow cell.", "Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al.  2008 Aquat Toxicol. 872:115 26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers  approximately 1 hpf. Eggs were then cleaned and unfertilised embryos were removed prior to the exposures.", "strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:silver bulk 0.6 1.6\u00b5m; 5 \u00b5g/L|barcode:GCTC", "GSM935118", "GSM935118: Dre 24h silver bulk; Danio rerio; OTHER", "GSM935118 1", "GSM935118: Dre 24h silver bulk", "1", null, "GEO Accession:GSM935118", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013309", null, null, "Dre_24h_bulk.gz", "fastq", 53296632.0, 1480462.0, "GSM935118 r1", "0:36", "A:8986044;C:17367907;G:13631579;T:13181001;N:130101", 36, null, null, null, 8986044, 17367907, 13631579, 13181001, 130101, "SRX148956", "SRS334485", "SRA053074", "GEO", "van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter", 1, 0.078, null, 0.00708, null, 0.96877, null, 0.4609, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "other", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2012-05-22", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [36379, "SRR499865", "SRX148955", "SRS334484", "SRP013309", "PRJNA167302", "Transcriptomic profiles of zebrafish embryos exposed to silver nanoparticles  bulk and ions using HT SuperSAGE in a Illumina GA2 platform", "GSE38125", "Other", "Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.", null, "pubmed:23758687", null, "Dre 24h silver NP", "GSM935117", null, "source name:Dre 24h silver NP|strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:silver nanoparticles 10nm; 5\u00b5g/L|barcode:GCAG", "Dre 24h silver NP", "FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. FASTQ to FASTA from the FASTX Toolkit was used to convert the fastq files to fasta files. FASTQ/A trimmer from the FASTX Toolkit was used to remove the barcodes the first 4 bases from the sequence. A Perl script was used to remove all bases post the last occurence of CATG NlaIII restriction site  used for sequence tag preparation in each of the sequences FASTX collapser was used to collapse the sequences and calculate the frequency of unique sequence tags unitags in each library Supplementary files format and content: tabulated text files include frequency of all unitags in the treatment library", "Dre 24h silver NP", "Stock solutions for Ag NP  Ag Bulk and silver nitrate were made up in ultrapure water  and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers  at 28+/  1\u00b0C with a 12h light: dark photoperiod. Immediately prior to the start of the exposures  glass chambers received 400 mL of ISO water  prepared according to OECD guidelines for zebrafish embryo experiments http://www.oecd.org/  containing 5 \u00b5g/L of 10nm Ag NP  5  \u00b5g/L of Ag Bulk or 0.25  \u00b5g/L of silver nitrate. A control chamber was set up containing water alone.  Solutions were replaced every 12h during the exposure period  and dead embryos were removed at the times of replacement of the exposure water. At 24h and 48h  3 pools of 50 embryos were removed from each exposure tank  immediately frozen in liquid nitrogen and stored at  80\u00b0C for analysis of gene expression. The experiment was terminated at 48 hpf.", "High throughput HT SuperSAGE libraries were prepared as described in Matsumura et al 2010  PLoS ONE 58:e12010. Samples were multiplexed on each lane of the Illumina flow cell.", "Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al.  2008 Aquat Toxicol. 872:115 26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers  approximately 1 hpf. Eggs were then cleaned and unfertilised embryos were removed prior to the exposures.", "strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:silver nanoparticles 10nm; 5\u00b5g/L|barcode:GCAG", "GSM935117", "GSM935117: Dre 24h silver NP; Danio rerio; OTHER", "GSM935117 1", "GSM935117: Dre 24h silver NP", "1", null, "GEO Accession:GSM935117", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013309", null, null, "Dre_24h_NP.gz", "fastq", 103827096.0, 2884086.0, "GSM935117 r1", "0:36", "A:22437552;C:29017806;G:28385826;T:23907583;N:78329", 36, null, null, null, 22437552, 29017806, 28385826, 23907583, 78329, "SRX148955", "SRS334484", "SRA053074", "GEO", "van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter", 1, 0.16321, null, 0.01606, null, 0.94631, null, 0.45783, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "other", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2012-05-22", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [36380, "SRR499864", "SRX148954", "SRS334483", "SRP013309", "PRJNA167302", "Transcriptomic profiles of zebrafish embryos exposed to silver nanoparticles  bulk and ions using HT SuperSAGE in a Illumina GA2 platform", "GSE38125", "Other", "Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.", null, "pubmed:23758687", null, "Dre 24h control", "GSM935116", null, "source name:Dre 24h control|strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:control|barcode:GCAT", "Dre 24h control", "FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. FASTQ to FASTA from the FASTX Toolkit was used to convert the fastq files to fasta files. FASTQ/A trimmer from the FASTX Toolkit was used to remove the barcodes the first 4 bases from the sequence. A Perl script was used to remove all bases post the last occurence of CATG NlaIII restriction site  used for sequence tag preparation in each of the sequences FASTX collapser was used to collapse the sequences and calculate the frequency of unique sequence tags unitags in each library Supplementary files format and content: tabulated text files include frequency of all unitags in the treatment library", "Dre 24h control", "Stock solutions for Ag NP  Ag Bulk and silver nitrate were made up in ultrapure water  and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers  at 28+/  1\u00b0C with a 12h light: dark photoperiod. Immediately prior to the start of the exposures  glass chambers received 400 mL of ISO water  prepared according to OECD guidelines for zebrafish embryo experiments http://www.oecd.org/  containing 5 \u00b5g/L of 10nm Ag NP  5  \u00b5g/L of Ag Bulk or 0.25  \u00b5g/L of silver nitrate. A control chamber was set up containing water alone.  Solutions were replaced every 12h during the exposure period  and dead embryos were removed at the times of replacement of the exposure water. At 24h and 48h  3 pools of 50 embryos were removed from each exposure tank  immediately frozen in liquid nitrogen and stored at  80\u00b0C for analysis of gene expression. The experiment was terminated at 48 hpf.", "High throughput HT SuperSAGE libraries were prepared as described in Matsumura et al 2010  PLoS ONE 58:e12010. Samples were multiplexed on each lane of the Illumina flow cell.", "Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al.  2008 Aquat Toxicol. 872:115 26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers  approximately 1 hpf. Eggs were then cleaned and unfertilised embryos were removed prior to the exposures.", "strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:control|barcode:GCAT", "GSM935116", "GSM935116: Dre 24h control; Danio rerio; OTHER", "GSM935116 1", "GSM935116: Dre 24h control", "1", null, "GEO Accession:GSM935116", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013309", null, null, "Dre_24h_control.gz", "fastq", 85032468.0, 2362013.0, "GSM935116 r1", "0:36", "A:16524315;C:24822030;G:21632275;T:21837611;N:216237", 36, null, null, null, 16524315, 24822030, 21632275, 21837611, 216237, "SRX148954", "SRS334483", "SRA053074", "GEO", "van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter", 1, 0.13983, null, 0.01175, null, 0.95966, null, 0.52467, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "other", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2012-05-22", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [41511, "SRR5004963", "SRX2336797", "SRS1790193", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "zebrafish embryos ythdf2 RIP rep2", "GSM2386192", null, "source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "zebrafish embryos ythdf2 RIP rep2", "Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample  reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples Supplementary files format and content: ythdf2 binding target.xls: ythdf2 binding targets identified by macs2 software", "zebrafish embryos", null, "For RIP seq  RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.", null, "genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "GSM2386192", "GSM2386192: zebrafish embryos ythdf2 RIP rep2; Danio rerio; RIP Seq", "GSM2386192", null, "1", "For RIP seq  RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.", "GEO Accession:GSM2386192", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP092907", null, null, "ythdf2_RIP_rep2_1.fastq.gz ythdf2_RIP_rep2_2.fastq.gz", "fastq fastq", 4007024510.0, 19836755.0, "GSM2386192 r1", "0:101 1:101", "A:769487104;C:1245093129;G:1251328145;T:740377823;N:738309", 101, 101, null, null, 769487104, 1245093129, 1251328145, 740377823, 738309, "SRX2336797", "SRS1790193", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.97768, 0.97802, 0.22786, 0.21743, 0.89885, 0.89968, 0.77584, 0.83808, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41512, "SRR5004962", "SRX2336796", "SRS1790194", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "zebrafish embryos ythdf2 RIP rep1", "GSM2386191", null, "source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "zebrafish embryos ythdf2 RIP rep1", "Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample  reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples Supplementary files format and content: ythdf2 binding target.xls: ythdf2 binding targets identified by macs2 software", "zebrafish embryos", null, "For RIP seq  RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.", null, "genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "GSM2386191", "GSM2386191: zebrafish embryos ythdf2 RIP rep1; Danio rerio; RIP Seq", "GSM2386191", null, "1", "For RIP seq  RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.", "GEO Accession:GSM2386191", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP092907", null, null, "ythdf2_RIP_rep1_1.fastq.gz ythdf2_RIP_rep1_2.fastq.gz", "fastq fastq", 6144583662.0, 30418731.0, "GSM2386191 r1", "0:101 1:101", "A:1227614258;C:1869131844;G:1825793436;T:1220118819;N:1925305", 101, 101, null, null, 1227614258, 1869131844, 1825793436, 1220118819, 1925305, "SRX2336796", "SRS1790194", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.96857, 0.96917, 0.23397, 0.22377, 0.89832, 0.90147, 0.78619, 0.8258, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41521, "SRR5004953", "SRX2336787", "SRS1790184", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "mettl3 morphant zebrafish embryos m6A IP rep2", "GSM2386182", null, "source name:zebrafish embryos|genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems", "mettl3 morphant zebrafish embryos m6A IP rep2", "Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: m6A peak locus.xls: m6A peaks indentified by macs2 software Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples", "zebrafish embryos", null, "For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.", null, "genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems", "GSM2386182", "GSM2386182: mettl3 morphant zebrafish embryos m6A IP rep2; Danio rerio; OTHER", "GSM2386182", null, "1", "For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.", "GEO Accession:GSM2386182", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP092907", null, null, "mettl3-mo_IP_rep2_1.fastq.gz mettl3-mo_IP_rep2_2.fastq.gz", "fastq fastq", 12246129204.0, 60624402.0, "GSM2386182 r1", "0:101 1:101", "A:3253814653;C:2887966071;G:2921051332;T:3179545005;N:3752143", 101, 101, null, null, 3253814653, 2887966071, 2921051332, 3179545005, 3752143, "SRX2336787", "SRS1790184", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.93906, 0.94462, 0.08073, 0.07972, 0.69148, 0.69394, 0.43224, 0.48778, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41522, "SRR5004952", "SRX2336785", "SRS1790183", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "mettl3 morphant zebrafish embryos m6A IP rep1", "GSM2386181", null, "source name:zebrafish embryos|genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems", "mettl3 morphant zebrafish embryos m6A IP rep1", "Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: m6A peak locus.xls: m6A peaks indentified by macs2 software Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples", "zebrafish embryos", null, "For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 151 bp.", null, "genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems", "GSM2386181", "GSM2386181: mettl3 morphant zebrafish embryos m6A IP rep1; Danio rerio; OTHER", "GSM2386181", null, "1", "For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 151 bp.", "GEO Accession:GSM2386181", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP092907", null, null, "mettl3-mo_IP_rep1_1.fastq.gz mettl3-mo_IP_rep1_2.fastq.gz", "fastq fastq", 22767872412.0, 75390306.0, "GSM2386181 r1", "0:151 1:151", "A:6356270201;C:5175380564;G:5545741592;T:5686194578;N:4285477", 151, 151, null, null, 6356270201, 5175380564, 5545741592, 5686194578, 4285477, "SRX2336785", "SRS1790183", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.94647, 0.95162, 0.07314, 0.07248, 0.70796, 0.71021, 0.54859, 0.54624, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41523, "SRR5004951", "SRX2336784", "SRS1790182", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "control zebrafish embryos input rep2", "GSM2386180", null, "source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "control zebrafish embryos input rep2", "Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples", "zebrafish embryos", null, "For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.", null, "genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "GSM2386180", "GSM2386180: control zebrafish embryos input rep2; Danio rerio; OTHER", "GSM2386180", null, "1", "For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.", "GEO Accession:GSM2386180", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP092907", null, null, "control_input_rep2_1.fastq.gz control_input_rep2_2.fastq.gz", "fastq fastq", 20629042748.0, 102123974.0, "GSM2386180 r1", "0:101 1:101", "A:5541548211;C:4810650367;G:4699999124;T:5571342766;N:5502280", 101, 101, null, null, 5541548211, 4810650367, 4699999124, 5571342766, 5502280, "SRX2336784", "SRS1790182", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.94898, 0.9511, 0.10842, 0.10266, 0.70465, 0.70481, 0.4986, 0.48915, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41524, "SRR5004950", "SRX2336783", "SRS1790181", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "control zebrafish embryos input rep1", "GSM2386179", null, "source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "control zebrafish embryos input rep1", "Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples", "zebrafish embryos", null, "For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 151 bp.", null, "genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "GSM2386179", "GSM2386179: control zebrafish embryos input rep1; Danio rerio; OTHER", "GSM2386179", null, "1", "For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 151 bp.", "GEO Accession:GSM2386179", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP092907", null, null, "control_input_rep1_1.fastq.gz control_input_rep1_2.fastq.gz", "fastq fastq", 27776308060.0, 91974530.0, "GSM2386179 r1", "0:151 1:151", "A:7467418896;C:6517753701;G:6333567394;T:7452805069;N:4763000", 151, 151, null, null, 7467418896, 6517753701, 6333567394, 7452805069, 4763000, "SRX2336783", "SRS1790181", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.95616, 0.95939, 0.10401, 0.09776, 0.72263, 0.73637, 0.57906, 0.58185, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41525, "SRR5004949", "SRX2336782", "SRS1790180", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "control zebrafish embryos m6A IP rep2", "GSM2386178", null, "source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems", "control zebrafish embryos m6A IP rep2", "Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: m6A peak locus.xls: m6A peaks indentified by macs2 software Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples", "zebrafish embryos", null, "For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.", null, "genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems", "GSM2386178", "GSM2386178: control zebrafish embryos m6A IP rep2; Danio rerio; OTHER", "GSM2386178", null, "1", "For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.", "GEO Accession:GSM2386178", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP092907", null, null, "control_IP_rep2_1.fastq.gz control_IP_rep2_2.fastq.gz", "fastq fastq", 11899573964.0, 58908782.0, "GSM2386178 r1", "0:101 1:101", "A:3146907590;C:2817914269;G:2838718195;T:3092392965;N:3640945", 101, 101, null, null, 3146907590, 2817914269, 2838718195, 3092392965, 3640945, "SRX2336782", "SRS1790180", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.93821, 0.94281, 0.08361, 0.08174, 0.69676, 0.69816, 0.4628, 0.46386, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41526, "SRR5004948", "SRX2336781", "SRS1790179", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "control zebrafish embryos m6A IP rep1", "GSM2386177", null, "source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems", "control zebrafish embryos m6A IP rep1", "Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: m6A peak locus.xls: m6A peaks indentified by macs2 software Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples", "zebrafish embryos", null, "For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 151 bp.", null, "genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems", "GSM2386177", "GSM2386177: control zebrafish embryos m6A IP rep1; Danio rerio; OTHER", "GSM2386177", null, "1", "For MeRIP seq  mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 151 bp.", "GEO Accession:GSM2386177", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP092907", null, null, "control_IP_rep1_1.fastq.gz control_IP_rep1_2.fastq.gz", "fastq fastq", 16582066208.0, 54907504.0, "GSM2386177 r1", "0:151 1:151", "A:4529890968;C:3812739433;G:4031512714;T:4204817283;N:3105810", 151, 151, null, null, 4529890968, 3812739433, 4031512714, 4204817283, 3105810, "SRX2336781", "SRS1790179", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.93701, 0.95377, 0.07009, 0.07008, 0.70972, 0.71173, 0.54711, 0.54995, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [50802, "SRR8298668", "SRX5113214", "SRS4122013", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 3", null, "4dpi#3", null, "breed:zebrafish|age:220 days|sex:missing|tissue:whole heart|time point:4 dpi|time replicate:4dpi#3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "4dpi rep3", "5940", "5940", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5940_S30_L006_R1_001.fastq.gz SID5940_S30_L006_R2_001.fastq.gz", "fastq fastq", 5188299450.0, 34588663.0, "SID5940 S30 L006 R1 001.fastq.gz", "0:75 1:75", "A:1444454822;C:1145256079;G:1148548307;T:1446499267;N:3540975", 75, 75, null, null, 1444454822, 1145256079, 1148548307, 1446499267, 3540975, "SRX5113214", "SRS4122013", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92184, 0.92415, 0.30116, 0.30149, 0.73592, 0.7399, 0.54201, 0.38073, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50803, "SRR8298669", "SRX5113213", "SRS4122012", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 1", null, "7dpi#1", null, "breed:zebrafish|age:273 days|sex:missing|tissue:whole heart|time