rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
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.,,,,Fish embryo mRNA germ ring PAL seq v4,GSM7716871,,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 “ m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7”. 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 “  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate”. 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; 4–7 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,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP455680,,,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,,,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,,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.,,,,Fish embryo mRNA germ ring PAL seq v4,GSM7716871,,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 “ m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7”. 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 “  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate”. 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; 4–7 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,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP455680,,,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,,,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,,52,255,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,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.,,,,Fish embryo mRNA zfs:0000015 PAL seq v4,GSM7716870,,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 “ m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7”. 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 “  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate”. 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; 4–7 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,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP455680,,,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,,,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,,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.,,,,Fish embryo mRNA zfs:0000015 PAL seq v4,GSM7716870,,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 “ m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7”. 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 “  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate”. 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; 4–7 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,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP455680,,,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,,,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,,52,255,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,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.,,,,Fish embryo mRNA sphere PAL seq v4,GSM7716869,,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 “ m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7”. 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 “  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate”. 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; 4–7 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,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP455680,,,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,,,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,,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.,,,,Fish embryo mRNA sphere PAL seq v4,GSM7716869,,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 “ m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7”. 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 “  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate”. 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; 4–7 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,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP455680,,,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,,,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,,52,255,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,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.,,,,Fish embryo mRNA 1024cell PAL seq v4,GSM7716868,,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 “ m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7”. 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 “  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate”. 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; 4–7 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,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP455680,,,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,,,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,,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.,,,,Fish embryo mRNA 1024cell PAL seq v4,GSM7716868,,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 “ m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7”. 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 “  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate”. 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; 4–7 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,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP455680,,,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,,,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,,52,255,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,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.,,,,Fish embryo mRNA 128cell PAL seq v4,GSM7716867,,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 “ m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7”. 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 “  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate”. 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; 4–7 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,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP455680,,,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,,,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,,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.,,,,Fish embryo mRNA 128cell PAL seq v4,GSM7716867,,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 “ m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7”. 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 “  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate”. 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; 4–7 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,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP455680,,,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,,,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,,52,255,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,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.,,,,Fish embryo mRNA 8cell PAL seq v4,GSM7716866,,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 “ m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7”. 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 “  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate”. 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; 4–7 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,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP455680,,,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,,,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,,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.,,,,Fish embryo mRNA 8cell PAL seq v4,GSM7716866,,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 “ m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7”. 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 “  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate”. 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; 4–7 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,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP455680,,,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,,,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,,52,255,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,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.,,,,Fish embryo mRNA 1cell PAL seq v4,GSM7716865,,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 “ m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7”. 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 “  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate”. 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; 4–7 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,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP455680,,,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,,,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,,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.,,,,Fish embryo mRNA 1cell PAL seq v4,GSM7716865,,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 “ m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7”. 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 “  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate”. 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; 4–7 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,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,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 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C 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°C 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 3ʹ 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 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C 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 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 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 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10–15 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 3ʹ adapter KXS013 was used for 3ʹ 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 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C 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 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP455680,,,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,,,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,,52,255,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2023-08-17,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28690,SRR26535341,SRX22238472,SRS19292733,SRP468564,PRJNA1032461,A syngeneic spontaneous zebrafish model oftp53 deficient  EGFRviii  and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo,GSE246295,Transcriptome Analysis,To build a patient relevantin vivomodel of human glioblastoma  we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life  with a gene expression signature similar to human glioblastoma of the mesenchymal subtype  along with a strong inflammatory component. Within early stage tumor lesions  and in an intact and endogenous tumor microenvironment  we visualized infiltration of phagocytic cells  as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages  suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore  CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context  while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether  we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging  high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation  with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains  we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells.  EGFRviii derived tumors were induced by microinjection of EGFRviii  PI3KCAH1047R  and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS  PI3KCAH1047R  GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3  KPG 1 3  alongside three control brains from injected siblings who did not develop tumors CTRL 1 3  were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition  resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.,,pubmed:39052000,,Pooled EPS brains  mScarlet ve Sorted Cells,GSM7866396,,source name:Sorted Cells|strain:CG1 p53null|tissue:Sorted Cells|geo loc name:missing|collection date:missing,Pooled EPS brains  mScarlet ve Sorted Cells,Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23  with entries manually added for GFP  mScarlet  EGFRviii  KRAS  and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments:  r    seqBias    mp  3    validateMappings    rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.,Sorted Cells,Fertilized embryos injected with either EPS or KPG construct mix,Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina  according to manufacturer’s recommendations,Zebrafish were housed and reared following approved animal use protocol,strain:CG1 p53null|tissue:Sorted Cells,GSM7866396,GSM7866396: Pooled EPS brains  mScarlet ve Sorted Cells; Danio rerio; RNA Seq,GSM7866396 r1,GSM7866396,1,Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina  according to manufacturer's recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP468564,,loader:fastq load.py,CS_Neg.fastq.gz,fastq,6384313020.0,63211020.0,GSM7866396 r1,0:101,A:1646899028;C:1504048934;G:1428638008;T:1804712211;N:14839,101,,,,1646899028,1504048934,1428638008,1804712211,14839,SRX22238472,SRS19292733,SRA1740017,"Hayes Lab, DSCB, Sickkids Research","Hayes Lab, DSCB, Sickkids Research",1,0.94094,,0.14273,,0.67416,,0.48471,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Canada,2023-10-26,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
