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
8091,ERR034124,ERX012650,ERS032265,ERP000635,PRJEB2512,The Zebrafish transcriptome during early development,KI-BN-JKE-DRERIO-RNASEQ-2011,Transcriptome Analysis,Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65%   73% reads were successfully mapped to the zebrafish genome and 36%   44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding  protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results  and to further investigate the developmental expression of specific genes  the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels  with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes  whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes  number of uniquely expressed genes and enrichment of GO molecular functions.,,,RNA extracted from zebrafish embryo at 1 cell stage,zebrafish embryo 1 cell,SAMEA791630,"Department of Biosciences and Nutrition, Karolinska Institutet, Sweden",ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791630|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition  Karolinska Institutet  Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 1cell|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 1cell|sex:mixed|strain:Tuebingen,,,,,,,,,Transcriptome profiling of early zebrafish development,KI BN JKE DRERIO RNASEQ 2011 1cell,JKE Drerio rna seq,Transcriptome profiling of 1 cell stage of zebrafish embryos.,Total RNA was extracted from approximately 150 embryos                 per developmental stage using Trireagent                 Sigma Aldrich. The total RNA was then processed                 further according to the Small RNA Expression Kit                 Applied Biosystems.,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ABI_SOLID,AB SOLiD System 3.0,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP000635,AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development,ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16,KI-BN-JKE-DRERIO-RNASEQ-2011-1cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-1cell_QV.qual.gz,SOLiD_native SOLiD_native,3676380950.0,73527619.0,KI BN JKE DRERIO RNASEQ 2011 1cell,0:50,,50,,,,,,,,,ERX012650,ERS032265,ERA029959,KI-BN|Department of Biosciences and Nutrition,"Department of Biosciences and Nutrition, Karolinska Institutet, Sweden",1,0.64855,,0.08432,,0.9052,,0.74223,,50,,B,,usable mapping rate,legacy,early,unknown,random_priming,unknown,bulk,unknown,unknown,,Sweden,2011-06-09,Zygote,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
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
28569,SRR26395043,SRX22100890,SRS19166016,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1 cell RNA seq rep8,,strain:AB x India|age:0.5 hpf|dev stage:1cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1 8|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1 cell replicate8,DR 027,DR 027,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1-8_1.fq.gz C1-8_2.fq.gz,fastq fastq,14524806800.0,51874310.0,C1 8 1.fq.gz,0:140 1:140,A:3808586515;C:3473203895;G:3505848142;T:3737124558;N:43690,140,140,,,3808586515,3473203895,3505848142,3737124558,43690,SRX22100890,SRS19166016,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95859,0.96129,0.01726,0.01698,0.85405,0.85374,0.47349,0.47931,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28570,SRR26395044,SRX22100889,SRS19166015,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1 cell RNA seq rep7,,strain:AB x India|age:0.5 hpf|dev stage:1cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1 7|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1 cell replicate7,DR 026,DR 026,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1-7_1.fq.gz C1-7_2.fq.gz,fastq fastq,20478629360.0,73137962.0,C1 7 1.fq.gz,0:140 1:140,A:5376265063;C:4892923429;G:4935127460;T:5274249841;N:63567,140,140,,,5376265063,4892923429,4935127460,5274249841,63567,SRX22100889,SRS19166015,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95971,0.96278,0.01686,0.01629,0.85411,0.85387,0.45729,0.47652,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28571,SRR26395045,SRX22100888,SRS19166014,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1 cell RNA seq rep6,,strain:AB x India|age:0.5 hpf|dev stage:1cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1 6|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1 cell replicate6,DR 025,DR 025,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1-6_1.fq.gz C1-6_2.fq.gz,fastq fastq,16358886880.0,58424596.0,C1 6 1.fq.gz,0:140 1:140,A:4287038412;C:3917335110;G:3953513580;T:4200950421;N:49357,140,140,,,4287038412,3917335110,3953513580,4200950421,49357,SRX22100888,SRS19166014,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.96027,0.96304,0.01855,0.01825,0.84271,0.84285,0.47803,0.47354,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28572,SRR26395046,SRX22100887,SRS19166013,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1 cell RNA seq rep5,,strain:AB x India|age:0.5 hpf|dev stage:1cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1 5|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1 cell replicate5,DR 024,DR 024,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1-5_1.fq.gz C1-5_2.fq.gz,fastq fastq,17004986600.0,60732095.0,C1 5 1.fq.gz,0:140 1:140,A:4459128776;C:4070413583;G:4104544139;T:4370848562;N:51540,140,140,,,4459128776,4070413583,4104544139,4370848562,51540,SRX22100887,SRS19166013,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95691,0.95965,0.01876,0.01822,0.84003,0.83934,0.47976,0.47873,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28573,SRR26395047,SRX22100886,SRS19166012,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1 cell RNA seq rep4,,strain:AB x India|age:0.5 hpf|dev stage:1cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1 4|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1 cell replicate4,DR 023,DR 023,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1-4_1.fq.gz C1-4_2.fq.gz,fastq fastq,17516685480.0,62559591.0,C1 4 1.fq.gz,0:140 1:140,A:4618802699;C:4171295741;G:4210242921;T:4516296296;N:47823,140,140,,,4618802699,4171295741,4210242921,4516296296,47823,SRX22100886,SRS19166012,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95994,0.96214,0.01942,0.01842,0.8421,0.84157,0.47848,0.47528,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28574,SRR26395048,SRX22100885,SRS19166011,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1 cell RNA seq rep3,,strain:AB x India|age:0.5 hpf|dev stage:1cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1 3|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1 cell replicate3,DR 022,DR 022,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1-3_1.fq.gz C1-3_2.fq.gz,fastq fastq,19515282360.0,69697437.0,C1 3 1.fq.gz,0:140 1:140,A:5115977218;C:4670888345;G:4717977881;T:5010379939;N:58977,140,140,,,5115977218,4670888345,4717977881,5010379939,58977,SRX22100885,SRS19166011,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95708,0.95865,0.02126,0.02102,0.84246,0.84216,0.46934,0.47058,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28575,SRR26395049,SRX22100884,SRS19166010,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1 cell RNA seq rep2,,strain:AB x India|age:0.5 hpf|dev stage:1cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1 2|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1 cell replicate2,DR 021,DR 021,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1-2_1.fq.gz C1-2_2.fq.gz,fastq fastq,20726034000.0,74021550.0,C1 2 1.fq.gz,0:140 1:140,A:5504115856;C:4899295944;G:4943875721;T:5378685883;N:60596,140,140,,,5504115856,4899295944,4943875721,5378685883,60596,SRX22100884,SRS19166010,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95721,0.95927,0.0207,0.01959,0.83287,0.8326,0.47491,0.47327,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28577,SRR26395052,SRX22100881,SRS19166007,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1 cell RNA seq rep1,,strain:AB x India|age:0.5 hpf|dev stage:1cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1 1|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1 cell replicate1,DR 020,DR 020,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1-1_1.fq.gz C1-1_2.fq.gz,fastq fastq,17399401600.0,62140720.0,C1 1 1.fq.gz,0:140 1:140,A:4537529281;C:4191810259;G:4227724301;T:4442283593;N:54166,140,140,,,4537529281,4191810259,4227724301,4442283593,54166,SRX22100881,SRS19166007,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.9597,0.96271,0.01629,0.01558,0.83909,0.83818,0.46855,0.46911,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28578,SRR26395053,SRX22100880,SRS19166006,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,fertilized egg RNA seq rep8,,strain:AB x India|age:0 hpf|dev stage:fertilized egg|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 0 8|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: fertilized egg replicate8,DR 019,DR 019,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C0-8_1.fq.gz C0-8_2.fq.gz,fastq fastq,18183625040.0,64941518.0,C0 8 1.fq.gz,0:140 1:140,A:4781555399;C:4337050646;G:4373956478;T:4691007549;N:54968,140,140,,,4781555399,4337050646,4373956478,4691007549,54968,SRX22100880,SRS19166006,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95834,0.96072,0.01841,0.01795,0.84577,0.84524,0.4829,0.48081,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28579,SRR26395054,SRX22100879,SRS19166005,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,fertilized egg RNA seq rep7,,strain:AB x India|age:0 hpf|dev stage:fertilized egg|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 0 7|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: fertilized egg replicate7,DR 018,DR 018,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C0-7_1.fq.gz C0-7_2.fq.gz,fastq fastq,15161389040.0,54147818.0,C0 7 1.fq.gz,0:140 