{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Zygote\" and experiment.library_layout = \"SINGLE\"", "rows": [[175, "DRR084197", "DRX078028", "DRS086522", "DRP004758", "PRJDB5490", "Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004758", "Other", "Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.", null, null, "natural paring early sample", "zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate2]", "SAMD00073604", null, "sample name:M 4th|replicate:biological replicate 2", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00073604", "DRX078028", "zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate2]", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004758", "Illumina HiSeq 2500 sequencing of SAMD00073604", null, null, null, 1389837888.0, 38606608.0, "DRR084197", "0:36", "A:320671418;C:336948866;G:347550258;T:381720581;N:2946765", 36, null, null, null, 320671418, 336948866, 347550258, 381720581, 2946765, "DRX078028", "DRS086522", "DRA005484", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.89763, null, 0.02235, null, 0.76445, null, 0.46381, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Zygote", "Embryo", "Multi-tissue", "Multi-system"], [181, "DRR084191", "DRX078022", "DRS086516", "DRP004758", "PRJDB5490", "Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004758", "Other", "Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.", null, null, "natural paring early sample", "zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate1]", "SAMD00073598", null, "sample name:M|replicate:biological replicate 1", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00073598", "DRX078022", "zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate1]", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004758", "Illumina HiSeq 2500 sequencing of SAMD00073598", null, null, null, 1050981012.0, 29193917.0, "DRR084191", "0:36", "A:241048832;C:256186268;G:260277071;T:293299597;N:169244", 36, null, null, null, 241048832, 256186268, 260277071, 293299597, 169244, "DRX078022", "DRS086516", "DRA005484", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.9088, null, 0.02369, null, 0.7624, null, 0.47998, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Zygote", "Embryo", "Multi-tissue", "Multi-system"], [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\u00ae 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.", null, null, "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", null, null, null, null, null, null, null, null, "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.", null, "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", null, 50, null, null, null, null, null, null, null, null, "ERX012650", "ERS032265", "ERA029959", "KI-BN|Department of Biosciences and Nutrition", "Department of Biosciences and Nutrition, Karolinska Institutet, Sweden", 1, 0.64855, null, 0.08432, null, 0.9052, null, 0.74223, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Sweden", "2011-06-09", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [15550, "ERR647595", "ERX604031", "ERS557915", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Egg", "SAMEA2796300", "UNIVERSITY OF AMSTERDAM", "Alias:Egg|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:29:23Z|INSDC status:public|SRA accession:ERS557915|Sample Name:ERS557915|Title:Zebrafish Egg samples|dev stage:Oocytes", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:25:29:391 1", "RID0024", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0024_016.fastq.gz", "fastq", 6684767188.0, 89052017.0, "ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:25:29:391 1", "0:75.07", "A:1523328157;C:1795624453;G:1849675240;T:1516139338;N:0", 75, null, null, null, 1523328157, 1795624453, 1849675240, 1516139338, 0, "ERX604031", "ERS557915", "ERA363845", "UNIVERSITY OF AMSTERDAM", "UNIVERSITY OF AMSTERDAM", 1, 0.89536, null, 0.15322, null, 0.91421, null, 0.69019, null, 73, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2014-10-01", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [24546, "ERR964671", "ERX1041634", "ERS792101", "ERP011038", "PRJEB9889", "The Zebrafish transcriptome during early development", "ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22", "Other", "Zebrafish has emerged as a model organism to investigate vertebrate development  and human genetic diseases. However  currently zebrafish annotation is still ongoing and clearly not sufficed  therefore  providing opportunity for novel transcript finding.  With the introduction of massive parallel sequencing  whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study  we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation.", null, null, null, "KI BN JKE DRERIO RNASEQ", "SAMEA3484816", "KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION", "ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484816|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 1cell|common name:zebrafish|dev stage:1cell|sample name:KI BN JKE DRERIO RNASEQ 2009 1cell|strain:Tuebingen", null, null, null, null, null, null, null, null, "AB SOLiD System 3.0 sequencing", "ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 5", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "ERP011038", "AB SOLiD System 3.0 sequencing", "ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16", "KI-BN-JKE-DRERIO-RNASEQ-20091014-1cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20091014-1cell_F3_QV.qual.gz", "SOLiD_native SOLiD_native", 2625510200.0, 52510204.0, "ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 5", "0:50", "0:677149824;1:606769571;2:761187530;3:578170290;.:2232985", 50, null, null, null, null, null, null, null, null, "ERX1041634", "ERS792101", "ERA458495", "KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive", "KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION", 1, 0.71662, null, 0.0994, null, 0.91644, null, 0.74578, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Sweden", "2015-07-15", "Zygote", "Embryo", "Undetermined", "Embryo Imprecise"], [24549, "ERR964667", "ERX1041630", "ERS792101", "ERP011038", "PRJEB9889", "The Zebrafish transcriptome during early development", "ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22", "Other", "Zebrafish has emerged as a model organism to investigate vertebrate development  and human genetic diseases. However  currently zebrafish annotation is still ongoing and clearly not sufficed  therefore  providing opportunity for novel transcript finding.  With the introduction of massive parallel sequencing  whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study  we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation.", null, null, null, "KI BN JKE DRERIO RNASEQ", "SAMEA3484816", "KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION", "ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484816|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 1cell|common name:zebrafish|dev stage:1cell|sample name:KI BN JKE DRERIO RNASEQ 2009 1cell|strain:Tuebingen", null, null, null, null, null, null, null, null, "AB SOLiD System 3.0 sequencing", "ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:870 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "ERP011038", "AB SOLiD System 3.0 sequencing", "ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16", "KI-BN-JKE-DRERIO-RNASEQ-20090709-1cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20090709-1cell_F3_QV.qual.gz", "SOLiD_native SOLiD_native", 5717685400.0, 114353708.0, "ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:870 1", "0:50", "0:1643444976;1:1261570333;2:1504304496;3:1282815913;.:25549682", 