28691,SRR26535342,SRX22238471,SRS19292732,SRP468564,PRJNA1032461,A syngeneic spontaneous zebrafish model oftp53 deficient  EGFRviii  and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo,GSE246295,Transcriptome Analysis,To build a patient relevantin vivomodel of human glioblastoma  we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life  with a gene expression signature similar to human glioblastoma of the mesenchymal subtype  along with a strong inflammatory component. Within early stage tumor lesions  and in an intact and endogenous tumor microenvironment  we visualized infiltration of phagocytic cells  as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages  suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore  CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context  while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether  we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging  high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation  with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains  we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells.  EGFRviii derived tumors were induced by microinjection of EGFRviii  PI3KCAH1047R  and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS  PI3KCAH1047R  GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3  KPG 1 3  alongside three control brains from injected siblings who did not develop tumors CTRL 1 3  were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition  resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.,,pubmed:39052000,,Pooled EPS brains  mScarlet+ve Sorted Cells,GSM7866395,,source name:Sorted Cells|strain:CG1 p53null|tissue:Sorted Cells|geo loc name:missing|collection date:missing,Pooled EPS brains  mScarlet+ve Sorted Cells,Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23  with entries manually added for GFP  mScarlet  EGFRviii  KRAS  and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments:  r    seqBias    mp  3    validateMappings    rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.,Sorted Cells,Fertilized embryos injected with either EPS or KPG construct mix,Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina  according to manufacturer’s recommendations,Zebrafish were housed and reared following approved animal use protocol,strain:CG1 p53null|tissue:Sorted Cells,GSM7866395,GSM7866395: Pooled EPS brains  mScarlet+ve Sorted Cells; Danio rerio; RNA Seq,GSM7866395 r1,GSM7866395,1,Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina  according to manufacturer's recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP468564,,loader:fastq load.py,CS_Pos.fastq.gz,fastq,6221936027.0,61603327.0,GSM7866395 r1,0:101,A:1586867899;C:1467436044;G:1398048259;T:1769569401;N:14424,101,,,,1586867899,1467436044,1398048259,1769569401,14424,SRX22238471,SRS19292732,SRA1740017,"Hayes Lab, DSCB, Sickkids Research","Hayes Lab, DSCB, Sickkids Research",1,0.88463,,0.14567,,0.69126,,0.48428,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Canada,2023-10-26,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
29025,SRR26974567,SRX22668017,SRS19663577,SRP474706,PRJNA1046144,Nlrc3 signaling is required for hematopoietic stem cell emergence by activating Notch signaling in vertebrates,GSE248871,Transcriptome Analysis,Purpose: Since Nlrc3 signaling is imperative for HSPCs production in zebrafish  to further determine the regulatory mechanism by which nlrc3 signaling regulates HSPCs. Bulk RNA sequencing analysis is performed to dissect the function and molecular mechanism between the control groups and the nlrc3 morphants groups. Methods: The GFP+ cells in Tgfli1a:eGFP zebrafish embryos at 28 hpf were sorted  which is the stage that EHT occurs in the VDA and the site of hemogenic endothelial cells onset. The mRNA profiles of these cells in wild type WT and Nlrc3 knockdown were deep sequencing  in triplicate  using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: Using an optimized data analysis workflow  we mapped about 35 million sequence reads per sample and identified 4153 transcripts showing differential expression between the of WT and  Nlrc3 morphants  with a fold change =1.5 and p value <0.05. Based on the results of RNA seq  some signaling pathways essential for  the the Nlrc3 regulates the onset of HSPCs in vertebrate are dissected. Including Notch  WNT  NF kB. Conclusions: Hemogenic endothelial cells mRNA profiles of WT groups and Nlrc3 knockdown groups were deep sequenced and anlysis. Based on the results of RNA seq  we performed  experiments to validate the up and downstream pathway involved in the the Nlrc3 regulates the onset of HSCPs in vertebrate. Overall design: mRNA profiling by high throughput sequencing to dissect the function and molecular mechanism by which nlrc3 signaling regulates the HSPCs in vertebrate.,,pubmed:38172511,,samples in nlrc3 MO rep3,GSM7921554,,source name:zebrafish embryos|tissue:GFP+ cells in Tgfli1a:eGFP|passage:28 hpf embryos|culture:no culture|geo loc name:missing|collection date:missing,samples in nlrc3 MO rep3,Illunima Casava 1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Supplementary files format and content: FPKM values for each Sample.,zebrafish embryos,,Total RNA was extracted using Trizol reagent Invitrogen  CA  USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent  CA  USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:GFP+ cells in Tgfli1a:eGFP|passage:28 hpf embryos|culture:no culture,GSM7921554,GSM7921554: samples in nlrc3 MO rep3; Danio rerio; RNA Seq,GSM7921554 r1,GSM7921554,1,Total RNA was extracted using Trizol reagent Invitrogen  CA  USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent  CA  USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474706,,loader:fastq load.py,Mo3_Clean_Data2.fq.gz Mo3_Clean_Data1.fq.gz,fastq fastq,5520729146.0,19885310.0,GSM7921554 r1,0:138.82 1:138.81,A:1394113679;C:1363204261;G:1378651437;T:1384757621;N:2148,138,138,,,1394113679,1363204261,1378651437,1384757621,2148,SRX22668017,SRS19663577,SRA1759375,Zhejiang university,Zhejiang university,2,0.9435,0.94469,0.05163,0.05105,0.7601,0.75958,0.46104,0.46669,141,141,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,bulk,bulk,,China,2023-11-28,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
29026,SRR26974568,SRX22668016,SRS19663576,SRP474706,PRJNA1046144,Nlrc3 signaling is required for hematopoietic stem cell emergence by activating Notch signaling in vertebrates,GSE248871,Transcriptome Analysis,Purpose: Since Nlrc3 signaling is imperative for HSPCs production in zebrafish  to further determine the regulatory mechanism by which nlrc3 signaling regulates HSPCs. Bulk RNA sequencing analysis is performed to dissect the function and molecular mechanism between the control groups and the nlrc3 morphants groups. Methods: The GFP+ cells in Tgfli1a:eGFP zebrafish embryos at 28 hpf were sorted  which is the stage that EHT occurs in the VDA and the site of hemogenic endothelial cells onset. The mRNA profiles of these cells in wild type WT and Nlrc3 knockdown were deep sequencing  in triplicate  using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: Using an optimized data analysis workflow  we mapped about 35 million sequence reads per sample and identified 4153 transcripts showing differential expression between the of WT and  Nlrc3 morphants  with a fold change =1.5 and p value <0.05. Based on the results of RNA seq  some signaling pathways essential for  the the Nlrc3 regulates the onset of HSPCs in vertebrate are dissected. Including Notch  WNT  NF kB. Conclusions: Hemogenic endothelial cells mRNA profiles of WT groups and Nlrc3 knockdown groups were deep sequenced and anlysis. Based on the results of RNA seq  we performed  experiments to validate the up and downstream pathway involved in the the Nlrc3 regulates the onset of HSCPs in vertebrate. Overall design: mRNA profiling by high throughput sequencing to dissect the function and molecular mechanism by which nlrc3 signaling regulates the HSPCs in vertebrate.,,pubmed:38172511,,samples in nlrc3 MO rep2,GSM7921553,,source name:zebrafish embryos|tissue:GFP+ cells in Tgfli1a:eGFP|passage:28 hpf embryos|culture:no culture|geo loc name:missing|collection date:missing,samples in nlrc3 MO rep2,Illunima Casava 1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Supplementary files format and content: FPKM values for each Sample.,zebrafish embryos,,Total RNA was extracted using Trizol reagent Invitrogen  CA  USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent  CA  USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:GFP+ cells in Tgfli1a:eGFP|passage:28 hpf embryos|culture:no culture,GSM7921553,GSM7921553: samples in nlrc3 MO rep2; Danio rerio; RNA Seq,GSM7921553 r1,GSM7921553,1,Total RNA was extracted using Trizol reagent Invitrogen  CA  USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent  CA  USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474706,,loader:fastq load.py,Mo2_Clean_Data1.fq.gz Mo2_Clean_Data2.fq.gz,fastq fastq,6532296488.0,23367662.0,GSM7921553 r1,0:139.78 1:139.77,A:1648685612;C:1610899197;G:1630932563;T:1641776735;N:2381,139,139,,,1648685612,1610899197,1630932563,1641776735,2381,SRX22668016,SRS19663576,SRA1759375,Zhejiang university,Zhejiang university,2,0.94588,0.94696,0.05065,0.05045,0.75891,0.75854,0.47315,0.47431,141,141,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,bulk,bulk,,China,2023-11-28,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