point:7 dpi|time replicate:7dpi#1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "7dpi rep1", "5941", "5941", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5941_S29_L006_R1_001.fastq.gz SID5941_S29_L006_R2_001.fastq.gz", "fastq fastq", 5015554500.0, 33437030.0, "SID5941 S29 L006 R1 001.fastq.gz", "0:75 1:75", "A:1408835824;C:1099569560;G:1095191795;T:1408578266;N:3379055", 75, 75, null, null, 1408835824, 1099569560, 1095191795, 1408578266, 3379055, "SRX5113213", "SRS4122012", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92786, 0.93052, 0.26842, 0.26815, 0.76881, 0.77061, 0.57369, 0.57478, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50804, "SRR8298670", "SRX5113212", "SRS4122011", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 1", null, "4dpi#1", null, "breed:zebrafish|age:220 days|sex:missing|tissue:whole heart|time point:4 dpi|time replicate:4dpi#1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "4dpi rep1", "5938", "5938", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5938_S31_L006_R1_001.fastq.gz SID5938_S31_L006_R2_001.fastq.gz", "fastq fastq", 4100604750.0, 27337365.0, "SID5938 S31 L006 R1 001.fastq.gz", "0:75 1:75", "A:1149519787;C:899546129;G:898736633;T:1150023754;N:2778447", 75, 75, null, null, 1149519787, 899546129, 898736633, 1150023754, 2778447, "SRX5113212", "SRS4122011", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92416, 0.92519, 0.28682, 0.28584, 0.74237, 0.74592, 0.56445, 0.56447, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50805, "SRR8298671", "SRX5113211", "SRS4122010", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 2", null, "4dpi#2", null, "breed:zebrafish|age:220 days|sex:missing|tissue:whole heart|time point:4 dpi|time replicate:4dpi#2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "4dpi rep2", "5939", "5939", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5939_S32_L006_R1_001.fastq.gz SID5939_S32_L006_R2_001.fastq.gz", "fastq fastq", 4921234500.0, 32808230.0, "SID5939 S32 L006 R1 001.fastq.gz", "0:75 1:75", "A:1378004009;C:1080255504;G:1081677671;T:1377977314;N:3320002", 75, 75, null, null, 1378004009, 1080255504, 1081677671, 1377977314, 3320002, "SRX5113211", "SRS4122010", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.91946, 0.92276, 0.29123, 0.29112, 0.74182, 0.74539, 0.54354, 0.53724, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50806, "SRR8298672", "SRX5113210", "SRS4122009", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 2", null, "1dpi#2", null, "breed:zebrafish|age:319 days|sex:missing|tissue:whole heart|time point:1 dpi|time replicate:1dpi#2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "1dpi rep2", "5936", "5936", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5936_S21_L005_R2_001.fastq.gz SID5936_S21_L005_R1_001.fastq.gz", "fastq fastq", 5881601400.0, 39210676.0, "SID5936 S21 L005 R1 001.fastq.gz", "0:75 1:75", "A:1644521714;C:1296876199;G:1294933688;T:1641742109;N:3527690", 75, 75, null, null, 1644521714, 1296876199, 1294933688, 1641742109, 3527690, "SRX5113210", "SRS4122009", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92098, 0.92581, 0.27799, 0.27825, 0.76181, 0.76402, 0.57268, 0.5784, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2018-12-11", "Adult", "Adult", "Heart", "Cardiovascular System"], [50807, "SRR8298673", "SRX5113209", "SRS4122008", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 3", null, "1dpi#3", null, "breed:zebrafish|age:319 days|sex:missing|tissue:whole heart|time point:1 dpi|time replicate:1dpi#3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "1dpi rep3", "5937", "5937", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5937_S22_L005_R2_001.fastq.gz SID5937_S22_L005_R1_001.fastq.gz", "fastq fastq", 3621605550.0, 24144037.0, "SID5937 S22 L005 R1 001.fastq.gz", "0:75 1:75", "A:1010499889;C:803727762;G:812481024;T:992740068;N:2156807", 75, 75, null, null, 1010499889, 803727762, 812481024, 992740068, 2156807, "SRX5113209", "SRS4122008", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.91363, 0.91424, 0.24399, 0.24106, 0.76006, 0.76684, 0.59983, 0.58985, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2018-12-11", "Adult", "Adult", "Heart", "Cardiovascular System"], [50808, "SRR8298674", "SRX5113208", "SRS4122007", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 3", null, "sham#3", null, "breed:zebrafish|age:288 days|sex:missing|tissue:whole heart|time point:sham|time replicate:sham#3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sham rep3", "5934", "5934", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5934_S24_L005_R1_001.fastq.gz SID5934_S24_L005_R2_001.fastq.gz", "fastq fastq", 3509520600.0, 23396804.0, "SID5934 S24 L005 R1 001.fastq.gz", "0:75 1:75", "A:983495990;C:772289722;G:772021702;T:979606291;N:2106895", 75, 75, null, null, 983495990, 772289722, 772021702, 979606291, 2106895, "SRX5113208", "SRS4122007", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92688, 0.92939, 0.27458, 0.27381, 0.78309, 0.78723, 0.56919, 0.57178, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50809, "SRR8298675", "SRX5113207", "SRS4122006", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 1", null, "1dpi#1", null, "breed:zebrafish|age:319 days|sex:missing|tissue:whole heart|time point:1 dpi|time replicate:1dpi#1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "1dpi rep1", "5935", "5935", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5935_S23_L005_R1_001.fastq.gz SID5935_S23_L005_R2_001.fastq.gz", "fastq fastq", 5314974300.0, 35433162.0, "SID5935 S23 L005 R1 001.fastq.gz", "0:75 1:75", "A:1507510407;C:1155668287;G:1144742973;T:1503897494;N:3155139", 75, 75, null, null, 1507510407, 1155668287, 1144742973, 1503897494, 3155139, "SRX5113207", "SRS4122006", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.91872, 0.92108, 0.26295, 0.26278, 0.78508, 0.78835, 0.77063, 0.77073, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50810, "SRR8298676", "SRX5113206", "SRS4122005", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 1", null, "sham#1", null, "breed:zebrafish|age:288 days|sex:missing|tissue:whole heart|time point:sham|time replicate:sham#1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sham rep1", "5932", "5932", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5932_S25_L005_R1_001.fastq.gz SID5932_S25_L005_R2_001.fastq.gz", "fastq fastq", 5425627650.0, 36170851.0, "SID5932 S25 L005 R1 001.fastq.gz", "0:75 1:75", "A:1521456861;C:1194916965;G:1177157390;T:1528831524;N:3264910", 75, 75, null, null, 1521456861, 1194916965, 1177157390, 1528831524, 3264910, "SRX5113206", "SRS4122005", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92306, 0.92597, 0.26707, 0.26536, 0.80677, 0.80971, 0.57418, 0.57898, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50811, "SRR8298677", "SRX5113205", "SRS4122004", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 2", null, "sham#2", null, "breed:zebrafish|age:288 days|sex:missing|tissue:whole heart|time point:sham|time replicate:sham#2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sham rep2", "5933", "5933", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5933_S26_L005_R1_001.fastq.gz SID5933_S26_L005_R2_001.fastq.gz", "fastq fastq", 5773503750.0, 38490025.0, "SID5933 S26 L005 R1 001.fastq.gz", "0:75 1:75", "A:1615221347;C:1273042064;G:1255074373;T:1626681961;N:3484005", 75, 75, null, null, 1615221347, 1273042064, 1255074373, 1626681961, 3484005, "SRX5113205", "SRS4122004", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92587, 0.92714, 0.27509, 0.27353, 0.79855, 0.80006, 0.57301, 0.57575, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50812, "SRR8298678", "SRX5113204", "SRS4122003", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 3", null, "AgeCtr120dpi#3", null, "breed:zebrafish|age:378 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy120dpi|time replicate:AgeCtr120dpi#3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "AgeMatchCtr120dpi rep3", "8900", "8900", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID8900_S6_L001_R1_001.fastq.gz SID8900_S6_L001_R2_001.fastq.gz", "fastq fastq", 4707897000.0, 31385980.0, "SID8900 S6 L001 R1 001.fastq.gz", "0:75 1:75", "A:1337630387;C:1014865394;G:1014074014;T:1340631407;N:695798", 75, 75, null, null, 1337630387, 1014865394, 1014074014, 1340631407, 695798, "SRX5113204", "SRS4122003", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.93145, 0.93312, 0.28428, 0.28539, 0.77666, 0.77958, 0.61824, 0.61733, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50813, "SRR8298679", "SRX5113203", "SRS4122001", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 1", null, "AgeCtr45dpi#1", null, "breed:zebrafish|age:302 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy45dpi|time replicate:AgeCtr45dpi#1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "AgeMatchCtr45dpi rep1", "8901", "8901", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID8901_S7_L002_R1_001.fastq.gz SID8901_S7_L002_R2_001.fastq.gz", "fastq fastq", 3952220100.0, 26348134.0, "SID8901 S7 L002 R1 001.fastq.gz", "0:75 1:75", "A:1117201923;C:857412505;G:861138833;T:1115890129;N:576710", 75, 75, null, null, 1117201923, 857412505, 861138833, 1115890129, 576710, "SRX5113203", "SRS4122001", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.93193, 0.93451, 0.28235, 0.28132, 0.77064, 0.77246, 0.60098, 0.60153, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50814, "SRR8298680", "SRX5113202", "SRS4122002", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 2", null, "21dpi#2", null, "breed:zebrafish|age:267 days|sex:missing|tissue:whole heart|time point:21 dpi|time replicate:21dpi#2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "21dpi rep2", "5948", "5948", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5948_S37_L007_R1_001.fastq.gz SID5948_S37_L007_R2_001.fastq.gz", "fastq fastq", 5483888850.0, 36559259.0, "SID5948 S37 