50, null, null, null, null, null, null, null, null, "ERX1041630", "ERS792101", "ERA458495", "KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive", "KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION", 1, 0.72274, null, 0.11151, null, 0.92348, null, 0.71904, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Sweden", "2015-07-15", "Zygote", "Embryo", "Undetermined", "Embryo Imprecise"], [25293, "SRR25764131", "SRX21486791", "SRS18719090", "SRP457111", "PRJNA1009808", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]", "GSE241754", "Transcriptome Analysis", "Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.", "parent bioproject:PRJNA1009800", "pubmed:39402326", null, "WT egg 0 hpf tRNA seq rep2", "GSM7734772", null, "source name:Unfertilized egg|strain:TLAB strain|tissue:Unfertilized egg|developmental stage:unfertilized egg 0 hpf|genotype:WT|geo loc name:missing|collection date:missing", "WT egg 0 hpf tRNA seq rep2", "Read demultiplexing and adapter trimming performed with cutadapt v3.5  where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained  and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5\u2019 RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters   species Drer   cluster id 0.93   min cov 0.001   max mismatches 0.075   control condition Egg   deconv cov ratio 0.4   remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters  and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts", "Unfertilized egg", "unperturbed growth conditions in E3 medium for zebrafish embryos.", "50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq", "Embryos were grown in standard housing conditions namely28\u00b0C at a 14/10 hour light/dark cycle.", "strain:TLAB strain|tissue:Unfertilized egg|developmental stage:unfertilized egg 0 hpf|genotype:WT", "GSM7734772", "GSM7734772: WT egg 0 hpf tRNA seq rep2; Danio rerio; ncRNA Seq", "GSM7734772 r1", "GSM7734772", "1", "50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP457111", null, null, "WT_tRNA_egg_2.fastq.gz", "fastq", 206374994.0, 3181706.0, "GSM7734772 r1", "0:64.86", "A:41195250;C:56578032;G:56479855;T:52121365;N:492", 64, null, null, null, 41195250, 56578032, 56479855, 52121365, 492, "SRX21486791", "SRS18719090", "SRA1700461", "Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry", "Max Planck Institute of Biochemistry", 1, 0.28659, null, 0.02017, null, 0.9207, null, 0.48536, null, 78, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [25294, "SRR25764132", "SRX21486790", "SRS18719089", "SRP457111", "PRJNA1009808", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]", "GSE241754", "Transcriptome Analysis", "Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.", "parent bioproject:PRJNA1009800", "pubmed:39402326", null, "WT egg 0 hpf tRNA seq rep1", "GSM7734771", null, "source name:Unfertilized egg|strain:TLAB strain|tissue:Unfertilized egg|developmental stage:unfertilized egg 0 hpf|genotype:WT|geo loc name:missing|collection date:missing", "WT egg 0 hpf tRNA seq rep1", "Read demultiplexing and adapter trimming performed with cutadapt v3.5  where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained  and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5\u2019 RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters   species Drer   cluster id 0.93   min cov 0.001   max mismatches 0.075   control condition Egg   deconv cov ratio 0.4   remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters  and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts", "Unfertilized egg", "unperturbed growth conditions in E3 medium for zebrafish embryos.", "50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq", "Embryos were grown in standard housing conditions namely28\u00b0C at a 14/10 hour light/dark cycle.", "strain:TLAB strain|tissue:Unfertilized egg|developmental stage:unfertilized egg 0 hpf|genotype:WT", "GSM7734771", "GSM7734771: WT egg 0 hpf tRNA seq rep1; Danio rerio; ncRNA Seq", "GSM7734771 r1", "GSM7734771", "1", "50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP457111", null, null, "WT_tRNA_egg_1.fastq.gz", "fastq", 86021968.0, 1304769.0, "GSM7734771 r1", "0:65.93", "A:17511521;C:23474625;G:23300759;T:21734864;N:199", 65, null, null, null, 17511521, 23474625, 23300759, 21734864, 199, "SRX21486790", "SRS18719089", "SRA1700461", "Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry", "Max Planck Institute of Biochemistry", 1, 0.29829, null, 0.02027, null, 0.92245, null, 0.48877, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:40246845", null, null, "1 cell Iso seq", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "PACBIO_SMRT", "Sequel", null, "SRP466518", null, null, "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, null, null, null, 560055059, 479061015, 485136981, 552323650, 0, "SRX22100871", "SRS19165997", "SRA1731898", "University of Michigan|Computational Medicine and Bioinformatics", "University of Michigan", 1, 0.44892, null, 0.00258, null, 0.90114, null, 0.50832, null, 32, null, "B", null, "usable mapping rate", "pacbio", "pacbio_modern", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2023-10-16", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28588, "SRR26395064", "SRX22100870", "SRS19165996", "SRP466518", "PRJNA1028258", "Zygotic activation of transposable elements during zebrafish early embryogenesis", "PRJNA1028258", "Other", "Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.", null, "pubmed:40246845", null, null, "fertilized egg Iso seq", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "PACBIO_SMRT", "Sequel", null, "SRP466518", null, null, "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, null, null, null, 990393181, 795168216, 861389798, 903654015, 0, "SRX22100870", "SRS19165996", "SRA1731898", "University of Michigan|Computational Medicine and Bioinformatics", "University of Michigan", 1, 0.33296, null, 0.00275, null, 0.95548, null, 0.552, null, 1155, null, "T", null, "long read", "pacbio", "pacbio_modern", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2023-10-16", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30772, "SRR28348938", "SRX23954958", "SRS20755379", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Embryo  0hpf  rep3", "GSM8147855", null, "source name:Whole embryo|tissue:Whole embryo|developmental stage:0hpf|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Embryo  0hpf  rep3", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Whole embryo", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Whole embryo|developmental stage:0hpf|genotype:AB  TF and TLF", "GSM8147855", "GSM8147855: Zebrafish Embryo  0hpf  rep3; Danio rerio; RNA Seq", "GSM8147855 r1", "GSM8147855", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "s_0hpf_3.fastq", "fastq", 1542142220.0, 20291345.0, "GSM8147855 r1", "0:76", "A:376857497;C:381518368;G:357117823;T:426581588;N:66944", 76, null, null, null, 376857497, 381518368, 357117823, 426581588, 66944, "SRX23954958", "SRS20755379", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Zygote", "Embryo", "Whole Organism", "All anatomical structures"], [30773, "SRR28348939", "SRX23954957", "SRS20755378", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Embryo  0hpf  rep2", "GSM8147854", null, "source name:Whole embryo|tissue:Whole embryo|developmental stage:0hpf|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Embryo  0hpf  rep2", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Whole embryo", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Whole embryo|developmental stage:0hpf|genotype:AB  TF and TLF", "GSM8147854", "GSM8147854: Zebrafish Embryo  0hpf  rep2; Danio rerio; RNA Seq", "GSM8147854 