29027,SRR26974569,SRX22668015,SRS19663575,SRP474706,PRJNA1046144,Nlrc3 signaling is required for hematopoietic stem cell emergence by activating Notch signaling in vertebrates,GSE248871,Transcriptome Analysis,Purpose: Since Nlrc3 signaling is imperative for HSPCs production in zebrafish  to further determine the regulatory mechanism by which nlrc3 signaling regulates HSPCs. Bulk RNA sequencing analysis is performed to dissect the function and molecular mechanism between the control groups and the nlrc3 morphants groups. Methods: The GFP+ cells in Tgfli1a:eGFP zebrafish embryos at 28 hpf were sorted  which is the stage that EHT occurs in the VDA and the site of hemogenic endothelial cells onset. The mRNA profiles of these cells in wild type WT and Nlrc3 knockdown were deep sequencing  in triplicate  using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: Using an optimized data analysis workflow  we mapped about 35 million sequence reads per sample and identified 4153 transcripts showing differential expression between the of WT and  Nlrc3 morphants  with a fold change =1.5 and p value <0.05. Based on the results of RNA seq  some signaling pathways essential for  the the Nlrc3 regulates the onset of HSPCs in vertebrate are dissected. Including Notch  WNT  NF kB. Conclusions: Hemogenic endothelial cells mRNA profiles of WT groups and Nlrc3 knockdown groups were deep sequenced and anlysis. Based on the results of RNA seq  we performed  experiments to validate the up and downstream pathway involved in the the Nlrc3 regulates the onset of HSCPs in vertebrate. Overall design: mRNA profiling by high throughput sequencing to dissect the function and molecular mechanism by which nlrc3 signaling regulates the HSPCs in vertebrate.,,pubmed:38172511,,samples in nlrc3 MO rep1,GSM7921552,,source name:zebrafish embryos|tissue:GFP+ cells in Tgfli1a:eGFP|passage:28 hpf embryos|culture:no culture|geo loc name:missing|collection date:missing,samples in nlrc3 MO rep1,Illunima Casava 1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Supplementary files format and content: FPKM values for each Sample.,zebrafish embryos,,Total RNA was extracted using Trizol reagent Invitrogen  CA  USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent  CA  USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:GFP+ cells in Tgfli1a:eGFP|passage:28 hpf embryos|culture:no culture,GSM7921552,GSM7921552: samples in nlrc3 MO rep1; Danio rerio; RNA Seq,GSM7921552 r1,GSM7921552,1,Total RNA was extracted using Trizol reagent Invitrogen  CA  USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent  CA  USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474706,,loader:fastq load.py,Mo1_Clean_Data1.fq.gz Mo1_Clean_Data2.fq.gz,fastq fastq,5812795813.0,20780108.0,GSM7921552 r1,0:139.86 1:139.87,A:1453223147;C:1447175836;G:1465655085;T:1446739519;N:2226,139,139,,,1453223147,1447175836,1465655085,1446739519,2226,SRX22668015,SRS19663575,SRA1759375,Zhejiang university,Zhejiang university,2,0.94733,0.94831,0.05436,0.05351,0.76059,0.76063,0.47936,0.47664,141,141,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,bulk,bulk,,China,2023-11-28,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
29028,SRR26974570,SRX22668014,SRS19663574,SRP474706,PRJNA1046144,Nlrc3 signaling is required for hematopoietic stem cell emergence by activating Notch signaling in vertebrates,GSE248871,Transcriptome Analysis,Purpose: Since Nlrc3 signaling is imperative for HSPCs production in zebrafish  to further determine the regulatory mechanism by which nlrc3 signaling regulates HSPCs. Bulk RNA sequencing analysis is performed to dissect the function and molecular mechanism between the control groups and the nlrc3 morphants groups. Methods: The GFP+ cells in Tgfli1a:eGFP zebrafish embryos at 28 hpf were sorted  which is the stage that EHT occurs in the VDA and the site of hemogenic endothelial cells onset. The mRNA profiles of these cells in wild type WT and Nlrc3 knockdown were deep sequencing  in triplicate  using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: Using an optimized data analysis workflow  we mapped about 35 million sequence reads per sample and identified 4153 transcripts showing differential expression between the of WT and  Nlrc3 morphants  with a fold change =1.5 and p value <0.05. Based on the results of RNA seq  some signaling pathways essential for  the the Nlrc3 regulates the onset of HSPCs in vertebrate are dissected. Including Notch  WNT  NF kB. Conclusions: Hemogenic endothelial cells mRNA profiles of WT groups and Nlrc3 knockdown groups were deep sequenced and anlysis. Based on the results of RNA seq  we performed  experiments to validate the up and downstream pathway involved in the the Nlrc3 regulates the onset of HSCPs in vertebrate. Overall design: mRNA profiling by high throughput sequencing to dissect the function and molecular mechanism by which nlrc3 signaling regulates the HSPCs in vertebrate.,,pubmed:38172511,,samples in control MO rep3,GSM7921551,,source name:zebrafish embryos|tissue:GFP+ cells in Tgfli1a:eGFP|passage:28 hpf embryos|culture:no culture|geo loc name:missing|collection date:missing,samples in control MO rep3,Illunima Casava 1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Supplementary files format and content: FPKM values for each Sample.,zebrafish embryos,,Total RNA was extracted using Trizol reagent Invitrogen  CA  USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent  CA  USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:GFP+ cells in Tgfli1a:eGFP|passage:28 hpf embryos|culture:no culture,GSM7921551,GSM7921551: samples in control MO rep3; Danio rerio; RNA Seq,GSM7921551 r1,GSM7921551,1,Total RNA was extracted using Trizol reagent Invitrogen  CA  USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent  CA  USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474706,,loader:fastq load.py,S3_Clean_Data1.fq.gz S3_Clean_Data2.fq.gz,fastq fastq,5643732705.0,20272868.0,GSM7921551 r1,0:139.20 1:139.19,A:1466198749;C:1349499199;G:1367008013;T:1461024521;N:2223,139,139,,,1466198749,1349499199,1367008013,1461024521,2223,SRX22668014,SRS19663574,SRA1759375,Zhejiang university,Zhejiang university,2,0.95103,0.95208,0.07142,0.07068,0.73428,0.73371,0.47064,0.47197,141,141,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,bulk,bulk,,China,2023-11-28,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
29029,SRR26974571,SRX22668013,SRS19663573,SRP474706,PRJNA1046144,Nlrc3 signaling is required for hematopoietic stem cell emergence by activating Notch signaling in vertebrates,GSE248871,Transcriptome Analysis,Purpose: Since Nlrc3 signaling is imperative for HSPCs production in zebrafish  to further determine the regulatory mechanism by which nlrc3 signaling regulates HSPCs. Bulk RNA sequencing analysis is performed to dissect the function and molecular mechanism between the control groups and the nlrc3 morphants groups. Methods: The GFP+ cells in Tgfli1a:eGFP zebrafish embryos at 28 hpf were sorted  which is the stage that EHT occurs in the VDA and the site of hemogenic endothelial cells onset. The mRNA profiles of these cells in wild type WT and Nlrc3 knockdown were deep sequencing  in triplicate  using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: Using an optimized data analysis workflow  we mapped about 35 million sequence reads per sample and identified 4153 transcripts showing differential expression between the of WT and  Nlrc3 morphants  with a fold change =1.5 and p value <0.05. Based on the results of RNA seq  some signaling pathways essential for  the the Nlrc3 regulates the onset of HSPCs in vertebrate are dissected. Including Notch  WNT  NF kB. Conclusions: Hemogenic endothelial cells mRNA profiles of WT groups and Nlrc3 knockdown groups were deep sequenced and anlysis. Based on the results of RNA seq  we performed  experiments to validate the up and downstream pathway involved in the the Nlrc3 regulates the onset of HSCPs in vertebrate. Overall design: mRNA profiling by high throughput sequencing to dissect the function and molecular mechanism by which nlrc3 signaling regulates the HSPCs in vertebrate.,,pubmed:38172511,,samples in control MO rep2,GSM7921550,,source name:zebrafish embryos|tissue:GFP+ cells in Tgfli1a:eGFP|passage:28 hpf embryos|culture:no culture|geo loc name:missing|collection date:missing,samples in control MO rep2,Illunima Casava 1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Supplementary files format and content: FPKM values for each Sample.,zebrafish embryos,,Total RNA was extracted using Trizol reagent Invitrogen  CA  USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent  CA  USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:GFP+ cells in Tgfli1a:eGFP|passage:28 hpf embryos|culture:no culture,GSM7921550,GSM7921550: samples in control MO rep2; Danio rerio; RNA Seq,GSM7921550 r1,GSM7921550,1,Total RNA was extracted using Trizol reagent Invitrogen  CA  USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent  CA  USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474706,,loader:fastq load.py,S2_Clean_Data1.fq.gz S2_Clean_Data2.fq.gz,fastq fastq,4436220529.0,15923512.0,GSM7921550 r1,0:139.30 1:139.29,A:1152960918;C:1060020216;G:1074069001;T:1149168714;N:1680,139,139,,,1152960918,1060020216,1074069001,1149168714,1680,SRX22668013,SRS19663573,SRA1759375,Zhejiang university,Zhejiang university,2,0.94868,0.94952,0.07127,0.07083,0.73438,0.73403,0.46822,0.46865,141,141,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,bulk,bulk,,China,2023-11-28,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
29030,SRR26974572,SRX22668012,SRS19663572,SRP474706,PRJNA1046144,Nlrc3 signaling is required for hematopoietic stem cell emergence by activating Notch signaling in vertebrates,GSE248871,Transcriptome Analysis,Purpose: Since Nlrc3 signaling is imperative for HSPCs production in zebrafish  to further determine the regulatory mechanism by which nlrc3 signaling regulates HSPCs. Bulk RNA sequencing analysis is performed to dissect the function and molecular mechanism between the control groups and the nlrc3 morphants groups. Methods: The GFP+ cells in Tgfli1a:eGFP zebrafish embryos at 28 hpf were sorted  which is the stage that EHT occurs in the VDA and the site of hemogenic endothelial cells onset. The mRNA profiles of these cells in wild type WT and Nlrc3 knockdown were deep sequencing  in triplicate  using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: Using an optimized data analysis workflow  we mapped about 35 million sequence reads per sample and identified 4153 transcripts showing differential expression between the of WT and  Nlrc3 morphants  with a fold change =1.5 and p value <0.05. Based on the results of RNA seq  some signaling pathways essential for  the the Nlrc3 regulates the onset of HSPCs in vertebrate are dissected. Including Notch  WNT  NF kB. Conclusions: Hemogenic endothelial cells mRNA profiles of WT groups and Nlrc3 knockdown groups were deep sequenced and anlysis. Based on the results of RNA seq  we performed  experiments to validate the up and downstream pathway involved in the the Nlrc3 regulates the onset of HSCPs in vertebrate. Overall design: mRNA profiling by high throughput sequencing to dissect the function and molecular mechanism by which nlrc3 signaling regulates the HSPCs in vertebrate.,,pubmed:38172511,,samples in control MO rep1,GSM7921549,,source name:zebrafish embryos|tissue:GFP+ cells in Tgfli1a:eGFP|passage:28 hpf embryos|culture:no culture|geo loc name:missing|collection date:missing,samples in control MO rep1,Illunima Casava 1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Supplementary files format and content: FPKM values for each Sample.,zebrafish embryos,,Total RNA was extracted using Trizol reagent Invitrogen  CA  USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent  CA  USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:GFP+ cells in Tgfli1a:eGFP|passage:28 hpf embryos|culture:no culture,GSM7921549,GSM7921549: samples in control MO rep1; Danio rerio; RNA Seq,GSM7921549 r1,GSM7921549,1,Total RNA was extracted using Trizol reagent Invitrogen  CA  USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent  CA  USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474706,,loader:fastq load.py,S1_Clean_Data1.fq.gz S1_Clean_Data2.fq.gz,fastq fastq,6121313766.0,21997860.0,GSM7921549 r1,0:139.14 1:139.13,A:1591232135;C:1462847585;G:1481777440;T:1585450214;N:6392,139,139,,,1591232135,1462847585,1481777440,1585450214,6392,SRX22668012,SRS19663572,SRA1759375,Zhejiang university,Zhejiang university,2,0.95177,0.95291,0.07145,0.07064,0.73322,0.73306,0.47372,0.47734,141,141,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,bulk,bulk,,China,2023-11-28,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