L007 R1 001.fastq.gz", "0:75 1:75", "A:1539988374;C:1201795186;G:1199710952;T:1539542582;N:2851756", 75, 75, null, null, 1539988374, 1201795186, 1199710952, 1539542582, 2851756, "SRX5113202", "SRS4122002", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92071, 0.92596, 0.28014, 0.27952, 0.77078, 0.77283, 0.59179, 0.59946, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50815, "SRR8298681", "SRX5113201", "SRS4122000", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 3", null, "21dpi#3", null, "breed:zebrafish|age:267 days|sex:missing|tissue:whole heart|time point:21 dpi|time replicate:21dpi#3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "21dpi rep3", "5949", "5949", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5949_S38_L007_R1_001.fastq.gz SID5949_S38_L007_R2_001.fastq.gz", "fastq fastq", 4819312650.0, 32128751.0, "SID5949 S38 L007 R1 001.fastq.gz", "0:75 1:75", "A:1361991024;C:1048571509;G:1043232390;T:1363001014;N:2516713", 75, 75, null, null, 1361991024, 1048571509, 1043232390, 1363001014, 2516713, "SRX5113201", "SRS4122000", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.90783, 0.91107, 0.27083, 0.26934, 0.77167, 0.77516, 0.61614, 0.61731, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50816, "SRR8298682", "SRX5113200", "SRS4121998", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 3", null, "14dpi#3", null, "breed:zebrafish|age:NA|sex:missing|tissue:whole heart|time point:14 dpi|time replicate:14dpi#3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "14dpi rep3", "5946", "5946", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5946_S35_L007_R1_001.fastq.gz SID5946_S35_L007_R2_001.fastq.gz", "fastq fastq", 4648725300.0, 30991502.0, "SID5946 S35 L007 R1 001.fastq.gz", "0:75 1:75", "A:1303485934;C:1019161225;G:1015495862;T:1308163547;N:2418732", 75, 75, null, null, 1303485934, 1019161225, 1015495862, 1308163547, 2418732, "SRX5113200", "SRS4121998", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92153, 0.92446, 0.28679, 0.28712, 0.77792, 0.78042, 0.57131, 0.56895, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [50817, "SRR8298683", "SRX5113199", "SRS4121999", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 1", null, "21dpi#1", null, "breed:zebrafish|age:267 days|sex:missing|tissue:whole heart|time point:21 dpi|time replicate:21dpi#1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "21dpi rep1", "5947", "5947", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5947_S36_L007_R2_001.fastq.gz SID5947_S36_L007_R1_001.fastq.gz", "fastq fastq", 5219275350.0, 34795169.0, "SID5947 S36 L007 R1 001.fastq.gz", "0:75 1:75", "A:1469045456;C:1139906507;G:1137109871;T:1470492666;N:2720850", 75, 75, null, null, 1469045456, 1139906507, 1137109871, 1470492666, 2720850, "SRX5113199", "SRS4121999", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.90788, 0.91129, 0.28166, 0.28101, 0.7624, 0.76712, 0.57412, 0.60264, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2018-12-11", "Adult", "Adult", "Heart", "Cardiovascular System"], [50818, "SRR8298684", "SRX5113198", "SRS4121997", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 1", null, "14dpi#1", null, "breed:zebrafish|age:NA|sex:missing|tissue:whole heart|time point:14 dpi|time replicate:14dpi#1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "14dpi rep1", "5944", "5944", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5944_S33_L007_R1_001.fastq.gz SID5944_S33_L007_R2_001.fastq.gz", "fastq fastq", 4880230050.0, 32534867.0, "SID5944 S33 L007 R1 001.fastq.gz", "0:75 1:75", "A:1375786208;C:1064869277;G:1049678552;T:1387347217;N:2548796", 75, 75, null, null, 1375786208, 1064869277, 1049678552, 1387347217, 2548796, "SRX5113198", "SRS4121997", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92418, 0.92876, 0.27259, 0.27339, 0.78526, 0.78888, 0.57372, 0.57769, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [50819, "SRR8298685", "SRX5113197", "SRS4121996", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 2", null, "14dpi#2", null, "breed:zebrafish|age:NA|sex:missing|tissue:whole heart|time point:14 dpi|time replicate:14dpi#2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "14dpi rep2", "5945", "5945", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5945_S34_L007_R1_001.fastq.gz SID5945_S34_L007_R2_001.fastq.gz", "fastq fastq", 4722657450.0, 31484383.0, "SID5945 S34 L007 R1 001.fastq.gz", "0:75 1:75", "A:1318733900;C:1041426176;G:1033500671;T:1326546335;N:2450368", 75, 75, null, null, 1318733900, 1041426176, 1033500671, 1326546335, 2450368, "SRX5113197", "SRS4121996", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92723, 0.92976, 0.27077, 0.27133, 0.76232, 0.76451, 0.57825, 0.57723, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [50820, "SRR8298686", "SRX5113196", "SRS4121995", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 2", null, "7dpi#2", null, "breed:zebrafish|age:273 days|sex:missing|tissue:whole heart|time point:7 dpi|time replicate:7dpi#2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "7dpi rep2", "5942", "5942", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5942_S28_L006_R1_001.fastq.gz SID5942_S28_L006_R2_001.fastq.gz", "fastq fastq", 5171801700.0, 34478678.0, "SID5942 S28 L006 R1 001.fastq.gz", "0:75 1:75", "A:1457147640;C:1127485743;G:1124661741;T:1459005403;N:3501173", 75, 75, null, null, 1457147640, 1127485743, 1124661741, 1459005403, 3501173, "SRX5113196", "SRS4121995", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92102, 0.92337, 0.28961, 0.28865, 0.75004, 0.75209, 0.55117, 0.55117, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50821, "SRR8298687", "SRX5113195", "SRS4121994", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 3", null, "7dpi#3", null, "breed:zebrafish|age:273 days|sex:missing|tissue:whole heart|time point:7 dpi|time replicate:7dpi#3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "7dpi rep3", "5943", "5943", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5943_S27_L006_R1_001.fastq.gz SID5943_S27_L006_R2_001.fastq.gz", "fastq fastq", 4517033100.0, 30113554.0, "SID5943 S27 L006 R1 001.fastq.gz", "0:75 1:75", "A:1291269833;C:967425221;G:965208852;T:1290075691;N:3053503", 75, 75, null, null, 1291269833, 967425221, 965208852, 1290075691, 3053503, "SRX5113195", "SRS4121994", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.91466, 0.91949, 0.29572, 0.2961, 0.7487, 0.75558, 0.55326, 0.5641, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50822, "SRR8298688", "SRX5113194", "SRS4121992", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 1", null, "160dpi#1", null, "breed:zebrafish|age:463 days|sex:missing|tissue:whole heart|time point:160 dpi|time replicate:160dpi#1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "160dpi rep1", "7275", "7275", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID7275_S22_L004_R1_001.fastq.gz SID7275_S22_L004_R2_001.fastq.gz", "fastq fastq", 4181854650.0, 27879031.0, "SID7275 S22 L004 R1 001.fastq.gz", "0:75 1:75", "A:1181005942;C:906846060;G:899205780;T:1194204939;N:591929", 75, 75, null, null, 1181005942, 906846060, 899205780, 1194204939, 591929, "SRX5113194", "SRS4121992", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.90318, 0.9002, 0.32768, 0.32822, 0.77102, 0.77384, 0.56468, 0.56558, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50823, "SRR8298689", "SRX5113193", "SRS4121991", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 2", null, "160dpi#2", null, "breed:zebrafish|age:463 days|sex:missing|tissue:whole heart|time point:160 dpi|time replicate:160dpi#2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "160dpi rep2", "7276", "7276", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID7276_S23_L004_R2_001.fastq.gz SID7276_S23_L004_R1_001.fastq.gz", "fastq fastq", 4146332250.0, 27642215.0, "SID7276 S23 L004 R1 001.fastq.gz", "0:75 1:75", "A:1159957610;C:910352523;G:906687072;T:1168748952;N:586093", 75, 75, null, null, 1159957610, 910352523, 906687072, 1168748952, 586093, "SRX5113193", "SRS4121991", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.90536, 0.90276, 0.29293, 0.29449, 0.77849, 0.77895, 0.58534, 0.34898, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50824, "SRR8298690", "SRX5113192", "SRS4121990", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 3", null, "160dpi#3", null, "breed:zebrafish|age:463 days|sex:missing|tissue:whole heart|time point:160 dpi|time replicate:160dpi#3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "160dpi rep3", "7277", "7277", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID7277_S24_L004_R1_001.fastq.gz SID7277_S24_L004_R2_001.fastq.gz", "fastq fastq", 5472079650.0, 36480531.0, "SID7277 S24 L004 R1 001.fastq.gz", "0:75 1:75", "A:1470665608;C:1262401410;G:1252027798;T:1486219756;N:765078", 75, 75, null, null, 1470665608, 1262401410, 1252027798, 1486219756, 765078, "SRX5113192", "SRS4121990", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.85132, 0.83282, 0.25703, 0.25354, 0.80099, 0.80142, 0.59842, 0.60563, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50825, "SRR8298691", "SRX5113191", "SRS4121993", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 1", null, "AgeCtr160dpi#1", null, "breed:zebrafish|age:463 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy160dpi|time replicate:AgeCtr160dpi#1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "AgeMatchCtr160dpi rep1", "8895", "8895", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID8895_S1_L001_R2_001.fastq.gz SID8895_S1_L001_R1_001.fastq.gz", "fastq fastq", 3296071950.0, 21973813.0, "SID8895 S1 L001 R1 001.fastq.gz", "0:75 1:75", "A:933363384;C:712077172;G:711836031;T:938304378;N:490985", 75, 75, null, null, 933363384, 712077172, 711836031, 938304378, 490985, "SRX5113191", "SRS4121993", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.91566, 0.91751, 0.29657, 0.29659, 0.76035, 0.76169, 0.56344, 