r1", "GSM8147854", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "s_0hpf_2.fastq", "fastq", 1775936764.0, 23367589.0, "GSM8147854 r1", "0:76", "A:430534781;C:442757587;G:423062009;T:479501608;N:80779", 76, null, null, null, 430534781, 442757587, 423062009, 479501608, 80779, "SRX23954957", "SRS20755378", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Zygote", "Embryo", "Whole Organism", "All anatomical structures"], [30774, "SRR28348940", "SRX23954956", "SRS20755377", "SRP495323", "PRJNA1088158", "Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.", "GSE261646", "Transcriptome Analysis", "The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Embryo  0hpf  rep1", "GSM8147853", null, "source name:Whole embryo|tissue:Whole embryo|developmental stage:0hpf|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing", "Zebrafish Embryo  0hpf  rep1", "Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates", "Whole embryo", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer\u2019s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer\u2019s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "tissue:Whole embryo|developmental stage:0hpf|genotype:AB  TF and TLF", "GSM8147853", "GSM8147853: Zebrafish Embryo  0hpf  rep1; Danio rerio; RNA Seq", "GSM8147853 r1", "GSM8147853", "1", "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "s_0hpf_1.fastq", "fastq", 1616867016.0, 21274566.0, "GSM8147853 r1", "0:76", "A:390223732;C:404962813;G:373130983;T:448474905;N:74583", 76, null, null, null, 390223732, 404962813, 373130983, 448474905, 74583, "SRX23954956", "SRS20755377", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Zygote", "Embryo", "Whole Organism", "All anatomical structures"], [34978, "SRR32588735", "SRX27895216", "SRS24266218", "SRP568323", "PRJNA1232602", "Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains", "PRJNA1232602", "Other", "In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.", null, null, null, "Iso Seq RNA from embryo zero hpf", "C2 F2 0", null, "strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:time 0 hours|dev stage:Embyoys|collection date:2024 06|geo loc name:USA|sex:female|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Iso Seq RNA from embyo 0 hpf", "C2 F2 0", "C2 F2 0", "The long Read Sequencing libraries was sequenced using PacBio Sequel II", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP568323", null, null, "m54313U_231110_180503.hifi_reads.flnc.fastq.gz", "fastq", 8144050440.0, 3744842.0, "m54313U 231110 180503.hifi reads.flnc.fastq.gz", "0:2174.74", "A:2267401658;C:1836982566;G:1935470734;T:2104195482;N:0", 2174, null, null, null, 2267401658, 1836982566, 1935470734, 2104195482, 0, "SRX27895216", "SRS24266218", "SRA2089085", "National Human Genome Research Institute|Translational and Functional Genomics Branch", "National Human Genome Research Institute National Human Genome Research Institute", 1, 0.76793, null, 0.00473, null, 0.80371, null, 0.50925, null, 1489, null, "T", null, "long read", "pacbio", "pacbio_modern", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-03-06", "Zygote", "Embryo", "Muscle", "Muscular System"], [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", null, "pubmed:21555364;pubmed:24586560;pubmed:23676078", null, "1 cell", "GSM564428", null, "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:\u00a0 Mapping was done using Applied Biosystems\u2019 SOLiD BioScope alignment for whole transcriptome analysis pipeline.\u00a0 Two mismatches were allowed in the 25bp color space seed sequence with extension alignment performed to find the full mapping location.\u00a0 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\u2122 Sequencing kit ABI according to manufacturer\u2019s instructions. About 200 280 \u00b5g 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 \u221280\u00b0C. Total RNA was extracted from whole embryos using Trizol Invitrogen according to manufacturer\u2019s 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", null, "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", null, null, null, null, 1175348550.0, 23506971.0, "GSM564428 1", "0:50", null, 50, null, null, null, null, null, null, null, null, "SRX025026", "SRS085805", "SRA022850", "GEO", "Computational and Systems Biology, Genome Institute of Singapore", 1, 0.75876, null, 0.05232, null, 0.86762, null, 0.50392, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2010-07-08", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36260, "SRR062657", "SRX025025", "SRS085804", "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", null, "pubmed:21555364;pubmed:24586560;pubmed:23676078", null, "Maternal", "GSM564427", null, "tissue:Unfertilized egg|background:AB; wild type|developmental stage:unfertilized eggs", "Maternal", "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:\u00a0 Mapping was done using Applied Biosystems\u2019 SOLiD BioScope alignment for whole transcriptome analysis pipeline.\u00a0 Two mismatches were allowed in the 25bp color space seed sequence with extension alignment performed to find the full mapping location.\u00a0 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.", "Unfertilized egg", "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\u2122 Sequencing kit ABI according to manufacturer\u2019s instructions. About 200 280 \u00b5g 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 \u221280\u00b0C. Total RNA was extracted from whole embryos using Trizol Invitrogen according to manufacturer\u2019s 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:unfertilized eggs", "GSM564427", "GSM564427: Maternal", "GSM564427: Maternal", "GSM564427: Maternal", "1", null, "GEO Accession:GSM564427", "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", null, null, null, null, 1566199300.0, 31323986.0, "GSM564427 1", "0:50", null, 50, null, null, null, null, null, null, null, null, "SRX025025", "SRS085804", "SRA022850", "GEO", "Computational and Systems Biology, Genome Institute of Singapore", 1, 0.72688, null, 0.05657, null, 0.876, null, 0.51223, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2010-07-08", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [36424, "SRR516545", "SRX156307", "SRS347187", "SRP013950", "PRJNA169500", "Danio rerio embryonic promoterome", "PRJNA169500", "Transcriptome Analysis", "Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain   unfertilized egg", "D. rerio unfertilized egg", "D. rerio unfertilized egg", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio unfertilized egg", "CAGE   D. rerio unfertilized egg run2", "D. rerio unfertilized egg", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, null, null, 115273233.0, 4269379.0, "CAGE   D. rerio unfertilized egg run1", "0:27", "A:29909511;C:24823784;G:32519899;T:28020039;N:0", 27, null, null, null, 29909511, 24823784, 32519899, 28020039, 0, "SRX156307", "SRS347187", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.49872, null, 0.07655, null, 0.81673, null, 0.80445, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2012-06-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [36425, "SRR516546", "SRX156307", "SRS347187", "SRP013950", "PRJNA169500", "Danio rerio embryonic promoterome", "PRJNA169500", "Transcriptome Analysis", "Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain   unfertilized egg", "D. rerio unfertilized egg", "D. rerio unfertilized egg", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio unfertilized egg", "CAGE   D. rerio unfertilized egg run2", "D. rerio unfertilized egg", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, null, null, 112673943.0, 4173109.0, "CAGE   D. rerio unfertilized egg