30024,SRR27732020,SRX23397628,SRS20258469,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 36 hpf embryo,zebrafish embryo 36hpf replicate 1,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 36hpf embryo,W 13,W 13,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT36h-1_1.fq.gz WT36h-1_2.fq.gz,fastq fastq,7292758500.0,24309195.0,WT36h 1 1.fq.gz,0:150 1:150,A:1908273664;C:1731632674;G:1760624671;T:1892167502;N:59989,150,150,,,1908273664,1731632674,1760624671,1892167502,59989,SRX23397628,SRS20258469,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94269,0.94089,0.07258,0.07222,0.69978,0.70143,0.45682,0.45348,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
30025,SRR27732021,SRX23397627,SRS20258468,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 24 hpf embryo,zebrafish embryo 24hpf replicate 3,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:24 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 24hpf embryo,W 12,W 12,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT24h-3_1.fq.gz WT24h-3_2.fq.gz,fastq fastq,6515838900.0,21719463.0,WT24h 3 1.fq.gz,0:150 1:150,A:1713953613;C:1537571365;G:1564392828;T:1699697009;N:224085,150,150,,,1713953613,1537571365,1564392828,1699697009,224085,SRX23397627,SRS20258468,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93632,0.9362,0.06541,0.06556,0.69992,0.70094,0.46899,0.46674,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
30026,SRR27732022,SRX23397626,SRS20258467,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 24 hpf embryo,zebrafish embryo 24hpf replicate 2,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:24 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 24hpf embryo,W 11,W 11,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT24h-2_1.fq.gz WT24h-2_2.fq.gz,fastq fastq,7161020400.0,23870068.0,WT24h 2 1.fq.gz,0:150 1:150,A:1879362459;C:1692535178;G:1727934369;T:1860947917;N:240477,150,150,,,1879362459,1692535178,1727934369,1860947917,240477,SRX23397626,SRS20258467,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93727,0.93618,0.06477,0.06473,0.69546,0.69534,0.46029,0.46325,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
30027,SRR27732023,SRX23397625,SRS20258466,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 24 hpf embryo,zebrafish embryo 24hpf replicate 1,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:24 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 24hpf embryo,W 10,W 10,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT24h-1_1.fq.gz WT24h-1_2.fq.gz,fastq fastq,6174518700.0,20581729.0,WT24h 1 1.fq.gz,0:150 1:150,A:1622124267;C:1458396393;G:1486147186;T:1607751720;N:99134,150,150,,,1622124267,1458396393,1486147186,1607751720,99134,SRX23397625,SRS20258466,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93835,0.93534,0.06486,0.06373,0.69934,0.70041,0.45483,0.45986,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
30028,SRR27732024,SRX23397624,SRS20258465,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 12 hpf embryo,zebrafish embryo 12hpf replicate 3,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:12 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 12hpf embryo,W 9,W 9,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT12h-3_1.fq.gz WT12h-3_2.fq.gz,fastq fastq,6455561100.0,21518537.0,WT12h 3 1.fq.gz,0:150 1:150,A:1703515693;C:1511743995;G:1560331864;T:1679864521;N:105027,150,150,,,1703515693,1511743995,1560331864,1679864521,105027,SRX23397624,SRS20258465,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94111,0.94086,0.06759,0.06714,0.74383,0.74479,0.46264,0.46309,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
30029,SRR27732025,SRX23397623,SRS20258464,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 12 hpf embryo,zebrafish embryo 12hpf replicate 2,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:12 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 12hpf embryo,W 8,W 8,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT12h-2_1.fq.gz WT12h-2_2.fq.gz,fastq fastq,6161839200.0,20539464.0,WT12h 2 1.fq.gz,0:150 1:150,A:1628002733;C:1440787634;G:1486546983;T:1606403484;N:98366,150,150,,,1628002733,1440787634,1486546983,1606403484,98366,SRX23397623,SRS20258464,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94064,0.93857,0.06897,0.06866,0.7457,0.74621,0.46575,0.46211,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
30030,SRR27732026,SRX23397622,SRS20258463,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 12 hpf embryo,zebrafish embryo 12hpf replicate 1,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:12 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 12hpf embryo,W 7,W 7,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT12h-1_2.fq.gz WT12h-1_1.fq.gz,fastq fastq,6395259000.0,21317530.0,WT12h 1 1.fq.gz,0:150 1:150,A:1700786034;C:1487669685;G:1530455534;T:1676243983;N:103764,150,150,,,1700786034,1487669685,1530455534,1676243983,103764,SRX23397622,SRS20258463,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94192,0.9393,0.07278,0.0714,0.74225,0.74414,0.46258,0.46623,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
30031,SRR27732027,SRX23397621,SRS20258462,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 8 hpf embryo,zebrafish embryo 8hpf replicate 3,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:8 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 8hpf embryo,W 6,W 6,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT8h-3_2.fq.gz WT8h-3_1.fq.gz,fastq fastq,6747267300.0,22490891.0,WT8h 3 1.fq.gz,0:150 1:150,A:1802220913;C:1560718919;G:1610360895;T:1773867706;N:98867,150,150,,,1802220913,1560718919,1610360895,1773867706,98867,SRX23397621,SRS20258462,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94669,0.94524,0.06343,0.06321,0.74517,0.74535,0.46737,0.46861,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
30032,SRR27732028,SRX23397620,SRS20258461,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 72 hpf embryo,zebrafish embryo 72hpf replicate 3,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:72 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 72hpf embryo,W 21,W 21,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT72h-3_1.fq.gz WT72h-3_2.fq.gz,fastq fastq,6611014500.0,22036715.0,WT72h 3 1.fq.gz,0:150 1:150,A:1772431295;C:1528499931;G:1545216909;T:1764783401;N:82964,150,150,,,1772431295,1528499931,1545216909,1764783401,82964,SRX23397620,SRS20258461,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93676,0.9346,0.10556,0.10444,0.66927,0.66991,0.46155,0.46025,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Larval,Larval,Embryo Imprecise,All anatomical structures
30033,SRR27732029,SRX23397619,SRS20258460,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 72 hpf embryo,zebrafish embryo 72hpf replicate 2,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:72 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 72hpf embryo,W 20,W 20,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT72h-2_1.fq.gz WT72h-2_2.fq.gz,fastq fastq,5844974100.0,19483247.0,WT72h 2 1.fq.gz,0:150 1:150,A:1570406354;C:1348972192;G:1363229634;T:1562318366;N:47554,150,150,,,1570406354,1348972192,1363229634,1562318366,47554,SRX23397619,SRS20258460,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93927,0.93723,0.10803,0.10754,0.66574,0.66959,0.45443,0.4547,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Larval,Larval,Embryo Imprecise,All anatomical structures
30034,SRR27732030,SRX23397618,SRS20258459,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 72 hpf embryo,zebrafish embryo 72hpf replicate 1,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:72 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 72hpf embryo,W 19,W 19,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT72h-1_1.fq.gz WT72h-1_2.fq.gz,fastq fastq,7024123200.0,23413744.0,WT72h 1 1.fq.gz,0:150 1:150,A:1870182203;C:1638926026;G:1656247404;T:1858679271;N:88296,150,150,,,1870182203,1638926026,1656247404,1858679271,88296,SRX23397618,SRS20258459,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93353,0.93369,0.09236,0.09181,0.6674,0.66789,0.44578,0.45563,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Larval,Larval,Embryo Imprecise,All anatomical structures
30035,SRR27732031,SRX23397617,SRS20258458,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 48 hpf embryo,zebrafish embryo 48hpf replicate 3,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:48 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 48hpf embryo,W 18,W 18,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT48h-3_1.fq.gz WT48h-3_2.fq.gz,fastq fastq,6520477800.0,21734926.0,WT48h 3 1.fq.gz,0:150 1:150,A:1739928482;C:1516508736;G:1531638319;T:1732180903;N:221360,150,150,,,1739928482,1516508736,1531638319,1732180903,221360,SRX23397617,SRS20258458,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93874,0.93954,0.09485,0.09438,0.67888,0.67913,0.46039,0.46026,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Hatching,Embryo,Embryo Imprecise,All anatomical structures
30036,SRR27732032,SRX23397616,SRS20258457,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 48 hpf embryo,zebrafish embryo 48hpf replicate 2,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:48 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 48hpf embryo,W 17,W 17,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT48h-2_2.fq.gz WT48h-2_1.fq.gz,fastq fastq,7046397300.0,23487991.0,WT48h 2 1.fq.gz,0:150 1:150,A:1865031055;C:1655796645;G:1670091105;T:1855237793;N:240702,150,150,,,1865031055,1655796645,1670091105,1855237793,240702,SRX23397616,SRS20258457,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94056,0.93987,0.08562,0.08535,0.68241,0.68288,0.46355,0.46204,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Hatching,Embryo,Embryo Imprecise,All anatomical structures
30037,SRR27732033,SRX23397615,SRS20258456,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 48 hpf embryo,zebrafish embryo 48hpf replicate 1,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:48 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 48hpf embryo,W 16,W 16,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT48h-1_1.fq.gz WT48h-1_2.fq.gz,fastq fastq,6851959800.0,22839866.0,WT48h 1 1.fq.gz,0:150 1:150,A:1813160204;C:1610483050;G:1626359291;T:1801871129;N:86126,150,150,,,1813160204,1610483050,1626359291,1801871129,86126,SRX23397615,SRS20258456,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94028,0.93857,0.08526,0.08523,0.68331,0.68477,0.45695,0.45202,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Hatching,Embryo,Embryo Imprecise,All anatomical structures
30038,SRR27732034,SRX23397614,SRS20258455,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 36 hpf embryo,zebrafish embryo 36hpf replicate 3,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 36hpf embryo,W 15,W 15,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT36h-3_1.fq.gz WT36h-3_2.fq.gz,fastq fastq,6607629600.0,22025432.0,WT36h 3 1.fq.gz,0:150 1:150,A:1740033364;C:1558025307;G:1585024036;T:1724491752;N:55141,150,150,,,1740033364,1558025307,1585024036,1724491752,55141,SRX23397614,SRS20258455,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94036,0.93863,0.07395,0.07343,0.69723,0.6994,0.46045,0.46325,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