0.56992, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2018-12-11", "Adult", "Adult", "Heart", "Cardiovascular System"], [50826, "SRR8298692", "SRX5113190", "SRS4121989", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 2", null, "AgeCtr160dpi#2", null, "breed:zebrafish|age:463 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy160dpi|time replicate:AgeCtr160dpi#2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "AgeMatchCtr160dpi rep2", "8896", "8896", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID8896_S2_L001_R2_001.fastq.gz SID8896_S2_L001_R1_001.fastq.gz", "fastq fastq", 4254029250.0, 28360195.0, "SID8896 S2 L001 R1 001.fastq.gz", "0:75 1:75", "A:1194195307;C:929727401;G:930645393;T:1198825951;N:635198", 75, 75, null, null, 1194195307, 929727401, 930645393, 1198825951, 635198, "SRX5113190", "SRS4121989", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92113, 0.92615, 0.29452, 0.29383, 0.7656, 0.76755, 0.5517, 0.5473, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2018-12-11", "Adult", "Adult", "Heart", "Cardiovascular System"], [50827, "SRR8298693", "SRX5113189", "SRS4121987", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 3", null, "AgeCtr160dpi#3", null, "breed:zebrafish|age:463 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy160dpi|time replicate:AgeCtr160dpi#3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "AgeMatchCtr160dpi rep3", "8897", "8897", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID8897_S3_L001_R1_001.fastq.gz SID8897_S3_L001_R2_001.fastq.gz", "fastq fastq", 4650028050.0, 31000187.0, "SID8897 S3 L001 R1 001.fastq.gz", "0:75 1:75", "A:1302193981;C:1017446128;G:1021800760;T:1307902725;N:684456", 75, 75, null, null, 1302193981, 1017446128, 1021800760, 1307902725, 684456, "SRX5113189", "SRS4121987", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.91652, 0.92167, 0.29435, 0.29352, 0.77285, 0.77453, 0.33726, 0.55364, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50828, "SRR8298694", "SRX5113188", "SRS4121988", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 1", null, "30dpi#1", null, "breed:zebrafish|age:241 days|sex:missing|tissue:whole heart|time point:30 dpi|time replicate:30dpi#1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "30dpi rep1", "5950", "5950", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5950_S39_L008_R1_001.fastq.gz SID5950_S39_L008_R2_001.fastq.gz", "fastq fastq", 4901662650.0, 32677751.0, "SID5950 S39 L008 R1 001.fastq.gz", "0:75 1:75", "A:1373803321;C:1078052071;G:1069535429;T:1377378449;N:2893380", 75, 75, null, null, 1373803321, 1078052071, 1069535429, 1377378449, 2893380, "SRX5113188", "SRS4121988", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92534, 0.92914, 0.24374, 0.24303, 0.78798, 0.79105, 0.59734, 0.59932, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50829, "SRR8298695", "SRX5113187", "SRS4121986", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 2", null, "30dpi#2", null, "breed:zebrafish|age:241 days|sex:missing|tissue:whole heart|time point:30 dpi|time replicate:30dpi#2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "30dpi rep2", "5951", "5951", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5951_S40_L008_R1_001.fastq.gz SID5951_S40_L008_R2_001.fastq.gz", "fastq fastq", 6092510850.0, 40616739.0, "SID5951 S40 L008 R1 001.fastq.gz", "0:75 1:75", "A:1688206071;C:1354066100;G:1339632797;T:1707023610;N:3582272", 75, 75, null, null, 1688206071, 1354066100, 1339632797, 1707023610, 3582272, "SRX5113187", "SRS4121986", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.91475, 0.91646, 0.25976, 0.25918, 0.76784, 0.77066, 0.59373, 0.36414, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50830, "SRR8298696", "SRX5113186", "SRS4121985", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 1", null, "AgeCtr120dpi#1", null, "breed:zebrafish|age:378 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy120dpi|time replicate:AgeCtr120dpi#1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "AgeMatchCtr120dpi rep1", "8898", "8898", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID8898_S4_L001_R2_001.fastq.gz SID8898_S4_L001_R1_001.fastq.gz", "fastq fastq", 4483909800.0, 29892732.0, "SID8898 S4 L001 R1 001.fastq.gz", "0:75 1:75", "A:1256860639;C:980027180;G:982979324;T:1263389080;N:653577", 75, 75, null, null, 1256860639, 980027180, 982979324, 1263389080, 653577, "SRX5113186", "SRS4121985", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92353, 0.92518, 0.29749, 0.29809, 0.76623, 0.76735, 0.58605, 0.58637, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50831, "SRR8298697", "SRX5113185", "SRS4121984", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 2", null, "AgeCtr120dpi#2", null, "breed:zebrafish|age:378 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy120dpi|time replicate:AgeCtr120dpi#2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "AgeMatchCtr120dpi rep2", "8899", "8899", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID8899_S5_L001_R2_001.fastq.gz SID8899_S5_L001_R1_001.fastq.gz", "fastq fastq", 3236079750.0, 21573865.0, "SID8899 S5 L001 R1 001.fastq.gz", "0:75 1:75", "A:924324675;C:694412856;G:683305315;T:933556442;N:480462", 75, 75, null, null, 924324675, 694412856, 683305315, 933556442, 480462, "SRX5113185", "SRS4121984", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.93623, 0.93903, 0.27394, 0.27249, 0.78305, 0.79397, 0.61872, 0.62189, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2018-12-11", "Adult", "Adult", "Heart", "Cardiovascular System"], [50832, "SRR8298698", "SRX5113184", "SRS4121982", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 3", null, "AgeCtr45dpi#3", null, "breed:zebrafish|age:302 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy45dpi|time replicate:AgeCtr45dpi#3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "AgeMatchCtr45dpi rep3", "8903", "8903", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID8903_S9_L002_R1_001.fastq.gz SID8903_S9_L002_R2_001.fastq.gz", "fastq fastq", 5771819400.0, 38478796.0, "SID8903 S9 L002 R1 001.fastq.gz", "0:75 1:75", "A:1626618253;C:1259436307;G:1254406150;T:1630506429;N:852261", 75, 75, null, null, 1626618253, 1259436307, 1254406150, 1630506429, 852261, "SRX5113184", "SRS4121982", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.93387, 0.93606, 0.26533, 0.26623, 0.7791, 0.78184, 0.60837, 0.6089, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50833, "SRR8298699", "SRX5113183", "SRS4121983", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 2", null, "AgeCtr45dpi#2", null, "breed:zebrafish|age:302 days|sex:missing|tissue:whole heart|time point:AgeMatchHealthy45dpi|time replicate:AgeCtr45dpi#2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "AgeMatchCtr45dpi rep2", "8902", "8902", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID8902_S8_L002_R1_001.fastq.gz SID8902_S8_L002_R2_001.fastq.gz", "fastq fastq", 4306880850.0, 28712539.0, "SID8902 S8 L002 R1 001.fastq.gz", "0:75 1:75", "A:1215412508;C:936746871;G:932596782;T:1221491491;N:633198", 75, 75, null, null, 1215412508, 936746871, 932596782, 1221491491, 633198, "SRX5113183", "SRS4121983", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92781, 0.93331, 0.28874, 0.28876, 0.78001, 0.78346, 0.60164, 0.59332, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50834, "SRR8298700", "SRX5113182", "SRS4121981", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 2", null, "AgeCtr5Month#2", null, "breed:zebrafish|age:154 days|sex:missing|tissue:whole heart|time point:Healthy5months|time replicate:AgeCtr5Month#2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Healthy 5months rep2", "8905", "8905", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID8905_S11_L002_R2_001.fastq.gz SID8905_S11_L002_R1_001.fastq.gz", "fastq fastq", 4929348150.0, 32862321.0, "SID8905 S11 L002 R1 001.fastq.gz", "0:75 1:75", "A:1391170271;C:1071161977;G:1070299973;T:1395997848;N:718081", 75, 75, null, null, 1391170271, 1071161977, 1070299973, 1395997848, 718081, "SRX5113182", "SRS4121981", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.93773, 0.93948, 0.26268, 0.26236, 0.77362, 0.77506, 0.57569, 0.57708, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2018-12-11", "Adult", "Adult", "Heart", "Cardiovascular System"], [50835, "SRR8298701", "SRX5113181", "SRS4121980", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 1", null, "AgeCtr5Month#1", null, "breed:zebrafish|age:154 days|sex:missing|tissue:whole heart|time point:Healthy5months|time replicate:AgeCtr5Month#1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Healthy 5months rep1", "8904", "8904", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID8904_S10_L002_R1_001.fastq.gz SID8904_S10_L002_R2_001.fastq.gz", "fastq fastq", 4600628100.0, 30670854.0, "SID8904 S10 L002 R1 001.fastq.gz", "0:75 1:75", "A:1299953049;C:997112028;G:995317490;T:1307572252;N:673281", 75, 75, null, null, 1299953049, 997112028, 995317490, 1307572252, 673281, "SRX5113181", "SRS4121980", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92985, 0.93317, 0.27378, 0.27505, 0.76708, 0.76928, 0.58583, 0.58459, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50836, "SRR8298702", "SRX5113180", "SRS4121979", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 3", null, "AgeCtr5Month#3", null, "breed:zebrafish|age:154 days|sex:missing|tissue:whole heart|time point:Healthy5months|time replicate:AgeCtr5Month#3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Healthy 5months rep3", "8906", "8906", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID8906_S12_L002_R1_001.fastq.gz SID8906_S12_L002_R2_001.fastq.gz", "fastq fastq", 4165039500.0, 27766930.0, "SID8906 S12 L002 R1 001.fastq.gz", "0:75 1:75", "A:1195051426;C:887781650;G:881955704;T:1199637740;N:612980", 75, 75, null, null, 1195051426, 887781650, 881955704, 1199637740, 612980, "SRX5113180", "SRS4121979", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.93095, 