1:140,A:3994107417;C:3609023200;G:3642319126;T:3915893474;N:45823,140,140,,,3994107417,3609023200,3642319126,3915893474,45823,SRX22100879,SRS19166005,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95744,0.95996,0.01875,0.01807,0.83725,0.83694,0.47055,0.46748,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28580,SRR26395055,SRX22100878,SRS19166004,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,fertilized egg RNA seq rep6,,strain:AB x India|age:0 hpf|dev stage:fertilized egg|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 0 6|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: fertilized egg replicate6,DR 017,DR 017,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C0-6_2.fq.gz C0-6_1.fq.gz,fastq fastq,18372330760.0,65615467.0,C0 6 1.fq.gz,0:140 1:140,A:4848831784;C:4365620714;G:4403697790;T:4754124527;N:55945,140,140,,,4848831784,4365620714,4403697790,4754124527,55945,SRX22100878,SRS19166004,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.96339,0.96549,0.01832,0.01765,0.84719,0.84699,0.47322,0.48081,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28581,SRR26395056,SRX22100877,SRS19166003,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,fertilized egg RNA seq rep5,,strain:AB x India|age:0 hpf|dev stage:fertilized egg|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 0 5|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: fertilized egg replicate5,DR 016,DR 016,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C0-5_1.fq.gz C0-5_2.fq.gz,fastq fastq,17733025240.0,63332233.0,C0 5 1.fq.gz,0:140 1:140,A:4656835082;C:4237633580;G:4277583056;T:4560919266;N:54256,140,140,,,4656835082,4237633580,4277583056,4560919266,54256,SRX22100877,SRS19166003,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95837,0.95974,0.01811,0.01704,0.85242,0.85184,0.4749,0.47361,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28582,SRR26395057,SRX22100876,SRS19166002,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,fertilized egg RNA seq rep4,,strain:AB x India|age:0 hpf|dev stage:fertilized egg|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 0 4|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: fertilized egg replicate4,DR 015,DR 015,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C0-4_1.fq.gz C0-4_2.fq.gz,fastq fastq,17317453440.0,61848048.0,C0 4 1.fq.gz,0:140 1:140,A:4549082241;C:4110729602;G:4198645748;T:4458943221;N:52628,140,140,,,4549082241,4110729602,4198645748,4458943221,52628,SRX22100876,SRS19166002,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.9524,0.95183,0.0196,0.01909,0.84443,0.84429,0.47269,0.47317,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28583,SRR26395058,SRX22100875,SRS19166001,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,fertilized egg RNA seq rep3,,strain:AB x India|age:0 hpf|dev stage:fertilized egg|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 0 3|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: fertilized egg replicate3,DR 014,DR 014,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C0-3_1.fq.gz C0-3_2.fq.gz,fastq fastq,20285193040.0,72447118.0,C0 3 1.fq.gz,0:140 1:140,A:5333425678;C:4804605480;G:4928569454;T:5218530436;N:61992,140,140,,,5333425678,4804605480,4928569454,5218530436,61992,SRX22100875,SRS19166001,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95386,0.95151,0.0188,0.01789,0.84226,0.8424,0.48241,0.47074,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28584,SRR26395059,SRX22100874,SRS19166000,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,fertilized egg RNA seq rep2,,strain:AB x India|age:0 hpf|dev stage:fertilized egg|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 0 2|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: fertilized egg replicate2,DR 013,DR 013,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C0-2_1.fq.gz C0-2_2.fq.gz,fastq fastq,18750583600.0,66966370.0,C0 2 1.fq.gz,0:140 1:140,A:4964845916;C:4440076965;G:4485931411;T:4859670521;N:58787,140,140,,,4964845916,4440076965,4485931411,4859670521,58787,SRX22100874,SRS19166000,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95711,0.95855,0.02082,0.01977,0.83733,0.83792,0.4711,0.47348,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28585,SRR26395060,SRX22100873,SRS19165999,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,fertilized egg RNA seq rep1,,strain:AB x India|age:0 hpf|dev stage:fertilized egg|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 0 1|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: fertilized egg replicate1,DR 012,DR 012,mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C0-1_1.fq.gz C0-1_2.fq.gz,fastq fastq,15875566560.0,56698452.0,C0 1 1.fq.gz,0:140 1:140,A:4193265882;C:3760934849;G:3804966904;T:4116350955;N:47970,140,140,,,4193265882,3760934849,3804966904,4116350955,47970,SRX22100873,SRS19165999,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95661,0.9602,0.02103,0.02033,0.84129,0.84092,0.48083,0.47857,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28587,SRR26395063,SRX22100871,SRS19165997,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1 cell Iso seq,,strain:AB x India|age:0.5 hpf|dev stage:1cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 2|BioSampleModel:Model organism or animal,,,,,,,,,PacBio Iso seq of zebrafish: 1 cell,DR 002,DR 002,Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN  CA  USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies  CA  USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies  CA  USA. RNA samples with a RIN  8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA  Inc.  Mountain View  CA  USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems  Wilmington  MA  USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently  two cDNA libraries <3 kb  >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences  Menlo Park  CA  USA and sequenced on the PacBio sequel II platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,PACBIO_SMRT,Sequel,,SRP466518,,,cell1_1.ccs.fq.gz cell1_2.ccs.fq.gz,fastq fastq,2076576705.0,1053386.0,cell1 1.ccs.fq.gz,0:1971.34,A:560055059;C:479061015;G:485136981;T:552323650;N:0,1971,,,,560055059,479061015,485136981,552323650,0,SRX22100871,SRS19165997,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,1,0.44892,,0.00258,,0.90114,,0.50832,,32,,B,,usable mapping rate,pacbio,pacbio_modern,full_length,poly_a,unknown,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
28588,SRR26395064,SRX22100870,SRS19165996,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,fertilized egg Iso seq,,strain:AB x India|age:0 hpf|dev stage:fertilized egg|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 1|BioSampleModel:Model organism or animal,,,,,,,,,PacBio Iso seq of zebrafish: fertilized egg,DR 001,DR 001,Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN  CA  USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies  CA  USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies  CA  USA. RNA samples with a RIN  8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA  Inc.  Mountain View  CA  USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems  Wilmington  MA  USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently  two cDNA libraries <3 kb  >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences  Menlo Park  CA  USA and sequenced on the PacBio sequel II platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,PACBIO_SMRT,Sequel,,SRP466518,,,cell0_1.ccs.fq.gz cell0_2.ccs.fq.gz cell0_3.ccs.fq.gz,fastq fastq fastq,3550605210.0,2083545.0,cell0 1.ccs.fq.gz,0:1704.12,A:990393181;C:795168216;G:861389798;T:903654015;N:0,1704,,,,990393181,795168216,861389798,903654015,0,SRX22100870,SRS19165996,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,1,0.33296,,0.00275,,0.95548,,0.552,,1155,,T,,long read,pacbio,pacbio_modern,full_length,poly_a,unknown,bulk,unknown,unknown,,United States,2023-10-16,Zygote,Embryo,Embryo Imprecise,All anatomical structures
36259,SRR062658,SRX025026,SRS085805,SRP003165,PRJNA127881,High throughput sequencing of mRNA from oocyte  1 cell  16/32 cells  128/256 cells  3.5hpf and 5.3hpf zebrafish embryos Wild type; AB line,GSE22830,Transcriptome Analysis,mRNA seq based approach to determine the transcriptome dynamics during early development To study the mechanisms regulating this developmental event in zebrafish  we applied RNA deep sequencing technology and generated comprehensive transcriptome profiles of 6 developmental stages from oocyte to early gastrulation. We determined the expression levels of maternal and zygotic transcripts and clustered them based on expression pattern. We identified a large number of novel transcribed regions in un annotated regions of the genome  as well as splice variants with an estimated frequency of 40 75% during early zebrafish embryogenesis. Our data constitute a useful resource for developmental studies  gene discovery  and genome annotation. Overall design: RNA was extracted from pooled embryos of desired stages and one RNA seq library was generated for each sample.  Totally 6 stages were selected: Maternal  1cell  16/32 cells  128/256 cells  3.5hpf and 5.3hpf,,pubmed:21555364;pubmed:24586560;pubmed:23676078,,1 cell,GSM564428,,tissue:developing embryos|background:AB; wild type|developmental stage:just fertilized 1cell embryos,1 cell,ABI pipeline BioScope v1.0.1 Data analysis: The SOLiD generated RNA Seq reads was in 50bp length and an initial filtering process was taken to remove any non desirable contamination sequences  such as rRNA  tRNA  and repeats etc. A seed and extension mapping approach was developed to map the 50bp reads into reference genome zv7 and also into the respective zv7 refGene annotation separately. During mapping of the reads to the refGene annotation  a splice junction database fasta file is generated to which the reads are mapped to. This database contains known and putative junction sequences  created by taking 46bp from the joining ends of adjacent and non adjacent exons for each gene and putting them together  simulating the genomic sequences of known and putative junctions respectively. The first 25bp of the 50bp read was used as the seed for alignment for each read. When an alignment cannot be found using these 25bp seed  the seed window is shifted and the next 25bp seed is taken from the 21st to the 45th base of the read. An extension step follows when the seed is able to map  and a score generated for each extended base to determine best alignment. A merging step is performed on the genome mapping and splice junction mapping to determine a set of alignments for each read  from which a unique alignment is found based on the score generated for these alignments. Mapping parameters:  Mapping was done using Applied Biosystems’ SOLiD BioScope alignment for whole transcriptome analysis pipeline.  