run2", "0:27", "A:28315221;C:24199098;G:32599482;T:27560142;N:0", 27, null, null, null, 28315221, 24199098, 32599482, 27560142, 0, "SRX156307", "SRS347187", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.46201, null, 0.06422, null, 0.82118, null, 0.82184, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2012-06-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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 \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0106", "GSM1483841", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 1100064, 790487, 836206, 1169251, 15697, "SRX684706", "SRS687823", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.72414, null, 0.09461, null, 0.96725, null, 0.4942, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38123, "SRR1555597", "SRX684705", "SRS687821", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0105", "GSM1483840", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 9524894, 6625944, 6696548, 9953576, 76183, "SRX684705", "SRS687821", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.74436, null, 0.07095, null, 0.88201, null, 0.47612, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38124, "SRR1555596", "SRX684704", "SRS687822", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0104", "GSM1483839", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 24075610, 16799998, 16694424, 25967423, 272565, "SRX684704", "SRS687822", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.7588, null, 0.07993, null, 0.84449, null, 0.49785, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38125, "SRR1555595", "SRX684703", "SRS687820", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0103", "GSM1483838", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 28361916, 19232789, 19589483, 30798968, 222994, "SRX684703", "SRS687820", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75509, null, 0.13429, null, 0.81117, null, 0.49102, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38126, "SRR1555594", "SRX684702", "SRS687819", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0102", "GSM1483837", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 55969077, 36880901, 37835921, 61101558, 1030378, "SRX684702", "SRS687819", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.73387, null, 0.17245, null, 0.80164, null, 0.48657, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38127, "SRR1555593", "SRX684701", "SRS687818", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0101", "GSM1483836", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 112191846, 73679996, 73185024, 114766825, 515764, "SRX684701", "SRS687818", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.83131, null, 0.16618, null, 0.77812, null, 0.49895, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38128, "SRR1555592", "SRX684700", "SRS687816", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0100", "GSM1483835", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 4361241, 3088134, 3269084, 4498093, 22868, "SRX684700", "SRS687816", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.7702, null, 0.17879, null, 0.92904, null, 0.505, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38129, "SRR1555591", "SRX684699", "SRS687817", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0099", "GSM1483834", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 81991733, 57440756, 58362818, 86010858, 390335, "SRX684699", "SRS687817", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.81284, null, 0.1715, null, 0.78468, null, 0.49472, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38130, "SRR1555590", "SRX684698", "SRS687815", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0098", "GSM1483833", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 70141725, 48500061, 50748992, 74478239, 375998, "SRX684698", "SRS687815", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.79668, null, 0.17718, null, 0.79271, null, 0.45966, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38131, "SRR1555589", "SRX684697", "SRS687814", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0097", "GSM1483832", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 62928172, 42420829, 43902946, 65803342, 292221, "SRX684697", "SRS687814", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.80605, null, 0.17396, null, 0.78873, null, 0.50241, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38132, "SRR1555588", "SRX684696", "SRS687813", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0096", "GSM1483831", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 4077402, 2837417, 2856511, 4200750, 20150, "SRX684696", "SRS687813", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.77543, null, 0.14778, null, 0.93288, null, 0.48967, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38133, "SRR1555587", "SRX684695", "SRS687811", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0095", "GSM1483830", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 86694666, 56953853, 57315219, 88811589, 376108, "SRX684695", "SRS687811", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.79098, null, 0.18155, null, 0.79034, null, 0.51338, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38134, "SRR1555586", "SRX684694", "SRS687810", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0094", "GSM1483829", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 186408265, 127218686, 131406509, 199399112, 990353, "SRX684694", "SRS687810", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.81184, null, 0.15572, null, 0.78496, null, 0.48733, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38135, "SRR1555585", "SRX684693", "SRS687812", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0093", "GSM1483828", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 24239984, 16625180, 16309055, 25123568, 276418, "SRX684693", "SRS687812", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75557, null, 0.14554, null, 0.82205, null, 0.49736, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38136, "SRR1555584", "SRX684692", "SRS687809", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0092", "GSM1483827", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 21349438, 14361391, 14472348, 21766197, 237531, "SRX684692", "SRS687809", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.74348, null, 0.13614, null, 0.8309, null, 0.51328, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38137, "SRR1555583", "SRX684691", "SRS687808", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0091", "GSM1483826", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 5374937, 3766785, 3774551, 5451369, 38298, "SRX684691", "SRS687808", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.74005, null, 0.11089, null, 0.91494, null, 0.49823, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38138, "SRR1555582", "SRX684690", "SRS687807", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0090", "GSM1483825", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 41371650, 28115945, 29356068, 42485478, 609124, "SRX684690", "SRS687807", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.71151, null, 0.17711, null, 0.82789, null, 0.52369, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38139, "SRR1555581", "SRX684689", "SRS687806", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0089", "GSM1483824", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 28763571, 20065085, 19332839, 31088193, 319327, "SRX684689", "SRS687806", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.74177, null, 0.13103, null, 0.81854, null, 