0.93609, 0.27404, 0.27418, 0.7667, 0.77047, 0.5912, 0.59542, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50837, "SRR8298703", "SRX5113179", "SRS4121978", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 3", null, "120dpi#3", null, "breed:zebrafish|age:378 days|sex:missing|tissue:whole heart|time point:120 dpi|time replicate:120dpi#3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "120dpi rep3", "5961", "5961", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5961_S11_L002_R1_001.fastq.gz SID5961_S11_L002_R2_001.fastq.gz", "fastq fastq", 4885501800.0, 32570012.0, "SID5961 S11 L002 R1 001.fastq.gz", "0:75 1:75", "A:1373358839;C:1068488355;G:1066801950;T:1372456422;N:4396234", 75, 75, null, null, 1373358839, 1068488355, 1066801950, 1372456422, 4396234, "SRX5113179", "SRS4121978", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.9246, 0.92659, 0.25833, 0.25787, 0.78127, 0.7836, 0.60281, 0.60025, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50838, "SRR8298704", "SRX5113178", "SRS4121976", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 2", null, "120dpi#2", null, "breed:zebrafish|age:378 days|sex:missing|tissue:whole heart|time point:120 dpi|time replicate:120dpi#2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "120dpi rep2", "5960", "5960", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5960_S12_L002_R2_001.fastq.gz SID5960_S12_L002_R1_001.fastq.gz", "fastq fastq", 3898224150.0, 25988161.0, "SID5960 S12 L002 R1 001.fastq.gz", "0:75 1:75", "A:1099131779;C:849905857;G:848167931;T:1097528051;N:3490532", 75, 75, null, null, 1099131779, 849905857, 848167931, 1097528051, 3490532, "SRX5113178", "SRS4121976", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92907, 0.93449, 0.2688, 0.26772, 0.78261, 0.78433, 0.60076, 0.59902, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2018-12-11", "Adult", "Adult", "Heart", "Cardiovascular System"], [50839, "SRR8298705", "SRX5113177", "SRS4121977", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 1", null, "120dpi#1", null, "breed:zebrafish|age:378 days|sex:missing|tissue:whole heart|time point:120 dpi|time replicate:120dpi#1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "120dpi rep1", "5959", "5959", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5959_S2_L001_R2_001.fastq.gz SID5959_S2_L001_R1_001.fastq.gz", "fastq fastq", 4162131150.0, 27747541.0, "SID5959 S2 L001 R1 001.fastq.gz", "0:75 1:75", "A:1179250180;C:902919196;G:895611442;T:1180890638;N:3459694", 75, 75, null, null, 1179250180, 902919196, 895611442, 1180890638, 3459694, "SRX5113177", "SRS4121977", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92816, 0.93221, 0.2657, 0.26641, 0.78835, 0.79028, 0.57814, 0.58497, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50840, "SRR8298706", "SRX5113176", "SRS4121975", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 3", null, "60dpi#3", null, "breed:zebrafish|age:265 days|sex:missing|tissue:whole heart|time point:60 dpi|time replicate:60dpi#3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "60dpi rep3", "5958", "5958", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5958_S6_L001_R1_001.fastq.gz SID5958_S6_L001_R2_001.fastq.gz", "fastq fastq", 8199799500.0, 54665330.0, "SID5958 S6 L001 R1 001.fastq.gz", "0:75 1:75", "A:2315697517;C:1786954487;G:1776061301;T:2314246361;N:6839834", 75, 75, null, null, 2315697517, 1786954487, 1776061301, 2314246361, 6839834, "SRX5113176", "SRS4121975", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92837, 0.92967, 0.27166, 0.2711, 0.79874, 0.80064, 0.58585, 0.58555, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50841, "SRR8298707", "SRX5113175", "SRS4121974", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 2", null, "60dpi#2", null, "breed:zebrafish|age:265 days|sex:missing|tissue:whole heart|time point:60 dpi|time replicate:60dpi#2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "60dpi rep2", "5957", "5957", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5957_S1_L001_R2_001.fastq.gz SID5957_S1_L001_R1_001.fastq.gz", "fastq fastq", 5076508950.0, 33843393.0, "SID5957 S1 L001 R1 001.fastq.gz", "0:75 1:75", "A:1419284178;C:1119499915;G:1116625755;T:1416893160;N:4205942", 75, 75, null, null, 1419284178, 1119499915, 1116625755, 1416893160, 4205942, "SRX5113175", "SRS4121974", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.91675, 0.91777, 0.24976, 0.24835, 0.80813, 0.80815, 0.59245, 0.59618, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2018-12-11", "Adult", "Adult", "Heart", "Cardiovascular System"], [50842, "SRR8298708", "SRX5113174", "SRS4121973", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 1", null, "60dpi#1", null, "breed:zebrafish|age:265 days|sex:missing|tissue:whole heart|time point:60 dpi|time replicate:60dpi#1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "60dpi rep1", "5956", "5956", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5956_S5_L001_R1_001.fastq.gz SID5956_S5_L001_R2_001.fastq.gz", "fastq fastq", 3037760250.0, 20251735.0, "SID5956 S5 L001 R1 001.fastq.gz", "0:75 1:75", "A:855319143;C:662784213;G:672270090;T:844860777;N:2526027", 75, 75, null, null, 855319143, 662784213, 672270090, 844860777, 2526027, "SRX5113174", "SRS4121973", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92385, 0.92129, 0.26517, 0.26397, 0.80125, 0.80545, 0.57571, 0.34016, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50843, "SRR8298709", "SRX5113173", "SRS4121972", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 3", null, "45dpi#3", null, "breed:zebrafish|age:302 days|sex:missing|tissue:whole heart|time point:45 dpi|time replicate:45dpi#3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "45dpi rep3", "5955", "5955", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5955_S4_L001_R1_001.fastq.gz SID5955_S4_L001_R2_001.fastq.gz", "fastq fastq", 4527734100.0, 30184894.0, "SID5955 S4 L001 R1 001.fastq.gz", "0:75 1:75", "A:1284400034;C:978356858;G:962329763;T:1298877592;N:3769853", 75, 75, null, null, 1284400034, 978356858, 962329763, 1298877592, 3769853, "SRX5113173", "SRS4121972", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.91901, 0.9216, 0.31343, 0.31336, 0.76585, 0.76749, 0.6169, 0.61439, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50844, "SRR8298710", "SRX5113172", "SRS4121969", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 2", null, "45dpi#2", null, "breed:zebrafish|age:302 days|sex:missing|tissue:whole heart|time point:45 dpi|time replicate:45dpi#2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "45dpi rep2", "5954", "5954", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5954_S3_L001_R1_001.fastq.gz SID5954_S3_L001_R2_001.fastq.gz", "fastq fastq", 4299485250.0, 28663235.0, "SID5954 S3 L001 R1 001.fastq.gz", "0:75 1:75", "A:1214156806;C:933962608;G:920087647;T:1227715898;N:3562291", 75, 75, null, null, 1214156806, 933962608, 920087647, 1227715898, 3562291, "SRX5113172", "SRS4121969", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.91583, 0.91783, 0.32439, 0.32427, 0.76471, 0.76678, 0.60158, 0.60172, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50845, "SRR8298711", "SRX5113171", "SRS4121970", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 1", null, "45dpi#1", null, "breed:zebrafish|age:302 days|sex:missing|tissue:whole heart|time point:45 dpi|time replicate:45dpi#1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "45dpi rep1", "5953", "5953", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5953_S44_L008_R1_001.fastq.gz SID5953_S44_L008_R2_001.fastq.gz", "fastq fastq", 5374207650.0, 35828051.0, "SID5953 S44 L008 R1 001.fastq.gz", "0:75 1:75", "A:1510807007;C:1174714817;G:1164085803;T:1521456074;N:3143949", 75, 75, null, null, 1510807007, 1174714817, 1164085803, 1521456074, 3143949, "SRX5113171", "SRS4121970", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92029, 0.9222, 0.3057, 0.30508, 0.76248, 0.76532, 0.62394, 0.62252, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [50846, "SRR8298712", "SRX5113170", "SRS4121971", "SRP173044", "PRJNA509429", "Delineating the transcriptomic response during Zebrafish heart regeneration", "PRJNA509429", "Other", "Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore  mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.", null, "pubmed:30597924", "Replicate 3", null, "30dpi#3", null, "breed:zebrafish|age:241 days|sex:missing|tissue:whole heart|time point:30 dpi|time replicate:30dpi#3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "30dpi rep3", "5952", "5952", "RNA was extracted using RNeasy Mini Kit Qiagen #74104 and 200 nanogram were used for library preparation with TruSeq Stranded Total RNA Library Prep Illumina #20020597", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP173044", null, null, "SID5952_S41_L008_R1_001.fastq.gz SID5952_S41_L008_R2_001.fastq.gz", "fastq fastq", 4010530950.0, 26736873.0, "SID5952 S41 L008 R1 001.fastq.gz", "0:75 1:75", "A:1111347218;C:892586235;G:885431304;T:1118779431;N:2386762", 75, 75, null, null, 1111347218, 892586235, 885431304, 1118779431, 2386762, "SRX5113170", "SRS4121971", "SRA821074", "University of Freiburg|Institute of Molecular Medicine and Cell Research", "University of Freiburg DeCaRe", 2, 0.92226, 0.92446, 0.2498, 0.24953, 0.7836, 0.78642, 0.55934, 0.55793, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2019-04-30", "Adult", "Adult", "Heart", "Cardiovascular System"], [66194, "SRR16096233", "SRX12382357", "SRS10353019", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 1cell Rep5", "GSM5599725", null, "tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 1cell Rep5", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 1cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599725", "GSM5599725: ZF zygote IP 1cell Rep5; Danio rerio; RIP Seq", "GSM5599725", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599725", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_1cell_Rep5_R1.fastq.gz