30039,SRR27732035,SRX23397613,SRS20258454,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 36 hpf embryo,zebrafish embryo 36hpf replicate 2,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 36hpf embryo,W 14,W 14,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT36h-2_1.fq.gz WT36h-2_2.fq.gz,fastq fastq,7848879900.0,26162933.0,WT36h 2 1.fq.gz,0:150 1:150,A:2065200572;C:1853008494;G:1880402891;T:2050169369;N:98574,150,150,,,2065200572,1853008494,1880402891,2050169369,98574,SRX23397613,SRS20258454,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.9395,0.93639,0.07562,0.07383,0.6969,0.69814,0.46478,0.45495,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
30040,SRR27732036,SRX23397612,SRS20258453,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 8 hpf embryo,zebrafish embryo 8hpf replicate 2,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:8 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 8hpf embryo,W 5,W 5,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT8h-2_1.fq.gz WT8h-2_2.fq.gz,fastq fastq,6832373100.0,22774577.0,WT8h 2 1.fq.gz,0:150 1:150,A:1819536066;C:1586031035;G:1634106671;T:1792464818;N:234510,150,150,,,1819536066,1586031035,1634106671,1792464818,234510,SRX23397612,SRS20258453,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94411,0.94402,0.0643,0.06343,0.7472,0.74775,0.47176,0.46993,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
30041,SRR27732037,SRX23397611,SRS20258452,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 8 hpf embryo,zebrafish embryo 8hpf replicate 1,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:8 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 8hpf embryo,W 4,W 4,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT8h-1_1.fq.gz WT8h-1_2.fq.gz,fastq fastq,5792885100.0,19309617.0,WT8h 1 1.fq.gz,0:150 1:150,A:1545377384;C:1341340578;G:1388087015;T:1517986965;N:93158,150,150,,,1545377384,1341340578,1388087015,1517986965,93158,SRX23397611,SRS20258452,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94512,0.9415,0.05988,0.05963,0.74345,0.74582,0.46534,0.46722,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
30042,SRR27730705,SRX23396353,SRS20257267,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  24 hpf embryo,zebrafish embryo hamp /  24hpf replicate 1,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:24 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 24hpf embryo,W 31,W 31,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp24h-1_1.fq.gz hamp24h-1_2.fq.gz,fastq fastq,6643634100.0,22145447.0,hamp24h 1 1.fq.gz,0:150 1:150,A:1742210141;C:1573249075;G:1600079934;T:1727989339;N:105611,150,150,,,1742210141,1573249075,1600079934,1727989339,105611,SRX23396353,SRS20257267,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93899,0.93556,0.06108,0.0602,0.6997,0.70179,0.47261,0.47417,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
30043,SRR27730706,SRX23396352,SRS20257266,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  12 hpf embryo,zebrafish embryo hamp /  12hpf replicate 3,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:12 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 12hpf embryo,W 30,W 30,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp12h-3_1.fq.gz hamp12h-3_2.fq.gz,fastq fastq,6380262000.0,21267540.0,hamp12h 3 1.fq.gz,0:150 1:150,A:1686482981;C:1496556670;G:1525661866;T:1671347887;N:212596,150,150,,,1686482981,1496556670,1525661866,1671347887,212596,SRX23396352,SRS20257266,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93955,0.93782,0.07021,0.07017,0.72541,0.72691,0.4754,0.47596,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
30044,SRR27730707,SRX23396351,SRS20257265,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  12 hpf embryo,zebrafish embryo hamp /  12hpf replicate 2,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:12 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 12hpf embryo,W 29,W 29,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp12h-2_1.fq.gz hamp12h-2_2.fq.gz,fastq fastq,6738373500.0,22461245.0,hamp12h 2 1.fq.gz,0:150 1:150,A:1793407846;C:1570428903;G:1600911780;T:1773421988;N:202983,150,150,,,1793407846,1570428903,1600911780,1773421988,202983,SRX23396351,SRS20257265,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93629,0.93637,0.07013,0.07043,0.72764,0.72912,0.47138,0.47279,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
30045,SRR27730708,SRX23396350,SRS20257264,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  12 hpf embryo,zebrafish embryo hamp /  12hpf replicate 1,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:12 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 12hpf embryo,W 28,W 28,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp12h-1_1.fq.gz hamp12h-1_2.fq.gz,fastq fastq,6882364200.0,22941214.0,hamp12h 1 1.fq.gz,0:150 1:150,A:1816338301;C:1617411981;G:1650700092;T:1797708715;N:205111,150,150,,,1816338301,1617411981,1650700092,1797708715,205111,SRX23396350,SRS20257264,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93465,0.93675,0.06811,0.06816,0.72863,0.72922,0.47838,0.47563,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
30046,SRR27730709,SRX23396349,SRS20257263,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  8 hpf embryo,zebrafish embryo hamp /  8hpf replicate 3,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:8 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 8hpf embryo,W 27,W 27,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp8h-3_1.fq.gz hamp8h-3_2.fq.gz,fastq fastq,6295202100.0,20984007.0,hamp8h 3 1.fq.gz,0:150 1:150,A:1694806329;C:1445372178;G:1488024762;T:1666904080;N:94751,150,150,,,1694806329,1445372178,1488024762,1666904080,94751,SRX23396349,SRS20257263,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94405,0.94297,0.06722,0.06702,0.76627,0.76828,0.48464,0.48699,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
30047,SRR27730710,SRX23396348,SRS20257262,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  8 hpf embryo,zebrafish embryo hamp /  8hpf replicate 2,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:8 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 8hpf embryo,W 26,W 26,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp8h-2_1.fq.gz hamp8h-2_2.fq.gz,fastq fastq,6148660800.0,20495536.0,hamp8h 2 1.fq.gz,0:150 1:150,A:1644992837;C:1420391182;G:1458975922;T:1624091150;N:209709,150,150,,,1644992837,1420391182,1458975922,1624091150,209709,SRX23396348,SRS20257262,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93828,0.93748,0.08438,0.08432,0.74681,0.74732,0.48765,0.48809,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
30048,SRR27730711,SRX23396347,SRS20257261,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  8 hpf embryo,zebrafish embryo hamp /  8hpf replicate 1,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:8 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 8hpf embryo,W 25,W 25,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp8h-1_1.fq.gz hamp8h-1_2.fq.gz,fastq fastq,7443429000.0,24811430.0,hamp8h 1 1.fq.gz,0:150 1:150,A:1989642168;C:1723187805;G:1770726575;T:1959761293;N:111159,150,150,,,1989642168,1723187805,1770726575,1959761293,111159,SRX23396347,SRS20257261,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94417,0.94323,0.06281,0.06203,0.76479,0.76706,0.47849,0.4799,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
30049,SRR27730712,SRX23396346,SRS20257260,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  72 hpf embryo,zebrafish embryo hamp /  72hpf replicate 3,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:72 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 72hpf embryo,W 42,W 42,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp72h-3_1.fq.gz hamp72h-3_2.fq.gz,fastq fastq,7124946000.0,23749820.0,hamp72h 3 1.fq.gz,0:150 1:150,A:1926386901;C:1633268260;G:1649597432;T:1915633812;N:59595,150,150,,,1926386901,1633268260,1649597432,1915633812,59595,SRX23396346,SRS20257260,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.9369,0.9352,0.10335,0.10255,0.66703,0.6686,0.47407,0.46796,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Larval,Larval,Embryo Imprecise,All anatomical structures
30050,SRR27730713,SRX23396345,SRS20257259,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  4 hpf embryo,zebrafish embryo hamp /  4hpf replicate 3,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:4 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 4hpf embryo,W 24,W 24,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp4h-3_2.fq.gz hamp4h-3_1.fq.gz,fastq fastq,6261088500.0,20870295.0,hamp4h 3 1.fq.gz,0:150 1:150,A:1668720393;C:1449635670;G:1495531397;T:1647100279;N:100761,150,150,,,1668720393,1449635670,1495531397,1647100279,100761,SRX23396345,SRS20257259,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94424,0.94159,0.04146,0.0415,0.75089,0.75201,0.48393,0.48457,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Blastula,Embryo,Embryo Imprecise,All anatomical structures
30051,SRR27730714,SRX23396344,SRS20257258,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  72 hpf embryo,zebrafish embryo hamp /  72hpf replicate 2,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:72 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 72hpf embryo,W 41,W 41,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp72h-2_1.fq.gz hamp72h-2_2.fq.gz,fastq fastq,6201979200.0,20673264.0,hamp72h 2 1.fq.gz,0:150 1:150,A:1657650097;C:1440501731;G:1451375517;T:1652374388;N:77467,150,150,,,1657650097,1440501731,1451375517,1652374388,77467,SRX23396344,SRS20257258,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93468,0.9333,0.0972,0.09614,0.66427,0.66588,0.46658,0.46539,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Larval,Larval,Embryo Imprecise,All anatomical structures
30052,SRR27730715,SRX23396343,SRS20257257,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  72 hpf embryo,zebrafish embryo hamp /  72hpf replicate 1,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:72 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 72hpf embryo,W 40,W 40,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp72h-1_1.fq.gz hamp72h-1_2.fq.gz,fastq fastq,6432009000.0,21440030.0,hamp72h 1 1.fq.gz,0:150 1:150,A:1734564732;C:1478070668;G:1490938268;T:1728354590;N:80742,150,150,,,1734564732,1478070668,1490938268,1728354590,80742,SRX23396343,SRS20257257,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93382,0.93132,0.10621,0.10453,0.66592,0.66667,0.46409,0.46541,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Larval,Larval,Embryo Imprecise,All anatomical structures
30053,SRR27730716,SRX23396342,SRS20257256,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  48 hpf embryo,zebrafish embryo hamp /  48hpf replicate 3,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:48 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 48hpf embryo,W 39,W 39,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp48h-3_1.fq.gz hamp48h-3_2.fq.gz,fastq fastq,7580570700.0,25268569.0,hamp48h 3 1.fq.gz,0:150 1:150,A:2019162299;C:1768225001;G:1782049665;T:2011039613;N:94122,150,150,,,2019162299,1768225001,1782049665,2011039613,94122,SRX23396342,SRS20257256,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93863,0.93681,0.08675,0.08582,0.68394,0.6857,0.46373,0.46321,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Hatching,Embryo,Embryo Imprecise,All anatomical structures