Two mismatches were allowed in the 25bp color space seed sequence with extension alignment performed to find the full mapping location.  A score is computed for each mapping location and any location that scored <22 were filtered. Generation of gff and bedgraph files: GFF files were produced by parsing the output BAM format and extracted for unique alignments with score >22. The bedgraph files are then produced with the resulting gff file.,developing embryos,Embryos were frozen at the desired developmental stages and RNAs was extracted for sequencing.,mRNA seq was performed by Mission Biotech Taiwan. SOLiD sequencing libraries were prepared using the Whole Transcriptome Library Preparation for SOLiD™ Sequencing kit ABI according to manufacturer’s instructions. About 200 280 µg of total RNAs were used as starting materials  which were subjected to polyA selection using Applied Biosystems PolyA Purist Kit AM1916  fragmentation  and library construction using distinct adapters for each library SOLiD Barcoding. From each library  equal volumes were pooled together and sequenced in SOLiD3 ABI platform generating 50bp tags.,Zebrafish embryos AB background collected just post fertilization  were reared and harvested at  desired time points.   Unfertilized oocytes were collected by squeezing the abdomen of spawning females. Harvested embryos were snap frozen in liquid nitrogen and stored in −80°C. Total RNA was extracted from whole embryos using Trizol Invitrogen according to manufacturer’s instructions. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. Integrity of RNA samples were determined using Agilent RNA 6000 Nano chip and size separated using Agilent 2100 Bioanalyzer. Total RNA obtained per 100 embryos at each developmental stage was calculated for data normalization purposes.,background:AB; wild type|developmental stage:just fertilized 1cell embryos,GSM564428,GSM564428: 1 cell,GSM564428: 1 cell,GSM564428: 1 cell,1,,GEO Accession:GSM564428,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP003165,,,,,1175348550.0,23506971.0,GSM564428 1,0:50,,50,,,,,,,,,SRX025026,SRS085805,SRA022850,GEO,"Computational and Systems Biology, Genome Institute of Singapore",1,0.75876,,0.05232,,0.86762,,0.50392,,50,,B,,usable mapping rate,legacy,early,full_length,poly_a,unknown,bulk,unknown,unknown,,Singapore,2010-07-08,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38122,SRR1555598,SRX684706,SRS687823,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0106,GSM1483841,,tissue:single embryo,Metazome ZF timecourse sample 0106,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:4240,GSM1483841,GSM1483841: Metazome ZF timecourse sample 0106; Danio rerio; RNA Seq,GSM1483841,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483841,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0106.fastq.gz,fastq,3911705.0,111763.0,GSM1483841 r1,0:35,A:1100064;C:790487;G:836206;T:1169251;N:15697,35,,,,1100064,790487,836206,1169251,15697,SRX684706,SRS687823,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.72414,,0.09461,,0.96725,,0.4942,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38123,SRR1555597,SRX684705,SRS687821,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0105,GSM1483840,,tissue:single embryo,Metazome ZF timecourse sample 0105,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:4200,GSM1483840,GSM1483840: Metazome ZF timecourse sample 0105; Danio rerio; RNA Seq,GSM1483840,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483840,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0105.fastq.gz,fastq,32877145.0,939347.0,GSM1483840 r1,0:35,A:9524894;C:6625944;G:6696548;T:9953576;N:76183,35,,,,9524894,6625944,6696548,9953576,76183,SRX684705,SRS687821,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.74436,,0.07095,,0.88201,,0.47612,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38124,SRR1555596,SRX684704,SRS687822,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0104,GSM1483839,,tissue:single embryo,Metazome ZF timecourse sample 0104,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:4160,GSM1483839,GSM1483839: Metazome ZF timecourse sample 0104; Danio rerio; RNA Seq,GSM1483839,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483839,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0104.fastq.gz,fastq,83810020.0,2394572.0,GSM1483839 r1,0:35,A:24075610;C:16799998;G:16694424;T:25967423;N:272565,35,,,,24075610,16799998,16694424,25967423,272565,SRX684704,SRS687822,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.7588,,0.07993,,0.84449,,0.49785,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38125,SRR1555595,SRX684703,SRS687820,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0103,GSM1483838,,tissue:single embryo,Metazome ZF timecourse sample 0103,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:4120,GSM1483838,GSM1483838: Metazome ZF timecourse sample 0103; Danio rerio; RNA Seq,GSM1483838,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483838,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0103.fastq.gz,fastq,98206150.0,2805890.0,GSM1483838 r1,0:35,A:28361916;C:19232789;G:19589483;T:30798968;N:222994,35,,,,28361916,19232789,19589483,30798968,222994,SRX684703,SRS687820,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75509,,0.13429,,0.81117,,0.49102,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38126,SRR1555594,SRX684702,SRS687819,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0102,GSM1483837,,tissue:single embryo,Metazome ZF timecourse sample 0102,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:4080,GSM1483837,GSM1483837: Metazome ZF timecourse sample 0102; Danio rerio; RNA Seq,GSM1483837,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483837,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0102.fastq.gz,fastq,192817835.0,5509081.0,GSM1483837 r1,0:35,A:55969077;C:36880901;G:37835921;T:61101558;N:1030378,35,,,,55969077,36880901,37835921,61101558,1030378,SRX684702,SRS687819,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.73387,,0.17245,,0.80164,,0.48657,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38127,SRR1555593,SRX684701,SRS687818,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0101,GSM1483836,,tissue:single embryo,Metazome ZF timecourse sample 0101,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:4040,GSM1483836,GSM1483836: Metazome ZF timecourse sample 0101; Danio rerio; RNA Seq,GSM1483836,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483836,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0101.fastq.gz,fastq,374339455.0,10695413.0,GSM1483836 r1,0:35,A:112191846;C:73679996;G:73185024;T:114766825;N:515764,35,,,,112191846,73679996,73185024,114766825,515764,SRX684701,SRS687818,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.83131,,0.16618,,0.77812,,0.49895,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38128,SRR1555592,SRX684700,SRS687816,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0100,GSM1483835,,tissue:single embryo,Metazome ZF timecourse sample 0100,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:4000,GSM1483835,GSM1483835: Metazome ZF timecourse sample 0100; Danio rerio; RNA Seq,GSM1483835,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483835,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0100.fastq.gz,fastq,15239420.0,435412.0,GSM1483835 r1,0:35,A:4361241;C:3088134;G:3269084;T:4498093;N:22868,35,,,,4361241,3088134,3269084,4498093,22868,SRX684700,SRS687816,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.7702,,0.17879,,0.92904,,0.505,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38129,SRR1555591,SRX684699,SRS687817,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0099,GSM1483834,,tissue:single embryo,Metazome ZF timecourse sample 0099,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3960,GSM1483834,GSM1483834: Metazome ZF timecourse sample 0099; Danio rerio; RNA Seq,GSM1483834,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483834,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0099.fastq.gz,fastq,284196500.0,8119900.0,GSM1483834 r1,0:35,A:81991733;C:57440756;G:58362818;T:86010858;N:390335,35,,,,81991733,57440756,58362818,86010858,390335,SRX684699,SRS687817,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.81284,,0.1715,,0.78468,,0.49472,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38130,SRR1555590,SRX684698,SRS687815,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0098,GSM1483833,,tissue:single embryo,Metazome ZF timecourse sample 0098,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3920,GSM1483833,GSM1483833: Metazome ZF timecourse sample 0098; Danio rerio; RNA Seq,GSM1483833,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483833,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0098.fastq.gz,fastq,244245015.0,6978429.0,GSM1483833 r1,0:35,A:70141725;C:48500061;G:50748992;T:74478239;N:375998,35,,,,70141725,48500061,50748992,74478239,375998,SRX684698,SRS687815,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.79668,,0.17718,,0.79271,,0.45966,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38131,SRR1555589,SRX684697,SRS687814,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0097,GSM1483832,,tissue:single