ZF_zygote_IP_1cell_Rep5_R2.fastq.gz", "fastq fastq", 3660517860.0, 35887430.0, "GSM5599725 r1", "0:51 1:51", "A:858138600;C:924733544;G:1002150083;T:875349961;N:145672", 51, 51, null, null, 858138600, 924733544, 1002150083, 875349961, 145672, "SRX12382357", "SRS10353019", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.83384, 0.82667, 0.09687, 0.11892, 0.79076, 0.79326, 0.63739, 0.60941, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66195, "SRR16096232", "SRX12382356", "SRS10353018", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 1cell Rep4", "GSM5599724", null, "tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 1cell Rep4", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 1cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599724", "GSM5599724: ZF zygote IP 1cell Rep4; Danio rerio; RIP Seq", "GSM5599724", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599724", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_1cell_Rep4_R1.fastq.gz ZF_zygote_IP_1cell_Rep4_R2.fastq.gz", "fastq fastq", 3660205842.0, 35884371.0, "GSM5599724 r1", "0:51 1:51", "A:895738659;C:880838836;G:971118499;T:912364119;N:145729", 51, 51, null, null, 895738659, 880838836, 971118499, 912364119, 145729, "SRX12382356", "SRS10353018", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.87258, 0.86932, 0.06573, 0.07958, 0.78044, 0.78374, 0.55531, 0.5462, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66196, "SRR16096231", "SRX12382355", "SRS10353016", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 1cell Rep3", "GSM5599723", null, "tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 1cell Rep3", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 1cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599723", "GSM5599723: ZF zygote IP 1cell Rep3; Danio rerio; RIP Seq", "GSM5599723", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599723", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_1cell_Rep3_R1.fastq.gz ZF_zygote_IP_1cell_Rep3_R2.fastq.gz", "fastq fastq", 2732409048.0, 26788324.0, "GSM5599723 r1", "0:51 1:51", "A:669345195;C:656715671;G:724415204;T:681825149;N:107829", 51, 51, null, null, 669345195, 656715671, 724415204, 681825149, 107829, "SRX12382355", "SRS10353016", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.85204, 0.83607, 0.06526, 0.08046, 0.78535, 0.78748, 0.60467, 0.50165, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66197, "SRR16096230", "SRX12382354", "SRS10353017", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 1cell Rep2", "GSM5599722", null, "tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 1cell Rep2", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 1cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599722", "GSM5599722: ZF zygote IP 1cell Rep2; Danio rerio; RIP Seq", "GSM5599722", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599722", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_1cell_Rep2_R1.fastq.gz ZF_zygote_IP_1cell_Rep2_R2.fastq.gz", "fastq fastq", 2235668028.0, 21918314.0, "GSM5599722 r1", "0:51 1:51", "A:552522700;C:535947981;G:588168855;T:558939713;N:88779", 51, 51, null, null, 552522700, 535947981, 588168855, 558939713, 88779, "SRX12382354", "SRS10353017", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.85597, 0.85298, 0.06663, 0.07927, 0.79058, 0.79237, 0.57626, 0.56525, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66198, "SRR16096229", "SRX12382353", "SRS10353015", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 1cell Rep1", "GSM5599721", null, "tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 1cell Rep1", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 1cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599721", "GSM5599721: ZF zygote IP 1cell Rep1; Danio rerio; RIP Seq", "GSM5599721", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599721", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_1cell_Rep1_R1.fastq.gz ZF_zygote_IP_1cell_Rep1_R2.fastq.gz", "fastq fastq", 1785761736.0, 17507468.0, "GSM5599721 r1", "0:51 1:51", "A:429081683;C:435813601;G:481376346;T:439419714;N:70392", 51, 51, null, null, 429081683, 435813601, 481376346, 439419714, 70392, "SRX12382353", "SRS10353015", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.75314, 0.75693, 0.0543, 0.06639, 0.79482, 0.79594, 0.57979, 0.56522, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66199, "SRR16096228", "SRX12382352", "SRS10353014", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 5cell Rep3", "GSM5599720", null, "tissue:ZF zygote IP 5cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 5cell Rep3", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 5cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599720", "GSM5599720: ZF zygote IP 5cell Rep3; Danio rerio; RIP Seq", "GSM5599720", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599720", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_5cell_Rep3_R1.fastq.gz ZF_zygote_IP_5cell_Rep3_R2.fastq.gz", "fastq fastq", 2179659420.0, 21369210.0, "GSM5599720 r1", "0:51 1:51", "A:539092949;C:513857324;G:569620218;T:556940661;N:148268", 51, 51, null, null, 539092949, 513857324, 569620218, 556940661, 148268, "SRX12382352", "SRS10353014", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.92028, 0.90706, 0.03967, 0.05572, 0.78431, 0.78886, 0.49727, 0.48541, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66200, "SRR16096227", "SRX12382351", "SRS10353012", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 5cell Rep2", "GSM5599719", null, "tissue:ZF zygote IP 5cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 5cell Rep2", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 5cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599719", "GSM5599719: ZF zygote IP 5cell Rep2; Danio rerio; RIP Seq", "GSM5599719", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599719", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_5cell_Rep2_R1.fastq.gz ZF_zygote_IP_5cell_Rep2_R2.fastq.gz", "fastq fastq", 2527184538.0, 24776319.0, "GSM5599719 r1", "0:51 1:51", "A:628307375;C:594702688;G:657847712;T:646151885;N:174878", 51, 51, null, null, 628307375, 594702688, 657847712, 646151885, 174878, "SRX12382351", "SRS10353012", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91811, 0.90487, 0.03919, 0.05376, 0.78315, 0.78729, 0.49414, 0.48564, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66201, "SRR16096226", "SRX12382350", "SRS10353011", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 5cell Rep1", "GSM5599718", null, "tissue:ZF zygote IP 5cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 5cell Rep1", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 5cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599718", "GSM5599718: ZF zygote IP 5cell Rep1; Danio rerio; RIP Seq", "GSM5599718", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599718", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_5cell_Rep1_R1.fastq.gz ZF_zygote_IP_5cell_Rep1_R2.fastq.gz", "fastq fastq", 3481342518.0, 34130809.0, "GSM5599718 r1", "0:51 1:51", "A:865680250;C:823420389;G:907146965;T:884854199;N:240715", 51, 51, null, null, 865680250, 823420389, 907146965, 884854199, 240715, "SRX12382350", "SRS10353011", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91893, 0.90939, 0.04544, 0.06005, 0.78025, 0.78348, 0.50569, 0.49155, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66202, "SRR16096225", "SRX12382349", "SRS10353013", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 10cell Rep3", "GSM5599717", null, "tissue:ZF zygote IP 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 10cell Rep3", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 10cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599717", "GSM5599717: ZF zygote IP 10cell Rep3; Danio rerio; RIP Seq", "GSM5599717", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599717", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_10cell_Rep3_R1.fastq.gz ZF_zygote_IP_10cell_Rep3_R2.fastq.gz", "fastq fastq", 2172362850.0, 21297675.0, "GSM5599717 r1", "0:51 1:51", "A:536043605;C:513512883;G:568368414;T:554284996;N:152952", 51, 51, null, null, 536043605, 513512883, 568368414, 554284996, 152952, "SRX12382349", "SRS10353013", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91859, 0.90522, 0.03736, 0.05214, 0.78715, 0.79129, 0.49736, 0.48681, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66203, "SRR16096224", "SRX12382348", "SRS10353010", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 10cell Rep2", "GSM5599716", null, "tissue:ZF zygote IP 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 10cell Rep2", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 10cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599716", "GSM5599716: ZF zygote IP 10cell Rep2; Danio rerio; RIP Seq", "GSM5599716", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599716", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_10cell_Rep2_R1.fastq.gz ZF_zygote_IP_10cell_Rep2_R2.fastq.gz", "fastq fastq", 1840839492.0, 18047446.0, "GSM5599716 r1", "0:51 1:51", "A:454385290;C:437082102;G:482351138;T:466893642;N:127320", 51, 51, null, null, 454385290, 437082102, 482351138, 466893642, 127320, "SRX12382348", "SRS10353010", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.92217, 0.90956, 0.04012, 0.05483, 0.78819, 0.79318, 0.49756, 0.48256, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66204, "SRR16096223", "SRX12382347", "SRS10353009", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 10cell Rep1", "GSM5599715", null, "tissue:ZF zygote IP 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 10cell Rep1", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 10cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599715", "GSM5599715: ZF zygote IP 10cell Rep1; Danio rerio; RIP Seq", "GSM5599715", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599715", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_10cell_Rep1_R1.fastq.gz