30054,SRR27730717,SRX23396341,SRS20257255,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  48 hpf embryo,zebrafish embryo hamp /  48hpf replicate 2,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:48 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 48hpf embryo,W 38,W 38,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp48h-2_1.fq.gz hamp48h-2_2.fq.gz,fastq fastq,7385330400.0,24617768.0,hamp48h 2 1.fq.gz,0:150 1:150,A:1971527478;C:1717463447;G:1738237873;T:1957858394;N:243208,150,150,,,1971527478,1717463447,1738237873,1957858394,243208,SRX23396341,SRS20257255,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93851,0.9369,0.09049,0.08988,0.68274,0.6843,0.45945,0.46042,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Hatching,Embryo,Embryo Imprecise,All anatomical structures
30055,SRR27730718,SRX23396340,SRS20257254,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  48 hpf embryo,zebrafish embryo hamp /  48hpf replicate 1,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:48 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 48hpf embryo,W 37,W 37,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp48h-1_1.fq.gz hamp48h-1_2.fq.gz,fastq fastq,6188343000.0,20627810.0,hamp48h 1 1.fq.gz,0:150 1:150,A:1649030143;C:1444577102;G:1461592285;T:1633092294;N:51176,150,150,,,1649030143,1444577102,1461592285,1633092294,51176,SRX23396340,SRS20257254,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94313,0.94006,0.08835,0.08702,0.6859,0.68702,0.45658,0.46001,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Hatching,Embryo,Embryo Imprecise,All anatomical structures
30056,SRR27730719,SRX23396339,SRS20257253,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  36 hpf embryo,zebrafish embryo hamp /  36hpf replicate 3,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 36hpf embryo,W 36,W 36,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp36h-3_1.fq.gz hamp36h-3_2.fq.gz,fastq fastq,6442851300.0,21476171.0,hamp36h 3 1.fq.gz,0:150 1:150,A:1696209844;C:1521086149;G:1542365512;T:1683136288;N:53507,150,150,,,1696209844,1521086149,1542365512,1683136288,53507,SRX23396339,SRS20257253,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.9446,0.94399,0.07193,0.07106,0.6955,0.69729,0.46483,0.46399,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
30057,SRR27730720,SRX23396338,SRS20257252,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  36 hpf embryo,zebrafish embryo hamp /  36hpf replicate 2,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 36hpf embryo,W 35,W 35,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp36h-2_1.fq.gz hamp36h-2_2.fq.gz,fastq fastq,8020366200.0,26734554.0,hamp36h 2 1.fq.gz,0:150 1:150,A:2103699528;C:1897760189;G:1928753070;T:2090039533;N:113880,150,150,,,2103699528,1897760189,1928753070,2090039533,113880,SRX23396338,SRS20257252,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94805,0.94701,0.07022,0.06985,0.69585,0.69777,0.46182,0.45694,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
30058,SRR27730721,SRX23396337,SRS20257251,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  36 hpf embryo,zebrafish embryo hamp /  36hpf replicate 1,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 36hpf embryo,W 34,W 34,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp36h-1_1.fq.gz hamp36h-1_2.fq.gz,fastq fastq,7319492100.0,24398307.0,hamp36h 1 1.fq.gz,0:150 1:150,A:1924726816;C:1727922135;G:1762476592;T:1904305780;N:60777,150,150,,,1924726816,1727922135,1762476592,1904305780,60777,SRX23396337,SRS20257251,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93938,0.93967,0.07121,0.07085,0.69581,0.69755,0.45448,0.45541,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
30059,SRR27730722,SRX23396336,SRS20257250,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  24 hpf embryo,zebrafish embryo hamp /  24hpf replicate 3,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:24 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 24hpf embryo,W 33,W 33,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp24h-3_1.fq.gz hamp24h-3_2.fq.gz,fastq fastq,6470874300.0,21569581.0,hamp24h 3 1.fq.gz,0:150 1:150,A:1698655936;C:1530916678;G:1555607788;T:1685479625;N:214273,150,150,,,1698655936,1530916678,1555607788,1685479625,214273,SRX23396336,SRS20257250,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93644,0.93637,0.06179,0.06156,0.70011,0.70134,0.47098,0.4709,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
30060,SRR27730723,SRX23396335,SRS20257249,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  24 hpf embryo,zebrafish embryo hamp /  24hpf replicate 2,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:24 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 24hpf embryo,W 32,W 32,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp24h-2_1.fq.gz hamp24h-2_2.fq.gz,fastq fastq,5875188900.0,19583963.0,hamp24h 2 1.fq.gz,0:150 1:150,A:1553428887;C:1379148744;G:1400831429;T:1541584152;N:195688,150,150,,,1553428887,1379148744,1400831429,1541584152,195688,SRX23396335,SRS20257249,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.9351,0.93566,0.06624,0.06643,0.69739,0.69875,0.47055,0.47049,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
30061,SRR27730724,SRX23396334,SRS20257248,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  4 hpf embryo,zebrafish embryo hamp /  4hpf replicate 2,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:4 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 4hpf embryo,W 23,W 23,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp4h-2_1.fq.gz hamp4h-2_2.fq.gz,fastq fastq,6140359800.0,20467866.0,hamp4h 2 1.fq.gz,0:150 1:150,A:1622433757;C:1437175847;G:1481587196;T:1599071088;N:91912,150,150,,,1622433757,1437175847,1481587196,1599071088,91912,SRX23396334,SRS20257248,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94763,0.94713,0.03975,0.03948,0.75045,0.75193,0.48915,0.48855,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Blastula,Embryo,Embryo Imprecise,All anatomical structures
30062,SRR27730725,SRX23396333,SRS20257247,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  4 hpf embryo,zebrafish embryo hamp /  4hpf replicate 1,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:4 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 4hpf embryo,W 22,W 22,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp4h-1_1.fq.gz hamp4h-1_2.fq.gz,fastq fastq,6482302500.0,21607675.0,hamp4h 1 1.fq.gz,0:150 1:150,A:1723398342;C:1504238189;G:1551942847;T:1702630056;N:93066,150,150,,,1723398342,1504238189,1551942847,1702630056,93066,SRX23396333,SRS20257247,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94434,0.94083,0.04297,0.04235,0.75327,0.75526,0.48487,0.4837,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Blastula,Embryo,Embryo Imprecise,All anatomical structures
30063,SRR27674233,SRX23341580,SRS20203706,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 4 phf embryo,zebrafish embryo 4 phf replicate 3,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:4 phf|dev stage:4 phf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 4hpf embryo,W 3,W 3,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT4h-3_1.fq.gz WT4h-3_2.fq.gz,fastq fastq,5799593100.0,19331977.0,WT4h 3 1.fq.gz,0:150 1:150,A:1543677690;C:1345529657;G:1387996505;T:1522341224;N:48024,150,150,,,1543677690,1345529657,1387996505,1522341224,48024,SRX23341580,SRS20203706,SRA1789158,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94823,0.94693,0.0386,0.03884,0.74686,0.74769,0.47863,0.48203,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-22,Blastula,Embryo,Embryo Imprecise,All anatomical structures
30064,SRR27674234,SRX23341579,SRS20203705,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 4 phf embryo,zebrafish embryo 4 phf replicate 2,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:4 phf|dev stage:4 phf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 4hpf embryo,W 2,W 2,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT4h-2_1.fq.gz WT4h-2_2.fq.gz,fastq fastq,6408374700.0,21361249.0,WT4h 2 1.fq.gz,0:150 1:150,A:1700326501;C:1489928909;G:1544130015;T:1673936668;N:52607,150,150,,,1700326501,1489928909,1544130015,1673936668,52607,SRX23341579,SRS20203705,SRA1789158,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94833,0.94724,0.03589,0.03528,0.74521,0.74665,0.47991,0.47552,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-22,Blastula,Embryo,Embryo Imprecise,All anatomical structures
30065,SRR27674235,SRX23341578,SRS20203704,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 4 phf embryo,zebrafish embryo 4 phf replicate 1,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:4 phf|dev stage:4 phf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 4hpf embryo,W 1,W 1,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT4h-1_1.fq.gz WT4h-1_2.fq.gz,fastq fastq,6176335500.0,20587785.0,WT4h 1 1.fq.gz,0:150 1:150,A:1639564255;C:1436792246;G:1481775020;T:1618153065;N:50914,150,150,,,1639564255,1436792246,1481775020,1618153065,50914,SRX23341578,SRS20203704,SRA1789158,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.94837,0.94497,0.03675,0.03629,0.74393,0.74497,0.48332,0.48392,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-22,Blastula,Embryo,Embryo Imprecise,All anatomical structures
31557,SRR28471021,SRX24074012,SRS20864401,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S16 slice 13,GSM8171995,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing,S16 slice 13,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:16 hpf,GSM8171995,GSM8171995: S16 slice 13; Danio rerio; RNA Seq,GSM8171995 r1,GSM8171995,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S16_2_13-R1.fq.gz S16_2_13-R2.fq.gz,fastq fastq,7021136766.0,24220886.0,GSM8171995 r1,0:143.40 1:146.48,A:1932409729;C:1613003140;G:1510879854;T:1964782006;N:62037,143,146,,,1932409729,1613003140,1510879854,1964782006,62037,SRX24074012,SRS20864401,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31558,SRR28471022,SRX24074011,SRS20864400,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S16 slice 12,GSM8171993,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing,S16 slice 12,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:16 hpf,GSM8171993,GSM8171993: S16 slice 12; Danio rerio; RNA Seq,GSM8171993 r1,GSM8171993,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S16_2_12-R1.fq.gz S16_2_12-R2.fq.gz,fastq fastq,6989496704.0,24013496.0,GSM8171993 r1,0:144.73 1:146.34,A:1973063613;C:1539634004;G:1502105630;T:1974633280;N:60177,144,146,,,1973063613,1539634004,1502105630,1974633280,60177,SRX24074011,SRS20864400,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31559,SRR28471023,SRX24074010,SRS20864399,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S16 slice 11,GSM8171992,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing,S16 slice 11,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:16 hpf,GSM8171992,GSM8171992: S16 slice 11; Danio rerio; RNA Seq,GSM8171992 r1,GSM8171992,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S16_2_11-R1.fq.gz S16_2_11-R2.fq.gz,fastq fastq,6658580843.0,22968779.0,GSM8171992 r1,0:143.28 1:146.62,A:1850547171;C:1505778383;G:1450300777;T:1851895401;N:59111,143,146,,,1850547171,1505778383,1450300777,1851895401,59111,SRX24074010,SRS20864399,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31560,SRR28471024,SRX24074009,SRS20864398,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S16 slice 10,GSM8171991,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing,S16 slice 10,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:16 hpf,GSM8171991,GSM8171991: S16 slice 10; Danio rerio; RNA Seq,GSM8171991 r1,GSM8171991,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S16_2_10-R1.fq.gz