embryo,Metazome ZF timecourse sample 0097,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3880,GSM1483832,GSM1483832: Metazome ZF timecourse sample 0097; Danio rerio; RNA Seq,GSM1483832,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483832,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0097.fastq.gz,fastq,215347510.0,6152786.0,GSM1483832 r1,0:35,A:62928172;C:42420829;G:43902946;T:65803342;N:292221,35,,,,62928172,42420829,43902946,65803342,292221,SRX684697,SRS687814,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80605,,0.17396,,0.78873,,0.50241,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38132,SRR1555588,SRX684696,SRS687813,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0096,GSM1483831,,tissue:single embryo,Metazome ZF timecourse sample 0096,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3840,GSM1483831,GSM1483831: Metazome ZF timecourse sample 0096; Danio rerio; RNA Seq,GSM1483831,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483831,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0096.fastq.gz,fastq,13992230.0,399778.0,GSM1483831 r1,0:35,A:4077402;C:2837417;G:2856511;T:4200750;N:20150,35,,,,4077402,2837417,2856511,4200750,20150,SRX684696,SRS687813,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.77543,,0.14778,,0.93288,,0.48967,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38133,SRR1555587,SRX684695,SRS687811,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0095,GSM1483830,,tissue:single embryo,Metazome ZF timecourse sample 0095,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3800,GSM1483830,GSM1483830: Metazome ZF timecourse sample 0095; Danio rerio; RNA Seq,GSM1483830,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483830,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0095.fastq.gz,fastq,290151435.0,8290041.0,GSM1483830 r1,0:35,A:86694666;C:56953853;G:57315219;T:88811589;N:376108,35,,,,86694666,56953853,57315219,88811589,376108,SRX684695,SRS687811,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.79098,,0.18155,,0.79034,,0.51338,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38134,SRR1555586,SRX684694,SRS687810,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0094,GSM1483829,,tissue:single embryo,Metazome ZF timecourse sample 0094,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3760,GSM1483829,GSM1483829: Metazome ZF timecourse sample 0094; Danio rerio; RNA Seq,GSM1483829,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483829,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0094.fastq.gz,fastq,645422925.0,18440655.0,GSM1483829 r1,0:35,A:186408265;C:127218686;G:131406509;T:199399112;N:990353,35,,,,186408265,127218686,131406509,199399112,990353,SRX684694,SRS687810,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.81184,,0.15572,,0.78496,,0.48733,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38135,SRR1555585,SRX684693,SRS687812,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0093,GSM1483828,,tissue:single embryo,Metazome ZF timecourse sample 0093,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3720,GSM1483828,GSM1483828: Metazome ZF timecourse sample 0093; Danio rerio; RNA Seq,GSM1483828,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483828,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0093.fastq.gz,fastq,82574205.0,2359263.0,GSM1483828 r1,0:35,A:24239984;C:16625180;G:16309055;T:25123568;N:276418,35,,,,24239984,16625180,16309055,25123568,276418,SRX684693,SRS687812,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75557,,0.14554,,0.82205,,0.49736,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38136,SRR1555584,SRX684692,SRS687809,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0092,GSM1483827,,tissue:single embryo,Metazome ZF timecourse sample 0092,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3680,GSM1483827,GSM1483827: Metazome ZF timecourse sample 0092; Danio rerio; RNA Seq,GSM1483827,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483827,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0092.fastq.gz,fastq,72186905.0,2062483.0,GSM1483827 r1,0:35,A:21349438;C:14361391;G:14472348;T:21766197;N:237531,35,,,,21349438,14361391,14472348,21766197,237531,SRX684692,SRS687809,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.74348,,0.13614,,0.8309,,0.51328,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38137,SRR1555583,SRX684691,SRS687808,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0091,GSM1483826,,tissue:single embryo,Metazome ZF timecourse sample 0091,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3640,GSM1483826,GSM1483826: Metazome ZF timecourse sample 0091; Danio rerio; RNA Seq,GSM1483826,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483826,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0091.fastq.gz,fastq,18405940.0,525884.0,GSM1483826 r1,0:35,A:5374937;C:3766785;G:3774551;T:5451369;N:38298,35,,,,5374937,3766785,3774551,5451369,38298,SRX684691,SRS687808,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.74005,,0.11089,,0.91494,,0.49823,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38138,SRR1555582,SRX684690,SRS687807,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0090,GSM1483825,,tissue:single embryo,Metazome ZF timecourse sample 0090,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3600,GSM1483825,GSM1483825: Metazome ZF timecourse sample 0090; Danio rerio; RNA Seq,GSM1483825,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483825,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0090.fastq.gz,fastq,141938265.0,4055379.0,GSM1483825 r1,0:35,A:41371650;C:28115945;G:29356068;T:42485478;N:609124,35,,,,41371650,28115945,29356068,42485478,609124,SRX684690,SRS687807,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.71151,,0.17711,,0.82789,,0.52369,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38139,SRR1555581,SRX684689,SRS687806,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0089,GSM1483824,,tissue:single embryo,Metazome ZF timecourse sample 0089,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3560,GSM1483824,GSM1483824: Metazome ZF timecourse sample 0089; Danio rerio; RNA Seq,GSM1483824,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483824,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0089.fastq.gz,fastq,99569015.0,2844829.0,GSM1483824 r1,0:35,A:28763571;C:20065085;G:19332839;T:31088193;N:319327,35,,,,28763571,20065085,19332839,31088193,319327,SRX684689,SRS687806,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.74177,,0.13103,,0.81854,,0.51184,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38140,SRR1555580,SRX684688,SRS687805,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0088,GSM1483823,,tissue:single embryo,Metazome ZF timecourse sample 0088,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3520,GSM1483823,GSM1483823: Metazome ZF timecourse sample 0088; Danio rerio; RNA Seq,GSM1483823,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483823,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0088.fastq.gz,fastq,168790055.0,4822573.0,GSM1483823 r1,0:35,A:49034449;C:32785565;G:33439918;T:52997820;N:532303,35,,,,49034449,32785565,33439918,52997820,532303,SRX684688,SRS687805,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.73454,,0.15775,,0.8047,,0.50587,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38141,SRR1555579,SRX684687,SRS687803,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0087,GSM1483822,,tissue:single embryo,Metazome ZF timecourse sample 0087,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3480,GSM1483822,GSM1483822: Metazome ZF timecourse sample 0087; Danio rerio; RNA Seq,GSM1483822,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483822,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0087.fastq.gz,fastq,83155975.0,2375885.0,GSM1483822 r1,0:35,A:23985678;C:16871573;G:17048421;T:25086100;N:164203,35,,,,23985678,16871573,17048421,25086100,164203,SRX684687,SRS687803,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75055,,0.10258,,0.83952,,0.49914,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38142,SRR1555578,SRX684686,SRS687804,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0086,GSM1483821,,tissue:single embryo,Metazome ZF timecourse sample 0086,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3440,GSM1483821,GSM1483821: Metazome ZF timecourse sample 0086; Danio rerio; RNA Seq,GSM1483821,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483821,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0086.fastq.gz,fastq,36772155.0,1050633.0,GSM1483821 r1,0:35,A:10536765;C:7377251;G:7701105;T:11014088;N:142946,35,,,,10536765,7377251,7701105,11014088,142946,SRX684686,SRS687804,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.745,,0.08312,,0.88209,,0.52632,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38143,SRR1555577,SRX684685,SRS687802,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0085,GSM1483820,,tissue:single embryo,Metazome ZF timecourse sample 0085,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3400,GSM1483820,GSM1483820: Metazome ZF timecourse sample 0085; Danio rerio; RNA Seq,GSM1483820,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483820,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0085.fastq.gz,fastq,142281650.0,4065190.0,GSM1483820 r1,0:35,A:41238155;C:28228882;G:28727190;T:43901346;N:186077,35,,,,41238155,28228882,28727190,43901346,186077,SRX684685,SRS687802,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80695,,0.14045,,0.80361,,0.5,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38144,SRR1555576,SRX684684,SRS687800,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0084,GSM1483819,,tissue:single embryo,Metazome ZF timecourse sample 0084,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3360,GSM1483819,GSM1483819: Metazome ZF timecourse sample 0084; Danio rerio; RNA