0.51184, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38140, "SRR1555580", "SRX684688", "SRS687805", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0088", "GSM1483823", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 49034449, 32785565, 33439918, 52997820, 532303, "SRX684688", "SRS687805", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.73454, null, 0.15775, null, 0.8047, null, 0.50587, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38141, "SRR1555579", "SRX684687", "SRS687803", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0087", "GSM1483822", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 23985678, 16871573, 17048421, 25086100, 164203, "SRX684687", "SRS687803", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75055, null, 0.10258, null, 0.83952, null, 0.49914, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38142, "SRR1555578", "SRX684686", "SRS687804", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0086", "GSM1483821", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 10536765, 7377251, 7701105, 11014088, 142946, "SRX684686", "SRS687804", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.745, null, 0.08312, null, 0.88209, null, 0.52632, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38143, "SRR1555577", "SRX684685", "SRS687802", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0085", "GSM1483820", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 41238155, 28228882, 28727190, 43901346, 186077, "SRX684685", "SRS687802", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.80695, null, 0.14045, null, 0.80361, null, 0.5, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38144, "SRR1555576", "SRX684684", "SRS687800", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0084", "GSM1483819", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 42100013, 30125860, 31767504, 43391728, 204190, "SRX684684", "SRS687800", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.80373, null, 0.08661, null, 0.83157, null, 0.51923, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38145, "SRR1555575", "SRX684683", "SRS687801", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0083", "GSM1483818", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 42533757, 29874233, 30500611, 44132167, 203217, "SRX684683", "SRS687801", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.80738, null, 0.08642, null, 0.82219, null, 0.49396, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38146, "SRR1555574", "SRX684682", "SRS687799", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0082", "GSM1483817", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 26768730, 19578598, 21713242, 28549716, 137449, "SRX684682", "SRS687799", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.80738, null, 0.09417, null, 0.85167, null, 0.50713, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38147, "SRR1555573", "SRX684681", "SRS687798", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0081", "GSM1483816", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 46939694, 31610300, 32050592, 47571349, 230960, "SRX684681", "SRS687798", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.78709, null, 0.11916, null, 0.82351, null, 0.48714, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38148, "SRR1555572", "SRX684680", "SRS687797", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0080", "GSM1483815", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 422951, 297837, 308257, 400778, 2552, "SRX684680", "SRS687797", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.7103, null, 0.12471, null, 0.9811, null, 0.57619, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38149, "SRR1555571", "SRX684679", "SRS687796", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0079", "GSM1483814", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 49235964, 34067309, 35846095, 52553397, 234875, "SRX684679", "SRS687796", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.79389, null, 0.14252, null, 0.81107, null, 0.50474, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38150, "SRR1555570", "SRX684678", "SRS687795", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0078", "GSM1483813", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 63723749, 43666354, 45504302, 67009596, 342949, "SRX684678", "SRS687795", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.80813, null, 0.1512, null, 0.80174, null, 0.49937, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38151, "SRR1555569", "SRX684677", "SRS687794", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0077", "GSM1483812", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 27102533, 18314712, 18498218, 29006764, 216448, "SRX684677", "SRS687794", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75818, null, 0.11499, null, 0.81572, null, 0.50169, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38152, "SRR1555568", "SRX684676", "SRS687793", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0076", "GSM1483811", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 33806370, 23395934, 24547522, 36374942, 387647, "SRX684676", "SRS687793", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75326, null, 0.1088, null, 0.81667, null, 0.49341, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38153, "SRR1555567", "SRX684675", "SRS687792", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0075", "GSM1483810", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 818327, 420638, 441967, 833315, 6278, "SRX684675", "SRS687792", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.7119, null, 0.22445, null, 0.97368, null, 0.51561, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38154, "SRR1555566", "SRX684674", "SRS687791", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0074", "GSM1483809", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 27032549, 18681500, 19490852, 29708978, 471831, "SRX684674", "SRS687791", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75216, null, 0.09004, null, 0.83469, null, 0.48768, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38155, "SRR1555565", "SRX684673", "SRS687790", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0073", "GSM1483808", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 42991931, 29913953, 30117935, 45803552, 338464, "SRX684673", "SRS687790", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.76488, null, 0.10545, null, 0.80586, null, 0.5046, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38156, "SRR1555564", "SRX684672", "SRS687789", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0072", "GSM1483807", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 61171233, 40047517, 44515900, 57461403, 633622, "SRX684672", "SRS687789", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.65225, null, 0.10254, null, 0.82014, null, 0.50437, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38157, "SRR1555563", "SRX684671", "SRS687788", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0071", "GSM1483806", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 30475809, 22092085, 22685204, 32400616, 240646, "SRX684671", "SRS687788", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.77637, null, 0.10375, null, 0.81574, null, 0.50918, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38158, "SRR1555562", "SRX684670", "SRS687787", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0070", "GSM1483805", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 29014067, 20865233, 21656956, 30738746, 500818, "SRX684670", "SRS687787", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.7643, null, 0.09535, null, 0.8325, null, 0.51201, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38159, "SRR1555561", "SRX684669", "SRS687786", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0069", "GSM1483804", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 