ZF_zygote_IP_10cell_Rep1_R2.fastq.gz", "fastq fastq", 2400553680.0, 23534840.0, "GSM5599715 r1", "0:51 1:51", "A:594878203;C:567573525;G:625488388;T:612448386;N:165178", 51, 51, null, null, 594878203, 567573525, 625488388, 612448386, 165178, "SRX12382347", "SRS10353009", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91641, 0.908, 0.03979, 0.05394, 0.78455, 0.7892, 0.48862, 0.47478, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66205, "SRR16096222", "SRX12382346", "SRS10353008", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote Input 10cell Rep2", "GSM5599714", null, "tissue:ZF zygote Input 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote Input 10cell Rep2", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote Input 10cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599714", "GSM5599714: ZF zygote Input 10cell Rep2; Danio rerio; RIP Seq", "GSM5599714", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599714", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_Input_10cell_Rep2_R1.fastq.gz ZF_zygote_Input_10cell_Rep2_R2.fastq.gz", "fastq fastq", 3842772582.0, 37674241.0, "GSM5599714 r1", "0:51 1:51", "A:843564828;C:1054412690;G:1130769812;T:813758353;N:266899", 51, 51, null, null, 843564828, 1054412690, 1130769812, 813758353, 266899, "SRX12382346", "SRS10353008", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91511, 0.90868, 0.32791, 0.38048, 0.89457, 0.89441, 0.81532, 0.75274, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66206, "SRR16096221", "SRX12382345", "SRS10353007", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote Input 10cell Rep1", "GSM5599713", null, "tissue:ZF zygote Input 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote Input 10cell Rep1", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote Input 10cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599713", "GSM5599713: ZF zygote Input 10cell Rep1; Danio rerio; RIP Seq", "GSM5599713", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599713", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_Input_10cell_Rep1_R1.fastq.gz ZF_zygote_Input_10cell_Rep1_R2.fastq.gz", "fastq fastq", 4029368016.0, 39503608.0, "GSM5599713 r1", "0:51 1:51", "A:893562237;C:1096986475;G:1180690796;T:857849967;N:278541", 51, 51, null, null, 893562237, 1096986475, 1180690796, 857849967, 278541, "SRX12382345", "SRS10353007", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91491, 0.90807, 0.32799, 0.37836, 0.89292, 0.89282, 0.81006, 0.73354, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [68382, "SRR17720609", "SRX13883476", "SRS11752245", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m7G Normoxia IP", "GSM5832287", null, "source name:zebrafish brain tissue|tissue:brain", "m7G Normoxia IP", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832287", "GSM5832287: m7G Normoxia IP; Danio rerio; OTHER", "GSM5832287 r1", "GSM5832287", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m7G_Normoxia_IP_R1.fastq.gz m7G_Normoxia_IP_R2.fastq.gz", "fastq fastq", 6634104000.0, 22113680.0, "GSM5832287 r1", "0:150 1:150", "A:1396464650;C:1688319426;G:2250091870;T:1299109891;N:118163", 150, 150, null, null, 1396464650, 1688319426, 2250091870, 1299109891, 118163, "SRX13883476", "SRS11752245", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.9266, 0.92801, 0.07275, 0.06866, 0.89964, 0.90601, 0.65995, 0.75535, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68383, "SRR17720610", "SRX13883475", "SRS11752244", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m7G Normoxia Input", "GSM5832286", null, "source name:zebrafish brain tissue|tissue:brain", "m7G Normoxia Input", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832286", "GSM5832286: m7G Normoxia Input; Danio rerio; OTHER", "GSM5832286 r1", "GSM5832286", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m7G_Normoxia_Input_R1.fastq.gz m7G_Normoxia_Input_R2.fastq.gz", "fastq fastq", 6839977800.0, 22799926.0, "GSM5832286 r1", "0:150 1:150", "A:1986780958;C:1411210049;G:1509902094;T:1932043482;N:41217", 150, 150, null, null, 1986780958, 1411210049, 1509902094, 1932043482, 41217, "SRX13883475", "SRS11752244", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.89709, 0.89888, 0.21747, 0.21725, 0.70021, 0.69936, 0.50469, 0.51865, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68384, "SRR17720611", "SRX13883474", "SRS11752243", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m7G Hypoxia IP", "GSM5832285", null, "source name:zebrafish brain tissue|tissue:brain", "m7G Hypoxia IP", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832285", "GSM5832285: m7G Hypoxia IP; Danio rerio; OTHER", "GSM5832285 r1", "GSM5832285", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m7G_Hypoxia_IP_R1.fastq.gz m7G_Hypoxia_IP_R2.fastq.gz", "fastq fastq", 7282575000.0, 24275250.0, "GSM5832285 r1", "0:150 1:150", "A:1512757767;C:1913587260;G:2472336371;T:1383764924;N:128678", 150, 150, null, null, 1512757767, 1913587260, 2472336371, 1383764924, 128678, "SRX13883474", "SRS11752243", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.94526, 0.9467, 0.05248, 0.05071, 0.91946, 0.91981, 0.69303, 0.78448, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68385, "SRR17720612", "SRX13883473", "SRS11752241", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m7G Hypoxia Input", "GSM5832284", null, "source name:zebrafish brain tissue|tissue:brain", "m7G Hypoxia Input", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832284", "GSM5832284: m7G Hypoxia Input; Danio rerio; OTHER", "GSM5832284 r1", "GSM5832284", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m7G_Hypoxia_Input_R1.fastq.gz m7G_Hypoxia_Input_R2.fastq.gz", "fastq fastq", 7492311600.0, 24974372.0, "GSM5832284 r1", "0:150 1:150", "A:2208863421;C:1521950436;G:1608371217;T:2153082842;N:43684", 150, 150, null, null, 2208863421, 1521950436, 1608371217, 2153082842, 43684, "SRX13883473", "SRS11752241", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.89264, 0.89479, 0.23239, 0.23163, 0.70496, 0.70311, 0.51741, 0.52135, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68386, "SRR17720613", "SRX13883472", "SRS11752242", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m6A Normoxia IP", "GSM5832283", null, "source name:zebrafish brain tissue|tissue:brain", "m6A Normoxia IP", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832283", "GSM5832283: m6A Normoxia IP; Danio rerio; OTHER", "GSM5832283 r1", "GSM5832283", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, null, "m6A_Normoxia_IP_R1.fastq.gz m6A_Normoxia_IP_R2.fastq.gz", "fastq fastq", 6583667700.0, 21945559.0, "GSM5832283 r1", "0:150 1:150", "A:1750230540;C:1500991424;G:1592129260;T:1740287575;N:28901", 150, 150, null, null, 1750230540, 1500991424, 1592129260, 1740287575, 28901, "SRX13883472", "SRS11752242", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.87682, 0.87986, 0.18203, 0.17239, 0.74671, 0.7472, 0.55638, 0.55861, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68387, "SRR17720614", "SRX13883471", "SRS11752240", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m6A Normoxia Input", "GSM5832282", null, "source name:zebrafish brain tissue|tissue:brain", "m6A Normoxia Input", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832282", "GSM5832282: m6A Normoxia Input; Danio rerio; OTHER", "GSM5832282 r1", "GSM5832282", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, "loader:fastq load.py", "m6A_Normoxia_Input_R1.fastq.gz m6A_Normoxia_Input_R2.fastq.gz", "fastq fastq", 6314076000.0, 21046920.0, "GSM5832282 r1", "0:150 1:150", "A:1815907910;C:1329572814;G:1378464668;T:1790102301;N:28307", 150, 150, null, null, 1815907910, 1329572814, 1378464668, 1790102301, 28307, "SRX13883471", "SRS11752240", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.91754, 0.91835, 0.21273, 0.20993, 0.69702, 0.69625, 0.53456, 0.53763, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68388, "SRR17720615", "SRX13883470", "SRS11752239", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m6A Hypoxia IP", "GSM5832281", null, "source name:zebrafish brain tissue|tissue:brain", "m6A Hypoxia IP", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832281", "GSM5832281: m6A Hypoxia IP; Danio rerio; OTHER", "GSM5832281 r1", "GSM5832281", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP356476", null, null, "m6A_Hypoxia_IP_R1.fastq.gz m6A_Hypoxia_IP_R2.fastq.gz", "fastq fastq", 6490349100.0, 21634497.0, "GSM5832281 r1", "0:150 1:150", "A:1714144102;C:1483635762;G:1606044832;T:1686496024;N:28380", 150, 150, null, null, 1714144102, 1483635762, 1606044832, 1686496024, 28380, "SRX13883470", "SRS11752239", "SRA1361294", "Affiliated Hospital of Guangdong Medical University", "Affiliated Hospital of Guangdong Medical University", 2, 0.87598, 0.88161, 0.16783, 0.16105, 0.74588, 0.74568, 0.55361, 0.55307, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "nebnext", "bulk", "bulk", "bulk", null, "China", "2022-01-24", "Adult", "Adult", "Brain", "Nervous System"], [68389, "SRR17720616", "SRX13883469", "SRS11752237", "SRP356476", "PRJNA800053", "Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq", "GSE194284", "Other", "The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.", null, "pubmed:35135476", null, "m6A Hypoxia Input", "GSM5832280", null, "source name:zebrafish brain tissue|tissue:brain", "m6A Hypoxia Input", "Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3\u2019 adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites", "zebrafish brain tissue", "Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq", null, "tissue:brain", "GSM5832280", "GSM5832280: m6A Hypoxia Input; Danio rerio; OTHER", "GSM5832280 r1", "GSM5832280", "1", "Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext\u00ae Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  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