S16_2_10-R2.fq.gz,fastq fastq,6764254234.0,23283773.0,GSM8171991 r1,0:143.52 1:146.99,A:1876570759;C:1531892471;G:1478929048;T:1876804139;N:57817,143,146,,,1876570759,1531892471,1478929048,1876804139,57817,SRX24074009,SRS20864398,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31561,SRR28471025,SRX24074008,SRS20864397,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S16 slice 9,GSM8171990,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing,S16 slice 9,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:16 hpf,GSM8171990,GSM8171990: S16 slice 9; Danio rerio; RNA Seq,GSM8171990 r1,GSM8171990,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S16_2_09-R1.fq.gz S16_2_09-R2.fq.gz,fastq fastq,6953469676.0,23939332.0,GSM8171990 r1,0:143.01 1:147.45,A:1887466615;C:1613826863;G:1550286679;T:1901843452;N:46067,143,147,,,1887466615,1613826863,1550286679,1901843452,46067,SRX24074008,SRS20864397,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31562,SRR28471026,SRX24074007,SRS20864396,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S16 slice 8,GSM8171989,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing,S16 slice 8,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:16 hpf,GSM8171989,GSM8171989: S16 slice 8; Danio rerio; RNA Seq,GSM8171989 r1,GSM8171989,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S16_2_08-R1.fq.gz S16_2_08-R2.fq.gz,fastq fastq,6932164944.0,23736001.0,GSM8171989 r1,0:144.93 1:147.12,A:1878823532;C:1592513147;G:1541045989;T:1919723182;N:59094,144,147,,,1878823532,1592513147,1541045989,1919723182,59094,SRX24074007,SRS20864396,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31563,SRR28471027,SRX24074006,SRS20864395,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S16 slice 7,GSM8171987,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing,S16 slice 7,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:16 hpf,GSM8171987,GSM8171987: S16 slice 7; Danio rerio; RNA Seq,GSM8171987 r1,GSM8171987,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S16_2_07-R1.fq.gz S16_2_07-R2.fq.gz,fastq fastq,7175124342.0,24613098.0,GSM8171987 r1,0:144.89 1:146.63,A:1955179901;C:1642901455;G:1556429416;T:2020550025;N:63545,144,146,,,1955179901,1642901455,1556429416,2020550025,63545,SRX24074006,SRS20864395,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31564,SRR28471028,SRX24074005,SRS20864394,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S16 slice 6,GSM8171986,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing,S16 slice 6,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:16 hpf,GSM8171986,GSM8171986: S16 slice 6; Danio rerio; RNA Seq,GSM8171986 r1,GSM8171986,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S16_2_06-R1.fq.gz S16_2_06-R2.fq.gz,fastq fastq,7015063214.0,24014594.0,GSM8171986 r1,0:145.26 1:146.86,A:1907017747;C:1603933957;G:1551829473;T:1952222046;N:59991,145,146,,,1907017747,1603933957,1551829473,1952222046,59991,SRX24074005,SRS20864394,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31565,SRR28471029,SRX24074004,SRS20864393,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S16 slice 5,GSM8171985,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing,S16 slice 5,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:16 hpf,GSM8171985,GSM8171985: S16 slice 5; Danio rerio; RNA Seq,GSM8171985 r1,GSM8171985,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S16_2_05-R1.fq.gz S16_2_05-R2.fq.gz,fastq fastq,6919538718.0,23740085.0,GSM8171985 r1,0:144.96 1:146.51,A:1882346373;C:1593041314;G:1504597309;T:1939492468;N:61254,144,146,,,1882346373,1593041314,1504597309,1939492468,61254,SRX24074004,SRS20864393,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31566,SRR28471030,SRX24074003,SRS20864392,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S16 slice 4,GSM8171984,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing,S16 slice 4,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:16 hpf,GSM8171984,GSM8171984: S16 slice 4; Danio rerio; RNA Seq,GSM8171984 r1,GSM8171984,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S16_2_04-R1.fq.gz S16_2_04-R2.fq.gz,fastq fastq,6868276226.0,23671591.0,GSM8171984 r1,0:144.21 1:145.94,A:1877392790;C:1565333202;G:1481973920;T:1943515595;N:60719,144,145,,,1877392790,1565333202,1481973920,1943515595,60719,SRX24074003,SRS20864392,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31567,SRR28471031,SRX24074002,SRS20864391,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S16 slice 3,GSM8171983,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing,S16 slice 3,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:16 hpf,GSM8171983,GSM8171983: S16 slice 3; Danio rerio; RNA Seq,GSM8171983 r1,GSM8171983,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S16_2_03-R1.fq.gz S16_2_03-R2.fq.gz,fastq fastq,6805653527.0,23393184.0,GSM8171983 r1,0:144.38 1:146.54,A:1865258599;C:1547577456;G:1497746987;T:1895011008;N:59477,144,146,,,1865258599,1547577456,1497746987,1895011008,59477,SRX24074002,SRS20864391,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31568,SRR28471032,SRX24074001,SRS20864390,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S16 slice 2,GSM8171981,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing,S16 slice 2,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:16 hpf,GSM8171981,GSM8171981: S16 slice 2; Danio rerio; RNA Seq,GSM8171981 r1,GSM8171981,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S16_2_02-R1.fq.gz S16_2_02-R2.fq.gz,fastq fastq,7023963229.0,24162141.0,GSM8171981 r1,0:144.12 1:146.58,A:1918527133;C:1603910134;G:1551695853;T:1949772309;N:57800,144,146,,,1918527133,1603910134,1551695853,1949772309,57800,SRX24074001,SRS20864390,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31569,SRR28471033,SRX24074000,SRS20864389,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S16 slice 1,GSM8171980,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:16 hpf|geo loc name:missing|collection date:missing,S16 slice 1,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:16 hpf,GSM8171980,GSM8171980: S16 slice 1; Danio rerio; RNA Seq,GSM8171980 r1,GSM8171980,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S16_2_01-R1.fq.gz S16_2_01-R2.fq.gz,fastq fastq,6619993068.0,22789527.0,GSM8171980 r1,0:143.43 1:147.06,A:1776228931;C:1542516186;G:1481044120;T:1820158687;N:45144,143,147,,,1776228931,1542516186,1481044120,1820158687,45144,SRX24074000,SRS20864389,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31570,SRR28471034,SRX24073999,SRS20864388,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S12 slice 12,GSM8171979,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing,S12 slice 12,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:12 hpf,GSM8171979,GSM8171979: S12 slice 12; Danio rerio; RNA Seq,GSM8171979 r1,GSM8171979,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S12_1_12-R1.fq.gz S12_1_12-R2.fq.gz,fastq fastq,6907282671.0,23557012.0,GSM8171979 r1,0:145.54 1:147.68,A:1862944199;C:1601198280;G:1521830219;T:1921292527;N:17446,145,147,,,1862944199,1601198280,1521830219,1921292527,17446,SRX24073999,SRS20864388,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31571,SRR28471035,SRX24073998,SRS20864387,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S12 slice 11,GSM8171978,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing,S12 slice 11,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:12 hpf,GSM8171978,GSM8171978: S12 slice 11; Danio rerio; RNA Seq,GSM8171978 r1,GSM8171978,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S12_1_11-R1.fq.gz S12_1_11-R2.fq.gz,fastq fastq,6831871099.0,23334246.0,GSM8171978 r1,0:145.23 1:147.56,A:1841130963;C:1590884839;G:1490156717;T:1909681306;N:17274,145,147,,,1841130963,1590884839,1490156717,1909681306,17274,SRX24073998,SRS20864387,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31572,SRR28471036,SRX24073997,SRS20864386,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S12 slice 10,GSM8171977,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing,S12 slice 10,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:12 hpf,GSM8171977,GSM8171977: S12 slice 10; Danio rerio; RNA Seq,GSM8171977 r1,GSM8171977,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S12_1_10-R1.fq.gz S12_1_10-R2.fq.gz,fastq fastq,5783041643.0,19665431.0,GSM8171977 r1,0:146.19 1:147.88,A:1581046379;C:1324978876;G:1248026718;T:1628974699;N:14971,146,147,,,1581046379,1324978876,1248026718,1628974699,14971,SRX24073997,SRS20864386,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31573,SRR28471037,SRX24073996,SRS20864385,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S12 slice 9,GSM8171976,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing,S12 slice 9,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:12 hpf,GSM8171976,GSM8171976: S12 slice 9; Danio rerio; RNA Seq,GSM8171976 r1,GSM8171976,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S12_1_09-R1.fq.gz S12_1_09-R2.fq.gz,fastq fastq,7123142895.0,24299296.0,GSM8171976 r1,0:145.49 1:147.66,A:1925297375;C:1659640314;G:1576196761;T:1961990580;N:17865,145,147,,,1925297375,1659640314,1576196761,1961990580,17865,SRX24073996,SRS20864385,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31574,SRR28471038,SRX24073995,SRS20864384,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S12 slice 8,GSM8171974,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing,S12 slice 8,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:12 hpf,GSM8171974,GSM8171974: S12 slice 8; Danio rerio; RNA Seq,GSM8171974 r1,GSM8171974,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S12_1_08-R1.fq.gz S12_1_08-R2.fq.gz,fastq fastq,7144819692.0,24316501.0,GSM8171974 r1,0:145.93 1:147.90,A:1915884877;C:1672968137;G:1576641332;T:1979307110;N:18236,145,147,,,1915884877,1672968137,1576641332,1979307110,18236,SRX24073995,SRS20864384,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31575,SRR28471039,SRX24073994,SRS20864383,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S12 slice 7,GSM8171973,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing,S12 slice 7,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:12 hpf,GSM8171973,GSM8171973: S12 slice 7; Danio rerio; RNA Seq,GSM8171973 r1,GSM8171973,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S12_1_07-R1.fq.gz S12_1_07-R2.fq.gz,fastq fastq,7379485401.0,25300209.0,GSM8171973 r1,0:143.87 1:147.81,A:1973584695;C:1736374415;G:1654430758;T:2015077010;N:18523,143,147,,,1973584695,1736374415,1654430758,2015077010,18523,SRX24073994,SRS20864383,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31576,SRR28471040,SRX24073993,SRS20864382,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S12 slice 6,GSM8171972,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing,S12 slice 6,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:12 hpf,GSM8171972,GSM8171972: S12 slice 6; Danio rerio; RNA Seq,GSM8171972 r1,GSM8171972,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S12_1_06-R1.fq.gz S12_1_06-R2.fq.gz,fastq fastq,6780830499.0,23111786.0,GSM8171972 r1,0:145.59 1:147.80,A:1809593504;C:1599719267;G:1512122288;T:1859381851;N:13589,145,147,,,1809593504,1599719267,1512122288,1859381851,13589,SRX24073993,SRS20864382,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31577,SRR28471041,SRX24073992,SRS20864381,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S12 slice 5,GSM8171971,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing,S12 slice 5,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:12 hpf,GSM8171971,GSM8171971: S12 slice 5; Danio rerio; RNA Seq,GSM8171971 r1,GSM8171971,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S12_1_05-R1.fq.gz