51610621, 35847602, 36898756, 54275519, 249947, "SRX684669", "SRS687786", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.81481, null, 0.1212, null, 0.80338, null, 0.48647, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38160, "SRR1555560", "SRX684668", "SRS687784", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0068", "GSM1483803", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 85968202, 57218562, 58533597, 87797178, 407236, "SRX684668", "SRS687784", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.78411, null, 0.12015, null, 0.80736, null, 0.5018, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38161, "SRR1555559", "SRX684667", "SRS687785", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0067", "GSM1483802", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 3757539, 2504848, 2608725, 3830804, 15439, "SRX684667", "SRS687785", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.77835, null, 0.12605, null, 0.92604, null, 0.45926, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38162, "SRR1555558", "SRX684666", "SRS687783", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0066", "GSM1483801", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 1490985, 1039675, 1088231, 1579040, 8109, "SRX684666", "SRS687783", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.77355, null, 0.11605, null, 0.96587, null, 0.48121, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38163, "SRR1555557", "SRX684665", "SRS687782", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0065", "GSM1483800", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 13699613, 9907599, 10751987, 15115154, 69267, "SRX684665", "SRS687782", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.81049, null, 0.12615, null, 0.86367, null, 0.51632, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38164, "SRR1555556", "SRX684664", "SRS687781", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0064", "GSM1483799", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 70332996, 49278360, 54252598, 73390003, 347243, "SRX684664", "SRS687781", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.80448, null, 0.14935, null, 0.80975, null, 0.54749, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38165, "SRR1555555", "SRX684663", "SRS687779", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0063", "GSM1483798", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 39999821, 27945450, 29190975, 42159133, 179516, "SRX684663", "SRS687779", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.80752, null, 0.14329, null, 0.81645, null, 0.50673, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38166, "SRR1555554", "SRX684662", "SRS687780", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0062", "GSM1483797", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 50196021, 35043121, 37861516, 53732194, 262878, "SRX684662", "SRS687780", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.81092, null, 0.13179, null, 0.8199, null, 0.49636, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38167, "SRR1555553", "SRX684661", "SRS687778", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0061", "GSM1483796", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 33678050, 23425078, 24368870, 35496994, 293818, "SRX684661", "SRS687778", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.71242, null, 0.11354, null, 0.83514, null, 0.51134, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38168, "SRR1555552", "SRX684660", "SRS687777", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0060", "GSM1483795", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 14629070, 9936986, 10066758, 15611930, 240481, "SRX684660", "SRS687777", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.74045, null, 0.14214, null, 0.84703, null, 0.50639, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38169, "SRR1555551", "SRX684659", "SRS687776", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0059", "GSM1483794", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 37661404, 25258511, 25987964, 39941302, 261724, "SRX684659", "SRS687776", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.74152, null, 0.13117, null, 0.81749, null, 0.51022, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38170, "SRR1555550", "SRX684658", "SRS687775", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0058", "GSM1483793", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 26231450, 17984688, 18624952, 28210031, 462924, "SRX684658", "SRS687775", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75933, null, 0.13326, null, 0.8294, null, 0.50639, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38171, "SRR1555549", "SRX684657", "SRS687774", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0057", "GSM1483792", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 73169774, 51240668, 52956333, 76957748, 619782, "SRX684657", "SRS687774", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75832, null, 0.11669, null, 0.80937, null, 0.50798, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38172, "SRR1555548", "SRX684656", "SRS687773", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0056", "GSM1483791", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 28266891, 20096113, 20730721, 29621152, 461823, "SRX684656", "SRS687773", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75342, null, 0.1218, null, 0.82982, null, 0.52199, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38173, "SRR1555547", "SRX684655", "SRS687772", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0055", "GSM1483790", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 43591040, 30002113, 30975524, 46254070, 304733, "SRX684655", "SRS687772", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75764, null, 0.12465, null, 0.81249, null, 0.51762, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38174, "SRR1555546", "SRX684654", "SRS687771", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0054", "GSM1483789", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 19683826, 13807471, 14484211, 20733707, 350580, "SRX684654", "SRS687771", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.68459, null, 0.10792, null, 0.85865, null, 0.53677, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38175, "SRR1555545", "SRX684653", "SRS687770", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0053", "GSM1483788", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 53654936, 37894425, 41404133, 58136035, 279901, "SRX684653", "SRS687770", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.80463, null, 0.1324, null, 0.81489, null, 0.49, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38176, "SRR1555544", "SRX684652", "SRS687768", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0052", "GSM1483787", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 63312652, 41647031, 43302090, 66999251, 303906, "SRX684652", "SRS687768", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.79312, null, 0.14581, null, 0.80748, null, 0.4943, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38177, "SRR1555543", "SRX684651", "SRS687769", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0051", "GSM1483786", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 85354255, 55749822, 57830877, 91385535, 417231, "SRX684651", "SRS687769", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.79714, null, 0.14915, null, 0.80351, null, 0.48212, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38178, "SRR1555542", "SRX684650", "SRS687767", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0050", "GSM1483785", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 