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206 rows where devstage_curation = "Zygote" and tissue_curation = "Embryo Imprecise"

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  • Embryo Imprecise · 206 ✖

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  • Zygote · 206 ✖
Link 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 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 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 superna…   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 superna…   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 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 superna…   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 superna…   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 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 superna…   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 superna…   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 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 superna…   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 superna…   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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;