Seq,GSM1483819,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483819,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0084.fastq.gz,fastq,147589295.0,4216837.0,GSM1483819 r1,0:35,A:42100013;C:30125860;G:31767504;T:43391728;N:204190,35,,,,42100013,30125860,31767504,43391728,204190,SRX684684,SRS687800,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80373,,0.08661,,0.83157,,0.51923,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38145,SRR1555575,SRX684683,SRS687801,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0083,GSM1483818,,tissue:single embryo,Metazome ZF timecourse sample 0083,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3320,GSM1483818,GSM1483818: Metazome ZF timecourse sample 0083; Danio rerio; RNA Seq,GSM1483818,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483818,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0083.fastq.gz,fastq,147243985.0,4206971.0,GSM1483818 r1,0:35,A:42533757;C:29874233;G:30500611;T:44132167;N:203217,35,,,,42533757,29874233,30500611,44132167,203217,SRX684683,SRS687801,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80738,,0.08642,,0.82219,,0.49396,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38146,SRR1555574,SRX684682,SRS687799,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0082,GSM1483817,,tissue:single embryo,Metazome ZF timecourse sample 0082,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3280,GSM1483817,GSM1483817: Metazome ZF timecourse sample 0082; Danio rerio; RNA Seq,GSM1483817,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483817,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0082.fastq.gz,fastq,96747735.0,2764221.0,GSM1483817 r1,0:35,A:26768730;C:19578598;G:21713242;T:28549716;N:137449,35,,,,26768730,19578598,21713242,28549716,137449,SRX684682,SRS687799,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80738,,0.09417,,0.85167,,0.50713,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38147,SRR1555573,SRX684681,SRS687798,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0081,GSM1483816,,tissue:single embryo,Metazome ZF timecourse sample 0081,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3240,GSM1483816,GSM1483816: Metazome ZF timecourse sample 0081; Danio rerio; RNA Seq,GSM1483816,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483816,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0081.fastq.gz,fastq,158402895.0,4525797.0,GSM1483816 r1,0:35,A:46939694;C:31610300;G:32050592;T:47571349;N:230960,35,,,,46939694,31610300,32050592,47571349,230960,SRX684681,SRS687798,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.78709,,0.11916,,0.82351,,0.48714,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38148,SRR1555572,SRX684680,SRS687797,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0080,GSM1483815,,tissue:single embryo,Metazome ZF timecourse sample 0080,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3200,GSM1483815,GSM1483815: Metazome ZF timecourse sample 0080; Danio rerio; RNA Seq,GSM1483815,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483815,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0080.fastq.gz,fastq,1432375.0,40925.0,GSM1483815 r1,0:35,A:422951;C:297837;G:308257;T:400778;N:2552,35,,,,422951,297837,308257,400778,2552,SRX684680,SRS687797,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.7103,,0.12471,,0.9811,,0.57619,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38149,SRR1555571,SRX684679,SRS687796,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0079,GSM1483814,,tissue:single embryo,Metazome ZF timecourse sample 0079,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3160,GSM1483814,GSM1483814: Metazome ZF timecourse sample 0079; Danio rerio; RNA Seq,GSM1483814,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483814,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0079.fastq.gz,fastq,171937640.0,4912504.0,GSM1483814 r1,0:35,A:49235964;C:34067309;G:35846095;T:52553397;N:234875,35,,,,49235964,34067309,35846095,52553397,234875,SRX684679,SRS687796,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.79389,,0.14252,,0.81107,,0.50474,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38150,SRR1555570,SRX684678,SRS687795,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0078,GSM1483813,,tissue:single embryo,Metazome ZF timecourse sample 0078,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3120,GSM1483813,GSM1483813: Metazome ZF timecourse sample 0078; Danio rerio; RNA Seq,GSM1483813,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483813,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0078.fastq.gz,fastq,220246950.0,6292770.0,GSM1483813 r1,0:35,A:63723749;C:43666354;G:45504302;T:67009596;N:342949,35,,,,63723749,43666354,45504302,67009596,342949,SRX684678,SRS687795,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80813,,0.1512,,0.80174,,0.49937,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38151,SRR1555569,SRX684677,SRS687794,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0077,GSM1483812,,tissue:single embryo,Metazome ZF timecourse sample 0077,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3080,GSM1483812,GSM1483812: Metazome ZF timecourse sample 0077; Danio rerio; RNA Seq,GSM1483812,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483812,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0077.fastq.gz,fastq,93138675.0,2661105.0,GSM1483812 r1,0:35,A:27102533;C:18314712;G:18498218;T:29006764;N:216448,35,,,,27102533,18314712,18498218,29006764,216448,SRX684677,SRS687794,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75818,,0.11499,,0.81572,,0.50169,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38152,SRR1555568,SRX684676,SRS687793,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0076,GSM1483811,,tissue:single embryo,Metazome ZF timecourse sample 0076,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3040,GSM1483811,GSM1483811: Metazome ZF timecourse sample 0076; Danio rerio; RNA Seq,GSM1483811,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483811,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0076.fastq.gz,fastq,118512415.0,3386069.0,GSM1483811 r1,0:35,A:33806370;C:23395934;G:24547522;T:36374942;N:387647,35,,,,33806370,23395934,24547522,36374942,387647,SRX684676,SRS687793,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75326,,0.1088,,0.81667,,0.49341,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38153,SRR1555567,SRX684675,SRS687792,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0075,GSM1483810,,tissue:single embryo,Metazome ZF timecourse sample 0075,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3000,GSM1483810,GSM1483810: Metazome ZF timecourse sample 0075; Danio rerio; RNA Seq,GSM1483810,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483810,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0075.fastq.gz,fastq,2520525.0,72015.0,GSM1483810 r1,0:35,A:818327;C:420638;G:441967;T:833315;N:6278,35,,,,818327,420638,441967,833315,6278,SRX684675,SRS687792,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.7119,,0.22445,,0.97368,,0.51561,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38154,SRR1555566,SRX684674,SRS687791,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0074,GSM1483809,,tissue:single embryo,Metazome ZF timecourse sample 0074,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2960,GSM1483809,GSM1483809: Metazome ZF timecourse sample 0074; Danio rerio; RNA Seq,GSM1483809,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483809,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0074.fastq.gz,fastq,95385710.0,2725306.0,GSM1483809 r1,0:35,A:27032549;C:18681500;G:19490852;T:29708978;N:471831,35,,,,27032549,18681500,19490852,29708978,471831,SRX684674,SRS687791,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75216,,0.09004,,0.83469,,0.48768,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38155,SRR1555565,SRX684673,SRS687790,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0073,GSM1483808,,tissue:single embryo,Metazome ZF timecourse sample 0073,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2920,GSM1483808,GSM1483808: Metazome ZF timecourse sample 0073; Danio rerio; RNA Seq,GSM1483808,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483808,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0073.fastq.gz,fastq,149165835.0,4261881.0,GSM1483808 r1,0:35,A:42991931;C:29913953;G:30117935;T:45803552;N:338464,35,,,,42991931,29913953,30117935,45803552,338464,SRX684673,SRS687790,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.76488,,0.10545,,0.80586,,0.5046,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38156,SRR1555564,SRX684672,SRS687789,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0072,GSM1483807,,tissue:single embryo,Metazome ZF timecourse sample 0072,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2880,GSM1483807,GSM1483807: Metazome ZF timecourse sample 0072; Danio rerio; RNA Seq,GSM1483807,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483807,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0072.fastq.gz,fastq,203829675.0,5823705.0,GSM1483807 r1,0:35,A:61171233;C:40047517;G:44515900;T:57461403;N:633622,35,,,,61171233,40047517,44515900,57461403,633622,SRX684672,SRS687789,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.65225,,0.10254,,0.82014,,0.50437,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38157,SRR1555563,SRX684671,SRS687788,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0071,GSM1483806,,tissue:single embryo,Metazome ZF timecourse sample 0071,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2840,GSM1483806,GSM1483806: Metazome ZF timecourse sample 0071; Danio rerio; RNA Seq,GSM1483806,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483806,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0071.fastq.gz,fastq,107894360.0,3082696.0,GSM1483806 