36640576, 24900786, 26610416, 39561545, 172512, "SRX684650", "SRS687767", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.80166, null, 0.14944, null, 0.81122, null, 0.46057, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38179, "SRR1555541", "SRX684649", "SRS687766", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0049", "GSM1483784", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 82273862, 55791356, 60225084, 90004597, 437321, "SRX684649", "SRS687766", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.80699, null, 0.14603, null, 0.80119, null, 0.50186, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38180, "SRR1555540", "SRX684648", "SRS687765", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0048", "GSM1483783", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 20988018, 14353166, 14709018, 21808886, 170422, "SRX684648", "SRS687765", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.7657, null, 0.12723, null, 0.82903, null, 0.51174, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38181, "SRR1555539", "SRX684647", "SRS687764", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0047", "GSM1483782", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 19374753, 13653921, 14376686, 20519427, 214963, "SRX684647", "SRS687764", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75951, null, 0.09929, null, 0.84372, null, 0.49457, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38182, "SRR1555538", "SRX684646", "SRS687763", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0046", "GSM1483781", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 22006761, 15565401, 16227173, 23236147, 173223, "SRX684646", "SRS687763", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.78187, null, 0.11068, null, 0.82408, null, 0.50229, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38183, "SRR1555537", "SRX684645", "SRS687762", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0045", "GSM1483780", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 39174780, 27210755, 28507642, 41999686, 690177, "SRX684645", "SRS687762", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75598, null, 0.12311, null, 0.81682, null, 0.5009, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38184, "SRR1555536", "SRX684644", "SRS687761", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0044", "GSM1483779", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 50342468, 34071199, 35445470, 53307736, 429907, "SRX684644", "SRS687761", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75753, null, 0.11777, null, 0.81055, null, 0.49526, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38185, "SRR1555535", "SRX684643", "SRS687760", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0043", "GSM1483778", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 24985086, 17224343, 17613830, 26349902, 429194, "SRX684643", "SRS687760", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75503, null, 0.11846, null, 0.82706, null, 0.50298, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38186, "SRR1555534", "SRX684642", "SRS687759", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0042", "GSM1483777", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 55128132, 36753131, 38260811, 58386915, 388306, "SRX684642", "SRS687759", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75676, null, 0.12061, null, 0.80442, null, 0.5035, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38187, "SRR1555533", "SRX684641", "SRS687758", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0041", "GSM1483776", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 28559457, 19637558, 20746011, 30190358, 508431, "SRX684641", "SRS687758", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.76108, null, 0.11637, null, 0.82751, null, 0.5096, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38188, "SRR1555532", "SRX684640", "SRS687757", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0040", "GSM1483775", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 19905778, 13336991, 13569868, 19599979, 88224, "SRX684640", "SRS687757", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.79612, null, 0.14476, null, 0.84421, null, 0.51356, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38189, "SRR1555531", "SRX684639", "SRS687756", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0039", "GSM1483774", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 26896148, 18075620, 18949224, 27276263, 125235, "SRX684639", "SRS687756", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.80286, null, 0.15016, null, 0.83195, null, 0.52775, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38190, "SRR1555530", "SRX684638", "SRS687755", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0038", "GSM1483773", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 30262327, 20264495, 20848086, 30389349, 138488, "SRX684638", "SRS687755", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.79914, null, 0.14724, null, 0.83047, null, 0.51145, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38191, "SRR1555529", "SRX684637", "SRS687754", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0037", "GSM1483772", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 23902634, 16036242, 17201817, 24155587, 120370, "SRX684637", "SRS687754", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.78827, null, 0.18587, null, 0.84674, null, 0.44219, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38192, "SRR1555528", "SRX684636", "SRS687752", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0036", "GSM1483771", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 22267492, 15517952, 15279496, 22807339, 99036, "SRX684636", "SRS687752", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.74377, null, 0.14648, null, 0.84348, null, 0.53283, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38193, "SRR1555527", "SRX684635", "SRS687753", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0035", "GSM1483770", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 402051, 272276, 287822, 429952, 2229, "SRX684635", "SRS687753", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.74877, null, 0.12157, null, 0.98646, null, 0.52724, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38194, "SRR1555526", "SRX684634", "SRS687751", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0034", "GSM1483769", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 10142602, 6989087, 7392583, 10442983, 47900, "SRX684634", "SRS687751", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.80122, null, 0.12241, null, 0.88402, null, 0.53072, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38195, "SRR1555525", "SRX684633", "SRS687749", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0033", "GSM1483768", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 17788769, 12319707, 13858738, 18933772, 89739, "SRX684633", "SRS687749", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.80408, null, 0.14198, null, 0.85802, null, 0.51504, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38196, "SRR1555524", "SRX684632", "SRS687750", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0032", "GSM1483767", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 15726201, 10988676, 11393651, 16764103, 171099, "SRX684632", "SRS687750", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75627, null, 0.11178, null, 0.84187, null, 0.51424, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38197, "SRR1555523", "SRX684631", "SRS687748", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0031", "GSM1483766", null, "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", null, "RNA