S12_1_05-R2.fq.gz,fastq fastq,6959350050.0,23769190.0,GSM8171971 r1,0:145.06 1:147.72,A:1875092128;C:1615063748;G:1550970555;T:1918160024;N:63595,145,147,,,1875092128,1615063748,1550970555,1918160024,63595,SRX24073992,SRS20864381,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31578,SRR28471042,SRX24073991,SRS20864380,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S12 slice 4,GSM8171970,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing,S12 slice 4,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:12 hpf,GSM8171970,GSM8171970: S12 slice 4; Danio rerio; RNA Seq,GSM8171970 r1,GSM8171970,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S12_1_04-R1.fq.gz S12_1_04-R2.fq.gz,fastq fastq,7016331930.0,23929575.0,GSM8171970 r1,0:145.36 1:147.85,A:1883672645;C:1639902329;G:1566256062;T:1926486960;N:13934,145,147,,,1883672645,1639902329,1566256062,1926486960,13934,SRX24073991,SRS20864380,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31579,SRR28471043,SRX24073990,SRS20864379,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S12 slice 3,GSM8171968,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing,S12 slice 3,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:12 hpf,GSM8171968,GSM8171968: S12 slice 3; Danio rerio; RNA Seq,GSM8171968 r1,GSM8171968,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S12_1_03-R1.fq.gz S12_1_03-R2.fq.gz,fastq fastq,7014757897.0,23928375.0,GSM8171968 r1,0:145.38 1:147.78,A:1893627672;C:1629188725;G:1555319202;T:1936558222;N:64076,145,147,,,1893627672,1629188725,1555319202,1936558222,64076,SRX24073990,SRS20864379,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31580,SRR28471044,SRX24073989,SRS20864378,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S12 slice 2,GSM8171967,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing,S12 slice 2,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:12 hpf,GSM8171967,GSM8171967: S12 slice 2; Danio rerio; RNA Seq,GSM8171967 r1,GSM8171967,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S12_1_02-R1.fq.gz S12_1_02-R2.fq.gz,fastq fastq,6840908671.0,23398529.0,GSM8171967 r1,0:144.87 1:147.50,A:1887167845;C:1555902053;G:1495740904;T:1902033708;N:64161,144,147,,,1887167845,1555902053,1495740904,1902033708,64161,SRX24073989,SRS20864378,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31581,SRR28471045,SRX24073988,SRS20864376,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S12 slice 1,GSM8171966,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:12 hpf|geo loc name:missing|collection date:missing,S12 slice 1,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:12 hpf,GSM8171966,GSM8171966: S12 slice 1; Danio rerio; RNA Seq,GSM8171966 r1,GSM8171966,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S12_1_01-R1.fq.gz S12_1_01-R2.fq.gz,fastq fastq,7278647579.0,24915967.0,GSM8171966 r1,0:144.68 1:147.45,A:1978225177;C:1677337831;G:1598910902;T:2024108056;N:65613,144,147,,,1978225177,1677337831,1598910902,2024108056,65613,SRX24073988,SRS20864376,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
31582,SRR28471046,SRX24073987,SRS20864375,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S10 slice 28,GSM8171965,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing,S10 slice 28,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:10 hpf,GSM8171965,GSM8171965: S10 slice 28; Danio rerio; RNA Seq,GSM8171965 r1,GSM8171965,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S10_2_28-R1.fq.gz S10_2_28-R2.fq.gz,fastq fastq,759288186.0,2615807.0,GSM8171965 r1,0:143.73 1:146.54,A:205364809;C:175246978;G:163844785;T:214825556;N:6058,143,146,,,205364809,175246978,163844785,214825556,6058,SRX24073987,SRS20864375,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
31583,SRR28471047,SRX24073986,SRS20864377,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S10 slice 27,GSM8171964,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing,S10 slice 27,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:10 hpf,GSM8171964,GSM8171964: S10 slice 27; Danio rerio; RNA Seq,GSM8171964 r1,GSM8171964,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S10_2_27-R1.fq.gz S10_2_27-R2.fq.gz,fastq fastq,6581985394.0,22700834.0,GSM8171964 r1,0:143.52 1:146.42,A:1794301951;C:1513541111;G:1430119165;T:1844015897;N:7270,143,146,,,1794301951,1513541111,1430119165,1844015897,7270,SRX24073986,SRS20864377,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
31584,SRR28471048,SRX24073985,SRS20864373,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S10 slice 26,GSM8171962,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing,S10 slice 26,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:10 hpf,GSM8171962,GSM8171962: S10 slice 26; Danio rerio; RNA Seq,GSM8171962 r1,GSM8171962,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S10_2_26-R1.fq.gz S10_2_26-R2.fq.gz,fastq fastq,7222374349.0,24651582.0,GSM8171962 r1,0:145.51 1:147.47,A:1979954857;C:1642503990;G:1569784440;T:2030123197;N:7865,145,147,,,1979954857,1642503990,1569784440,2030123197,7865,SRX24073985,SRS20864373,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
31585,SRR28471049,SRX24073984,SRS20864374,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S10 slice 25,GSM8171961,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing,S10 slice 25,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:10 hpf,GSM8171961,GSM8171961: S10 slice 25; Danio rerio; RNA Seq,GSM8171961 r1,GSM8171961,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S10_2_25-R1.fq.gz S10_2_25-R2.fq.gz,fastq fastq,6912437288.0,23704050.0,GSM8171961 r1,0:144.17 1:147.45,A:1886377008;C:1583136289;G:1524973541;T:1917942644;N:7806,144,147,,,1886377008,1583136289,1524973541,1917942644,7806,SRX24073984,SRS20864374,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
31586,SRR28471050,SRX24073983,SRS20864372,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S10 slice 24,GSM8171960,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing,S10 slice 24,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:10 hpf,GSM8171960,GSM8171960: S10 slice 24; Danio rerio; RNA Seq,GSM8171960 r1,GSM8171960,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S10_2_24-R1.fq.gz S10_2_24-R2.fq.gz,fastq fastq,6839477961.0,23381494.0,GSM8171960 r1,0:145.10 1:147.42,A:1878952639;C:1564093766;G:1477542759;T:1918881626;N:7171,145,147,,,1878952639,1564093766,1477542759,1918881626,7171,SRX24073983,SRS20864372,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
31587,SRR28471051,SRX24073982,SRS20864371,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S10 slice 23,GSM8171959,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing,S10 slice 23,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:10 hpf,GSM8171959,GSM8171959: S10 slice 23; Danio rerio; RNA Seq,GSM8171959 r1,GSM8171959,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S10_2_23-R1.fq.gz S10_2_23-R2.fq.gz,fastq fastq,7167273237.0,24443101.0,GSM8171959 r1,0:145.85 1:147.38,A:1939464339;C:1670904264;G:1550365240;T:2006531554;N:7840,145,147,,,1939464339,1670904264,1550365240,2006531554,7840,SRX24073982,SRS20864371,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
31588,SRR28471052,SRX24073981,SRS20864369,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S10 slice 22,GSM8171958,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing,S10 slice 22,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:10 hpf,GSM8171958,GSM8171958: S10 slice 22; Danio rerio; RNA Seq,GSM8171958 r1,GSM8171958,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S10_2_22-R1.fq.gz S10_2_22-R2.fq.gz,fastq fastq,7201833997.0,24595383.0,GSM8171958 r1,0:145.55 1:147.26,A:1961492345;C:1657551460;G:1566181731;T:2016600464;N:7997,145,147,,,1961492345,1657551460,1566181731,2016600464,7997,SRX24073981,SRS20864369,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
31589,SRR28471053,SRX24073980,SRS20864370,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S10 slice 21,GSM8171957,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing,S10 slice 21,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:10 hpf,GSM8171957,GSM8171957: S10 slice 21; Danio rerio; RNA Seq,GSM8171957 r1,GSM8171957,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S10_2_21-R1.fq.gz S10_2_21-R2.fq.gz,fastq fastq,7200671307.0,24658175.0,GSM8171957 r1,0:145.00 1:147.02,A:1952177571;C:1673984272;G:1548414880;T:2026087466;N:7118,145,147,,,1952177571,1673984272,1548414880,2026087466,7118,SRX24073980,SRS20864370,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
31590,SRR28471054,SRX24073979,SRS20864368,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S10 slice 20,GSM8171955,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing,S10 slice 20,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:10 hpf,GSM8171955,GSM8171955: S10 slice 20; Danio rerio; RNA Seq,GSM8171955 r1,GSM8171955,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S10_2_20-R1.fq.gz S10_2_20-R2.fq.gz,fastq fastq,7029384198.0,24038713.0,GSM8171955 r1,0:145.27 1:147.15,A:1927499291;C:1610291489;G:1509165690;T:1982420962;N:6766,145,147,,,1927499291,1610291489,1509165690,1982420962,6766,SRX24073979,SRS20864368,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
31591,SRR28471055,SRX24073978,SRS20864367,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S10 slice 19,GSM8171954,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing,S10 slice 19,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:10 hpf,GSM8171954,GSM8171954: S10 slice 19; Danio rerio; RNA Seq,GSM8171954 r1,GSM8171954,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S10_2_19-R1.fq.gz S10_2_19-R2.fq.gz,fastq fastq,6805088018.0,23209224.0,GSM8171954 r1,0:145.80 1:147.41,A:1868791398;C:1559085219;G:1478313464;T:1898890630;N:7307,145,147,,,1868791398,1559085219,1478313464,1898890630,7307,SRX24073978,SRS20864367,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
31592,SRR28471056,SRX24073977,SRS20864366,SRP498123,PRJNA1092581,Construction of Danio rerio Asymmetrical Maps DreAM,GSE262578,Transcriptome Analysis,Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods:  We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references  we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates  establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis  and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally  we difined a hox score  and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf  12 hpf and 16 hpf.,,,,S10 slice 18,GSM8171953,,source name:embryonic cells|tissue:embryonic cells|strain:AB|age:10 hpf|geo loc name:missing|collection date:missing,S10 slice 18,Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds  files include count matrixes and slice position information post running the processing steps.,embryonic cells,Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,Zebrafish embryos were raised in 0.3x Danieau buffer  and were then embedded in OCT at the required developmental stages of 10 hpf  12hpf and 16 hpf.,tissue:embryonic cells|strain:AB|age:10 hpf,GSM8171953,GSM8171953: S10 slice 18; Danio rerio; RNA Seq,GSM8171953 r1,GSM8171953,1,RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498123,,loader:fastq load.py,S10_2_18-R1.fq.gz S10_2_18-R2.fq.gz,fastq fastq,6840069197.0,23337475.0,GSM8171953 r1,0:145.70 1:147.40,A:1857694353;C:1583014737;G:1489270628;T:1910082435;N:7044,145,147,,,1857694353,1583014737,1489270628,1910082435,7044,SRX24073977,SRS20864366,SRA1834502,"Institute of genetics, Zhejiang University","Institute of genetics, Zhejiang University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2024-03-27,Gastrula,Embryo,Embryo Imprecise,All anatomical structures