r1,0:35,A:30475809;C:22092085;G:22685204;T:32400616;N:240646,35,,,,30475809,22092085,22685204,32400616,240646,SRX684671,SRS687788,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.77637,,0.10375,,0.81574,,0.50918,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38158,SRR1555562,SRX684670,SRS687787,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0070,GSM1483805,,tissue:single embryo,Metazome ZF timecourse sample 0070,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2800,GSM1483805,GSM1483805: Metazome ZF timecourse sample 0070; Danio rerio; RNA Seq,GSM1483805,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483805,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0070.fastq.gz,fastq,102775820.0,2936452.0,GSM1483805 r1,0:35,A:29014067;C:20865233;G:21656956;T:30738746;N:500818,35,,,,29014067,20865233,21656956,30738746,500818,SRX684670,SRS687787,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.7643,,0.09535,,0.8325,,0.51201,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38159,SRR1555561,SRX684669,SRS687786,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0069,GSM1483804,,tissue:single embryo,Metazome ZF timecourse sample 0069,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2760,GSM1483804,GSM1483804: Metazome ZF timecourse sample 0069; Danio rerio; RNA Seq,GSM1483804,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483804,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0069.fastq.gz,fastq,178882445.0,5110927.0,GSM1483804 r1,0:35,A:51610621;C:35847602;G:36898756;T:54275519;N:249947,35,,,,51610621,35847602,36898756,54275519,249947,SRX684669,SRS687786,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.81481,,0.1212,,0.80338,,0.48647,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38160,SRR1555560,SRX684668,SRS687784,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0068,GSM1483803,,tissue:single embryo,Metazome ZF timecourse sample 0068,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2720,GSM1483803,GSM1483803: Metazome ZF timecourse sample 0068; Danio rerio; RNA Seq,GSM1483803,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483803,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0068.fastq.gz,fastq,289924775.0,8283565.0,GSM1483803 r1,0:35,A:85968202;C:57218562;G:58533597;T:87797178;N:407236,35,,,,85968202,57218562,58533597,87797178,407236,SRX684668,SRS687784,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.78411,,0.12015,,0.80736,,0.5018,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38161,SRR1555559,SRX684667,SRS687785,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0067,GSM1483802,,tissue:single embryo,Metazome ZF timecourse sample 0067,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2680,GSM1483802,GSM1483802: Metazome ZF timecourse sample 0067; Danio rerio; RNA Seq,GSM1483802,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483802,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0067.fastq.gz,fastq,12717355.0,363353.0,GSM1483802 r1,0:35,A:3757539;C:2504848;G:2608725;T:3830804;N:15439,35,,,,3757539,2504848,2608725,3830804,15439,SRX684667,SRS687785,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.77835,,0.12605,,0.92604,,0.45926,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38162,SRR1555558,SRX684666,SRS687783,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0066,GSM1483801,,tissue:single embryo,Metazome ZF timecourse sample 0066,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2640,GSM1483801,GSM1483801: Metazome ZF timecourse sample 0066; Danio rerio; RNA Seq,GSM1483801,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483801,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0066.fastq.gz,fastq,5206040.0,148744.0,GSM1483801 r1,0:35,A:1490985;C:1039675;G:1088231;T:1579040;N:8109,35,,,,1490985,1039675,1088231,1579040,8109,SRX684666,SRS687783,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.77355,,0.11605,,0.96587,,0.48121,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38163,SRR1555557,SRX684665,SRS687782,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0065,GSM1483800,,tissue:single embryo,Metazome ZF timecourse sample 0065,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2600,GSM1483800,GSM1483800: Metazome ZF timecourse sample 0065; Danio rerio; RNA Seq,GSM1483800,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483800,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0065.fastq.gz,fastq,49543620.0,1415532.0,GSM1483800 r1,0:35,A:13699613;C:9907599;G:10751987;T:15115154;N:69267,35,,,,13699613,9907599,10751987,15115154,69267,SRX684665,SRS687782,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.81049,,0.12615,,0.86367,,0.51632,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38164,SRR1555556,SRX684664,SRS687781,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0064,GSM1483799,,tissue:single embryo,Metazome ZF timecourse sample 0064,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2560,GSM1483799,GSM1483799: Metazome ZF timecourse sample 0064; Danio rerio; RNA Seq,GSM1483799,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483799,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0064.fastq.gz,fastq,247601200.0,7074320.0,GSM1483799 r1,0:35,A:70332996;C:49278360;G:54252598;T:73390003;N:347243,35,,,,70332996,49278360,54252598,73390003,347243,SRX684664,SRS687781,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80448,,0.14935,,0.80975,,0.54749,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38165,SRR1555555,SRX684663,SRS687779,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0063,GSM1483798,,tissue:single embryo,Metazome ZF timecourse sample 0063,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2520,GSM1483798,GSM1483798: Metazome ZF timecourse sample 0063; Danio rerio; RNA Seq,GSM1483798,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483798,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0063.fastq.gz,fastq,139474895.0,3984997.0,GSM1483798 r1,0:35,A:39999821;C:27945450;G:29190975;T:42159133;N:179516,35,,,,39999821,27945450,29190975,42159133,179516,SRX684663,SRS687779,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80752,,0.14329,,0.81645,,0.50673,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38166,SRR1555554,SRX684662,SRS687780,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0062,GSM1483797,,tissue:single embryo,Metazome ZF timecourse sample 0062,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2480,GSM1483797,GSM1483797: Metazome ZF timecourse sample 0062; Danio rerio; RNA Seq,GSM1483797,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483797,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0062.fastq.gz,fastq,177095730.0,5059878.0,GSM1483797 r1,0:35,A:50196021;C:35043121;G:37861516;T:53732194;N:262878,35,,,,50196021,35043121,37861516,53732194,262878,SRX684662,SRS687780,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.81092,,0.13179,,0.8199,,0.49636,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38167,SRR1555553,SRX684661,SRS687778,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0061,GSM1483796,,tissue:single embryo,Metazome ZF timecourse sample 0061,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2440,GSM1483796,GSM1483796: Metazome ZF timecourse sample 0061; Danio rerio; RNA Seq,GSM1483796,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483796,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0061.fastq.gz,fastq,117262810.0,3350366.0,GSM1483796 r1,0:35,A:33678050;C:23425078;G:24368870;T:35496994;N:293818,35,,,,33678050,23425078,24368870,35496994,293818,SRX684661,SRS687778,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.71242,,0.11354,,0.83514,,0.51134,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38168,SRR1555552,SRX684660,SRS687777,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0060,GSM1483795,,tissue:single embryo,Metazome ZF timecourse sample 0060,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2400,GSM1483795,GSM1483795: Metazome ZF timecourse sample 0060; Danio rerio; RNA Seq,GSM1483795,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483795,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0060.fastq.gz,fastq,50485225.0,1442435.0,GSM1483795 r1,0:35,A:14629070;C:9936986;G:10066758;T:15611930;N:240481,35,,,,14629070,9936986,10066758,15611930,240481,SRX684660,SRS687777,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.74045,,0.14214,,0.84703,,0.50639,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38169,SRR1555551,SRX684659,SRS687776,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0059,GSM1483794,,tissue:single embryo,Metazome ZF timecourse sample 0059,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2360,GSM1483794,GSM1483794: Metazome ZF timecourse sample 0059; Danio rerio; RNA Seq,GSM1483794,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483794,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0059.fastq.gz,fastq,129110905.0,3688883.0,GSM1483794 r1,0:35,A:37661404;C:25258511;G:25987964;T:39941302;N:261724,35,,,,37661404,25258511,25987964,39941302,261724,SRX684659,SRS687776,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.74152,,0.13117,,0.81749,,0.51022,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38170,SRR1555550,SRX684658,SRS687775,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0058,GSM1483793,,tissue:single embryo,Metazome ZF timecourse sample 0058,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2320,GSM1483793,GSM1483793: Metazome ZF timecourse sample 0058; Danio rerio; RNA Seq,GSM1483793,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483793,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0058.fastq.gz,fastq,91514045.0,2614687.0,GSM1483793 r1,0:35,A:26231450;C:17984688;G:18624952;T:28210031;N:462924,35,,,,26231450,17984688,18624952,28210031,462924,SRX684658,SRS687775,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75933,,0.13326,,0.8294,,0.50639,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38171,SRR1555549,SRX684657,SRS687774,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0057,GSM1483792,,tissue:single embryo,Metazome ZF timecourse sample 0057,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2280,GSM1483792,GSM1483792: Metazome ZF timecourse sample 0057; Danio rerio; RNA Seq,GSM1483792,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483792,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0057.fastq.gz,fastq,254944305.0,7284123.0,GSM1483792 r1,0:35,A:73169774;C:51240668;G:52956333;T:76957748;N:619782,35,,,,73169774,51240668,52956333,76957748,619782,SRX684657,SRS687774,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75832,,0.11669,,0.80937,,0.50798,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38172,SRR1555548,SRX684656,SRS687773,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0056,GSM1483791,,tissue:single embryo,Metazome ZF timecourse sample 0056,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2240,GSM1483791,GSM1483791: Metazome ZF timecourse sample 0056; Danio rerio; RNA Seq,GSM1483791,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483791,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0056.fastq.gz,fastq,99176700.0,2833620.0,GSM1483791 r1,0:35,A:28266891;C:20096113;G:20730721;T:29621152;N:461823,35,,,,28266891,20096113,20730721,29621152,461823,SRX684656,SRS687773,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75342,,0.1218,,0.82982,,0.52199,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38173,SRR1555547,SRX684655,SRS687772,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0055,GSM1483790,,tissue:single embryo,Metazome ZF timecourse sample 0055,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2200,GSM1483790,GSM1483790: Metazome ZF timecourse sample 0055; Danio rerio; RNA Seq,GSM1483790,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483790,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0055.fastq.gz,fastq,151127480.0,4317928.0,GSM1483790 r1,0:35,A:43591040;C:30002113;G:30975524;T:46254070;N:304733,35,,,,43591040,30002113,30975524,46254070,304733,SRX684655,SRS687772,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75764,,0.12465,,0.81249,,0.51762,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38174,SRR1555546,SRX684654,SRS687771,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0054,GSM1483789,,tissue:single embryo,Metazome ZF timecourse sample 0054,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2160,GSM1483789,GSM1483789: Metazome ZF timecourse sample 0054; Danio rerio; RNA Seq,GSM1483789,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483789,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0054.fastq.gz,fastq,69059795.0,1973137.0,GSM1483789 r1,0:35,A:19683826;C:13807471;G:14484211;T:20733707;N:350580,35,,,,19683826,13807471,14484211,20733707,350580,SRX684654,SRS687771,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.68459,,0.10792,,0.85865,,0.53677,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38175,SRR1555545,SRX684653,SRS687770,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0053,GSM1483788,,tissue:single embryo,Metazome ZF timecourse sample 0053,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2120,GSM1483788,GSM1483788: Metazome ZF timecourse sample 0053; Danio rerio; RNA Seq,GSM1483788,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483788,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0053.fastq.gz,fastq,191369430.0,5467698.0,GSM1483788 r1,0:35,A:53654936;C:37894425;G:41404133;T:58136035;N:279901,35,,,,53654936,37894425,41404133,58136035,279901,SRX684653,SRS687770,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80463,,0.1324,,0.81489,,0.49,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38176,SRR1555544,SRX684652,SRS687768,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0052,GSM1483787,,tissue:single embryo,Metazome ZF timecourse sample 0052,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2080,GSM1483787,GSM1483787: Metazome ZF timecourse sample 0052; Danio rerio; RNA Seq,GSM1483787,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483787,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0052.fastq.gz,fastq,215564930.0,6158998.0,GSM1483787 r1,0:35,A:63312652;C:41647031;G:43302090;T:66999251;N:303906,35,,,,63312652,41647031,43302090,66999251,303906,SRX684652,SRS687768,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.79312,,0.14581,,0.80748,,0.4943,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38177,SRR1555543,SRX684651,SRS687769,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0051,GSM1483786,,tissue:single embryo,Metazome ZF timecourse sample 0051,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2040,GSM1483786,GSM1483786: Metazome ZF timecourse sample 0051; Danio rerio; RNA Seq,GSM1483786,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483786,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0051.fastq.gz,fastq,290737720.0,8306792.0,GSM1483786 r1,0:35,A:85354255;C:55749822;G:57830877;T:91385535;N:417231,35,,,,85354255,55749822,57830877,91385535,417231,SRX684651,SRS687769,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.79714,,0.14915,,0.80351,,0.48212,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38178,SRR1555542,SRX684650,SRS687767,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0050,GSM1483785,,tissue:single embryo,Metazome ZF timecourse sample 0050,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2000,GSM1483785,GSM1483785: Metazome ZF timecourse sample 0050; Danio rerio; RNA Seq,GSM1483785,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483785,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0050.fastq.gz,fastq,127885835.0,3653881.0,GSM1483785 r1,0:35,A:36640576;C:24900786;G:26610416;T:39561545;N:172512,35,,,,36640576,24900786,26610416,39561545,172512,SRX684650,SRS687767,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80166,,0.14944,,0.81122,,0.46057,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38179,SRR1555541,SRX684649,SRS687766,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0049,GSM1483784,,tissue:single embryo,Metazome ZF timecourse sample 0049,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1960,GSM1483784,GSM1483784: Metazome ZF timecourse sample 0049; Danio rerio; RNA Seq,GSM1483784,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483784,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0049.fastq.gz,fastq,288732220.0,8249492.0,GSM1483784 r1,0:35,A:82273862;C:55791356;G:60225084;T:90004597;N:437321,35,,,,82273862,55791356,60225084,90004597,437321,SRX684649,SRS687766,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80699,,0.14603,,0.80119,,0.50186,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38180,SRR1555540,SRX684648,SRS687765,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0048,GSM1483783,,tissue:single embryo,Metazome ZF timecourse sample 0048,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1920,GSM1483783,GSM1483783: Metazome ZF timecourse sample 0048; Danio rerio; RNA Seq,GSM1483783,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483783,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0048.fastq.gz,fastq,72029510.0,2057986.0,GSM1483783 r1,0:35,A:20988018;C:14353166;G:14709018;T:21808886;N:170422,35,,,,20988018,14353166,14709018,21808886,170422,SRX684648,SRS687765,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.7657,,0.12723,,0.82903,,0.51174,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38181,SRR1555539,SRX684647,SRS687764,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0047,GSM1483782,,tissue:single embryo,Metazome ZF timecourse sample 0047,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1880,GSM1483782,GSM1483782: Metazome ZF timecourse sample 0047; Danio rerio; RNA Seq,GSM1483782,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483782,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0047.fastq.gz,fastq,68139750.0,1946850.0,GSM1483782 r1,0:35,A:19374753;C:13653921;G:14376686;T:20519427;N:214963,35,,,,19374753,13653921,14376686,20519427,214963,SRX684647,SRS687764,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75951,,0.09929,,0.84372,,0.49457,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38182,SRR1555538,SRX684646,SRS687763,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0046,GSM1483781,,tissue:single embryo,Metazome ZF timecourse sample 0046,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1840,GSM1483781,GSM1483781: Metazome ZF timecourse sample 0046; Danio rerio; RNA Seq,GSM1483781,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483781,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0046.fastq.gz,fastq,77208705.0,2205963.0,GSM1483781 r1,0:35,A:22006761;C:15565401;G:16227173;T:23236147;N:173223,35,,,,22006761,15565401,16227173,23236147,173223,SRX684646,SRS687763,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.78187,,0.11068,,0.82408,,0.50229,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38183,SRR1555537,SRX684645,SRS687762,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0045,GSM1483780,,tissue:single embryo,Metazome ZF timecourse sample 0045,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1800,GSM1483780,GSM1483780: Metazome ZF timecourse sample 0045; Danio rerio; RNA Seq,GSM1483780,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483780,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0045.fastq.gz,fastq,137583040.0,3930944.0,GSM1483780 r1,0:35,A:39174780;C:27210755;G:28507642;T:41999686;N:690177,35,,,,39174780,27210755,28507642,41999686,690177,SRX684645,SRS687762,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75598,,0.12311,,0.81682,,0.5009,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38184,SRR1555536,SRX684644,SRS687761,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0044,GSM1483779,,tissue:single embryo,Metazome ZF timecourse sample 0044,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1760,GSM1483779,GSM1483779: Metazome ZF timecourse sample 0044; Danio rerio; RNA Seq,GSM1483779,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483779,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0044.fastq.gz,fastq,173596780.0,4959908.0,GSM1483779 