was isolated using TRIzol as previously described 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", null, "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", null, "SRP045679", null, null, "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, null, null, null, 32037252, 22024337, 23195973, 34219811, 352352, "SRX684631", "SRS687748", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.76499, null, 0.1174, null, 0.81931, null, 0.48818, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38198, "SRR1555522", "SRX684630", "SRS687746", "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 \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0030", "GSM1483765", null, "tissue:single embryo", "Metazome ZF timecourse sample 0030", "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", null, "RNA was isolated using TRIzol as previously described 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:1200", "GSM1483765", "GSM1483765: Metazome ZF timecourse sample 0030; Danio rerio; RNA Seq", "GSM1483765", null, "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:GSM1483765", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0030.fastq.gz", "fastq", 84687400.0, 2419640.0, "GSM1483765 r1", "0:35", "A:24536411;C:16814066;G:17686889;T:25482053;N:167981", 35, null, null, null, 24536411, 16814066, 17686889, 25482053, 167981, "SRX684630", "SRS687746", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75435, null, 0.12963, null, 0.8324, null, 0.50593, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38199, "SRR1555521", "SRX684629", "SRS687747", "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 \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0029", "GSM1483764", null, "tissue:single embryo", "Metazome ZF timecourse sample 0029", "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", null, "RNA was isolated using TRIzol as previously described 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:1160", "GSM1483764", "GSM1483764: Metazome ZF timecourse sample 0029; Danio rerio; RNA Seq", "GSM1483764", null, "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:GSM1483764", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0029.fastq.gz", "fastq", 50860390.0, 1453154.0, "GSM1483764 r1", "0:35", "A:14144967;C:10007963;G:10985572;T:15526449;N:195439", 35, null, null, null, 14144967, 10007963, 10985572, 15526449, 195439, "SRX684629", "SRS687747", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75525, null, 0.10789, null, 0.85622, null, 0.50316, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38200, "SRR1555520", "SRX684628", "SRS687745", "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 \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0028", "GSM1483763", null, "tissue:single embryo", "Metazome ZF timecourse sample 0028", "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", null, "RNA was isolated using TRIzol as previously described 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:1120", "GSM1483763", "GSM1483763: Metazome ZF timecourse sample 0028; Danio rerio; RNA Seq", "GSM1483763", null, "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:GSM1483763", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0028.fastq.gz", "fastq", 57701210.0, 1648606.0, "GSM1483763 r1", "0:35", "A:16640840;C:11312049;G:11835693;T:17776215;N:136413", 35, null, null, null, 16640840, 11312049, 11835693, 17776215, 136413, "SRX684628", "SRS687745", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.76575, null, 0.12571, null, 0.83782, null, 0.5033, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38201, "SRR1555519", "SRX684627", "SRS687744", "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 \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0027", "GSM1483762", null, "tissue:single embryo", "Metazome ZF timecourse sample 0027", "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", null, "RNA was isolated using TRIzol as previously described 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:1080", "GSM1483762", "GSM1483762: Metazome ZF timecourse sample 0027; Danio rerio; RNA Seq", "GSM1483762", null, "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:GSM1483762", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0027.fastq.gz", "fastq", 91053760.0, 2601536.0, "GSM1483762 r1", "0:35", "A:26661426;C:17590689;G:18376834;T:28126871;N:297940", 35, null, null, null, 26661426, 17590689, 18376834, 28126871, 297940, "SRX684627", "SRS687744", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.74007, null, 0.12423, null, 0.82935, null, 0.5148, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38202, "SRR1555518", "SRX684626", "SRS687743", "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 \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0026", "GSM1483761", null, "tissue:single embryo", "Metazome ZF timecourse sample 0026", "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", null, "RNA was isolated using TRIzol as previously described 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:1040", "GSM1483761", "GSM1483761: Metazome ZF timecourse sample 0026; Danio rerio; RNA Seq", "GSM1483761", null, "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:GSM1483761", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0026.fastq.gz", "fastq", 87302040.0, 2494344.0, "GSM1483761 r1", "0:35", "A:24959745;C:16874893;G:18128821;T:27123743;N:214838", 35, null, null, null, 24959745, 16874893, 18128821, 27123743, 214838, "SRX684626", "SRS687743", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.74837, null, 0.12743, null, 0.83629, null, 0.50606, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38203, "SRR1555517", "SRX684625", "SRS687742", "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 \u201cphylotypic stage\u201d 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 \u2018zootypic\u2019 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", null, "Metazome ZF timecourse sample 0025", "GSM1483760", null, "tissue:single embryo", "Metazome ZF timecourse sample 0025", "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", null, "RNA was isolated using TRIzol as previously described 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:1000", "GSM1483760", "GSM1483760: Metazome ZF timecourse sample 0025; Danio rerio; RNA Seq", "GSM1483760", null, "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:GSM1483760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0025.fastq.gz", "fastq", 57471750.0, 1642050.0, "GSM1483760 r1", "0:35", "A:16365571;C:11318721;G:11982274;T:17500837;N:304347", 35, null, null, null, 16365571, 11318721, 11982274, 17500837, 304347, "SRX684625", "SRS687742", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.7636, null, 0.10031, null, 0.8507, null, 0.50098, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 277, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", 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tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"devstage_curation\" = :p0 and \"experiment.library_layout\" = :p1 order by rowid limit 101", "params": {"p0": "Zygote", "p1": "SINGLE"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Zygote&experiment.library_layout=SINGLE", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 229, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Zygote&experiment.library_layout=SINGLE&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "OTHER", "label": "OTHER", "count": 20, "toggle_url": 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