r1,0:35,A:50342468;C:34071199;G:35445470;T:53307736;N:429907,35,,,,50342468,34071199,35445470,53307736,429907,SRX684644,SRS687761,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75753,,0.11777,,0.81055,,0.49526,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38185,SRR1555535,SRX684643,SRS687760,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0043,GSM1483778,,tissue:single embryo,Metazome ZF timecourse sample 0043,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1720,GSM1483778,GSM1483778: Metazome ZF timecourse sample 0043; Danio rerio; RNA Seq,GSM1483778,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483778,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0043.fastq.gz,fastq,86602355.0,2474353.0,GSM1483778 r1,0:35,A:24985086;C:17224343;G:17613830;T:26349902;N:429194,35,,,,24985086,17224343,17613830,26349902,429194,SRX684643,SRS687760,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75503,,0.11846,,0.82706,,0.50298,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38186,SRR1555534,SRX684642,SRS687759,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0042,GSM1483777,,tissue:single embryo,Metazome ZF timecourse sample 0042,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1680,GSM1483777,GSM1483777: Metazome ZF timecourse sample 0042; Danio rerio; RNA Seq,GSM1483777,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483777,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0042.fastq.gz,fastq,188917295.0,5397637.0,GSM1483777 r1,0:35,A:55128132;C:36753131;G:38260811;T:58386915;N:388306,35,,,,55128132,36753131,38260811,58386915,388306,SRX684642,SRS687759,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75676,,0.12061,,0.80442,,0.5035,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38187,SRR1555533,SRX684641,SRS687758,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0041,GSM1483776,,tissue:single embryo,Metazome ZF timecourse sample 0041,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1640,GSM1483776,GSM1483776: Metazome ZF timecourse sample 0041; Danio rerio; RNA Seq,GSM1483776,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483776,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0041.fastq.gz,fastq,99641815.0,2846909.0,GSM1483776 r1,0:35,A:28559457;C:19637558;G:20746011;T:30190358;N:508431,35,,,,28559457,19637558,20746011,30190358,508431,SRX684641,SRS687758,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.76108,,0.11637,,0.82751,,0.5096,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38188,SRR1555532,SRX684640,SRS687757,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0040,GSM1483775,,tissue:single embryo,Metazome ZF timecourse sample 0040,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1600,GSM1483775,GSM1483775: Metazome ZF timecourse sample 0040; Danio rerio; RNA Seq,GSM1483775,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483775,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0040.fastq.gz,fastq,66500840.0,1900024.0,GSM1483775 r1,0:35,A:19905778;C:13336991;G:13569868;T:19599979;N:88224,35,,,,19905778,13336991,13569868,19599979,88224,SRX684640,SRS687757,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.79612,,0.14476,,0.84421,,0.51356,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38189,SRR1555531,SRX684639,SRS687756,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0039,GSM1483774,,tissue:single embryo,Metazome ZF timecourse sample 0039,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1560,GSM1483774,GSM1483774: Metazome ZF timecourse sample 0039; Danio rerio; RNA Seq,GSM1483774,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483774,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0039.fastq.gz,fastq,91322490.0,2609214.0,GSM1483774 r1,0:35,A:26896148;C:18075620;G:18949224;T:27276263;N:125235,35,,,,26896148,18075620,18949224,27276263,125235,SRX684639,SRS687756,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80286,,0.15016,,0.83195,,0.52775,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38190,SRR1555530,SRX684638,SRS687755,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0038,GSM1483773,,tissue:single embryo,Metazome ZF timecourse sample 0038,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1520,GSM1483773,GSM1483773: Metazome ZF timecourse sample 0038; Danio rerio; RNA Seq,GSM1483773,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483773,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0038.fastq.gz,fastq,101902745.0,2911507.0,GSM1483773 r1,0:35,A:30262327;C:20264495;G:20848086;T:30389349;N:138488,35,,,,30262327,20264495,20848086,30389349,138488,SRX684638,SRS687755,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.79914,,0.14724,,0.83047,,0.51145,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38191,SRR1555529,SRX684637,SRS687754,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0037,GSM1483772,,tissue:single embryo,Metazome ZF timecourse sample 0037,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1480,GSM1483772,GSM1483772: Metazome ZF timecourse sample 0037; Danio rerio; RNA Seq,GSM1483772,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483772,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0037.fastq.gz,fastq,81416650.0,2326190.0,GSM1483772 r1,0:35,A:23902634;C:16036242;G:17201817;T:24155587;N:120370,35,,,,23902634,16036242,17201817,24155587,120370,SRX684637,SRS687754,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.78827,,0.18587,,0.84674,,0.44219,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38192,SRR1555528,SRX684636,SRS687752,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0036,GSM1483771,,tissue:single embryo,Metazome ZF timecourse sample 0036,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1440,GSM1483771,GSM1483771: Metazome ZF timecourse sample 0036; Danio rerio; RNA Seq,GSM1483771,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483771,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0036.fastq.gz,fastq,75971315.0,2170609.0,GSM1483771 r1,0:35,A:22267492;C:15517952;G:15279496;T:22807339;N:99036,35,,,,22267492,15517952,15279496,22807339,99036,SRX684636,SRS687752,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.74377,,0.14648,,0.84348,,0.53283,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38193,SRR1555527,SRX684635,SRS687753,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0035,GSM1483770,,tissue:single embryo,Metazome ZF timecourse sample 0035,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1400,GSM1483770,GSM1483770: Metazome ZF timecourse sample 0035; Danio rerio; RNA Seq,GSM1483770,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483770,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0035.fastq.gz,fastq,1394330.0,39838.0,GSM1483770 r1,0:35,A:402051;C:272276;G:287822;T:429952;N:2229,35,,,,402051,272276,287822,429952,2229,SRX684635,SRS687753,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.74877,,0.12157,,0.98646,,0.52724,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38194,SRR1555526,SRX684634,SRS687751,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0034,GSM1483769,,tissue:single embryo,Metazome ZF timecourse sample 0034,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1360,GSM1483769,GSM1483769: Metazome ZF timecourse sample 0034; Danio rerio; RNA Seq,GSM1483769,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483769,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0034.fastq.gz,fastq,35015155.0,1000433.0,GSM1483769 r1,0:35,A:10142602;C:6989087;G:7392583;T:10442983;N:47900,35,,,,10142602,6989087,7392583,10442983,47900,SRX684634,SRS687751,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80122,,0.12241,,0.88402,,0.53072,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38195,SRR1555525,SRX684633,SRS687749,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0033,GSM1483768,,tissue:single embryo,Metazome ZF timecourse sample 0033,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1320,GSM1483768,GSM1483768: Metazome ZF timecourse sample 0033; Danio rerio; RNA Seq,GSM1483768,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483768,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0033.fastq.gz,fastq,62990725.0,1799735.0,GSM1483768 r1,0:35,A:17788769;C:12319707;G:13858738;T:18933772;N:89739,35,,,,17788769,12319707,13858738,18933772,89739,SRX684633,SRS687749,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80408,,0.14198,,0.85802,,0.51504,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38196,SRR1555524,SRX684632,SRS687750,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0032,GSM1483767,,tissue:single embryo,Metazome ZF timecourse sample 0032,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1280,GSM1483767,GSM1483767: Metazome ZF timecourse sample 0032; Danio rerio; RNA Seq,GSM1483767,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483767,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0032.fastq.gz,fastq,55043730.0,1572678.0,GSM1483767 r1,0:35,A:15726201;C:10988676;G:11393651;T:16764103;N:171099,35,,,,15726201,10988676,11393651,16764103,171099,SRX684632,SRS687750,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75627,,0.11178,,0.84187,,0.51424,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures
38197,SRR1555523,SRX684631,SRS687748,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0031,GSM1483766,,tissue:single embryo,Metazome ZF timecourse sample 0031,Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1240,GSM1483766,GSM1483766: Metazome ZF timecourse sample 0031; Danio rerio; RNA Seq,GSM1483766,,1,RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483766,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0031.fastq.gz,fastq,111829725.0,3195135.0,GSM1483766 r1,0:35,A:32037252;C:22024337;G:23195973;T:34219811;N:352352,35,,,,32037252,22024337,23195973,34219811,352352,SRX684631,SRS687748,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.76499,,0.1174,,0.81931,,0.48818,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures