rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse 38122,SRR1555598,SRX684706,SRS687823,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0106,GSM1483841,,tissue:single embryo,Metazome ZF timecourse sample 0106,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:4240,GSM1483841,GSM1483841: Metazome ZF timecourse sample 0106; Danio rerio; RNA Seq,GSM1483841,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483841,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0106.fastq.gz,fastq,3911705.0,111763.0,GSM1483841 r1,0:35,A:1100064;C:790487;G:836206;T:1169251;N:15697,35,,,,1100064,790487,836206,1169251,15697,SRX684706,SRS687823,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.72414,,0.09461,,0.96725,,0.4942,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38123,SRR1555597,SRX684705,SRS687821,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0105,GSM1483840,,tissue:single embryo,Metazome ZF timecourse sample 0105,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:4200,GSM1483840,GSM1483840: Metazome ZF timecourse sample 0105; Danio rerio; RNA Seq,GSM1483840,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483840,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0105.fastq.gz,fastq,32877145.0,939347.0,GSM1483840 r1,0:35,A:9524894;C:6625944;G:6696548;T:9953576;N:76183,35,,,,9524894,6625944,6696548,9953576,76183,SRX684705,SRS687821,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.74436,,0.07095,,0.88201,,0.47612,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38124,SRR1555596,SRX684704,SRS687822,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0104,GSM1483839,,tissue:single embryo,Metazome ZF timecourse sample 0104,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:4160,GSM1483839,GSM1483839: Metazome ZF timecourse sample 0104; Danio rerio; RNA Seq,GSM1483839,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483839,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0104.fastq.gz,fastq,83810020.0,2394572.0,GSM1483839 r1,0:35,A:24075610;C:16799998;G:16694424;T:25967423;N:272565,35,,,,24075610,16799998,16694424,25967423,272565,SRX684704,SRS687822,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.7588,,0.07993,,0.84449,,0.49785,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38125,SRR1555595,SRX684703,SRS687820,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0103,GSM1483838,,tissue:single embryo,Metazome ZF timecourse sample 0103,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:4120,GSM1483838,GSM1483838: Metazome ZF timecourse sample 0103; Danio rerio; RNA Seq,GSM1483838,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483838,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0103.fastq.gz,fastq,98206150.0,2805890.0,GSM1483838 r1,0:35,A:28361916;C:19232789;G:19589483;T:30798968;N:222994,35,,,,28361916,19232789,19589483,30798968,222994,SRX684703,SRS687820,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75509,,0.13429,,0.81117,,0.49102,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38126,SRR1555594,SRX684702,SRS687819,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0102,GSM1483837,,tissue:single embryo,Metazome ZF timecourse sample 0102,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:4080,GSM1483837,GSM1483837: Metazome ZF timecourse sample 0102; Danio rerio; RNA Seq,GSM1483837,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483837,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0102.fastq.gz,fastq,192817835.0,5509081.0,GSM1483837 r1,0:35,A:55969077;C:36880901;G:37835921;T:61101558;N:1030378,35,,,,55969077,36880901,37835921,61101558,1030378,SRX684702,SRS687819,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.73387,,0.17245,,0.80164,,0.48657,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38127,SRR1555593,SRX684701,SRS687818,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0101,GSM1483836,,tissue:single embryo,Metazome ZF timecourse sample 0101,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:4040,GSM1483836,GSM1483836: Metazome ZF timecourse sample 0101; Danio rerio; RNA Seq,GSM1483836,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483836,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0101.fastq.gz,fastq,374339455.0,10695413.0,GSM1483836 r1,0:35,A:112191846;C:73679996;G:73185024;T:114766825;N:515764,35,,,,112191846,73679996,73185024,114766825,515764,SRX684701,SRS687818,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.83131,,0.16618,,0.77812,,0.49895,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38128,SRR1555592,SRX684700,SRS687816,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0100,GSM1483835,,tissue:single embryo,Metazome ZF timecourse sample 0100,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:4000,GSM1483835,GSM1483835: Metazome ZF timecourse sample 0100; Danio rerio; RNA Seq,GSM1483835,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483835,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0100.fastq.gz,fastq,15239420.0,435412.0,GSM1483835 r1,0:35,A:4361241;C:3088134;G:3269084;T:4498093;N:22868,35,,,,4361241,3088134,3269084,4498093,22868,SRX684700,SRS687816,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.7702,,0.17879,,0.92904,,0.505,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38129,SRR1555591,SRX684699,SRS687817,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0099,GSM1483834,,tissue:single embryo,Metazome ZF timecourse sample 0099,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3960,GSM1483834,GSM1483834: Metazome ZF timecourse sample 0099; Danio rerio; RNA Seq,GSM1483834,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483834,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0099.fastq.gz,fastq,284196500.0,8119900.0,GSM1483834 r1,0:35,A:81991733;C:57440756;G:58362818;T:86010858;N:390335,35,,,,81991733,57440756,58362818,86010858,390335,SRX684699,SRS687817,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.81284,,0.1715,,0.78468,,0.49472,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38130,SRR1555590,SRX684698,SRS687815,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0098,GSM1483833,,tissue:single embryo,Metazome ZF timecourse sample 0098,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3920,GSM1483833,GSM1483833: Metazome ZF timecourse sample 0098; Danio rerio; RNA Seq,GSM1483833,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483833,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0098.fastq.gz,fastq,244245015.0,6978429.0,GSM1483833 r1,0:35,A:70141725;C:48500061;G:50748992;T:74478239;N:375998,35,,,,70141725,48500061,50748992,74478239,375998,SRX684698,SRS687815,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.79668,,0.17718,,0.79271,,0.45966,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38131,SRR1555589,SRX684697,SRS687814,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0097,GSM1483832,,tissue:single embryo,Metazome ZF timecourse sample 0097,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3880,GSM1483832,GSM1483832: Metazome ZF timecourse sample 0097; Danio rerio; RNA Seq,GSM1483832,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483832,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0097.fastq.gz,fastq,215347510.0,6152786.0,GSM1483832 r1,0:35,A:62928172;C:42420829;G:43902946;T:65803342;N:292221,35,,,,62928172,42420829,43902946,65803342,292221,SRX684697,SRS687814,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80605,,0.17396,,0.78873,,0.50241,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38132,SRR1555588,SRX684696,SRS687813,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0096,GSM1483831,,tissue:single embryo,Metazome ZF timecourse sample 0096,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3840,GSM1483831,GSM1483831: Metazome ZF timecourse sample 0096; Danio rerio; RNA Seq,GSM1483831,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483831,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0096.fastq.gz,fastq,13992230.0,399778.0,GSM1483831 r1,0:35,A:4077402;C:2837417;G:2856511;T:4200750;N:20150,35,,,,4077402,2837417,2856511,4200750,20150,SRX684696,SRS687813,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.77543,,0.14778,,0.93288,,0.48967,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38133,SRR1555587,SRX684695,SRS687811,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0095,GSM1483830,,tissue:single embryo,Metazome ZF timecourse sample 0095,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3800,GSM1483830,GSM1483830: Metazome ZF timecourse sample 0095; Danio rerio; RNA Seq,GSM1483830,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483830,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0095.fastq.gz,fastq,290151435.0,8290041.0,GSM1483830 r1,0:35,A:86694666;C:56953853;G:57315219;T:88811589;N:376108,35,,,,86694666,56953853,57315219,88811589,376108,SRX684695,SRS687811,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.79098,,0.18155,,0.79034,,0.51338,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38134,SRR1555586,SRX684694,SRS687810,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0094,GSM1483829,,tissue:single embryo,Metazome ZF timecourse sample 0094,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3760,GSM1483829,GSM1483829: Metazome ZF timecourse sample 0094; Danio rerio; RNA Seq,GSM1483829,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483829,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0094.fastq.gz,fastq,645422925.0,18440655.0,GSM1483829 r1,0:35,A:186408265;C:127218686;G:131406509;T:199399112;N:990353,35,,,,186408265,127218686,131406509,199399112,990353,SRX684694,SRS687810,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.81184,,0.15572,,0.78496,,0.48733,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38135,SRR1555585,SRX684693,SRS687812,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0093,GSM1483828,,tissue:single embryo,Metazome ZF timecourse sample 0093,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3720,GSM1483828,GSM1483828: Metazome ZF timecourse sample 0093; Danio rerio; RNA Seq,GSM1483828,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483828,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0093.fastq.gz,fastq,82574205.0,2359263.0,GSM1483828 r1,0:35,A:24239984;C:16625180;G:16309055;T:25123568;N:276418,35,,,,24239984,16625180,16309055,25123568,276418,SRX684693,SRS687812,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75557,,0.14554,,0.82205,,0.49736,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38136,SRR1555584,SRX684692,SRS687809,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0092,GSM1483827,,tissue:single embryo,Metazome ZF timecourse sample 0092,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3680,GSM1483827,GSM1483827: Metazome ZF timecourse sample 0092; Danio rerio; RNA Seq,GSM1483827,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483827,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0092.fastq.gz,fastq,72186905.0,2062483.0,GSM1483827 r1,0:35,A:21349438;C:14361391;G:14472348;T:21766197;N:237531,35,,,,21349438,14361391,14472348,21766197,237531,SRX684692,SRS687809,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.74348,,0.13614,,0.8309,,0.51328,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38137,SRR1555583,SRX684691,SRS687808,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0091,GSM1483826,,tissue:single embryo,Metazome ZF timecourse sample 0091,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3640,GSM1483826,GSM1483826: Metazome ZF timecourse sample 0091; Danio rerio; RNA Seq,GSM1483826,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483826,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0091.fastq.gz,fastq,18405940.0,525884.0,GSM1483826 r1,0:35,A:5374937;C:3766785;G:3774551;T:5451369;N:38298,35,,,,5374937,3766785,3774551,5451369,38298,SRX684691,SRS687808,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.74005,,0.11089,,0.91494,,0.49823,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38138,SRR1555582,SRX684690,SRS687807,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0090,GSM1483825,,tissue:single embryo,Metazome ZF timecourse sample 0090,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3600,GSM1483825,GSM1483825: Metazome ZF timecourse sample 0090; Danio rerio; RNA Seq,GSM1483825,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483825,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0090.fastq.gz,fastq,141938265.0,4055379.0,GSM1483825 r1,0:35,A:41371650;C:28115945;G:29356068;T:42485478;N:609124,35,,,,41371650,28115945,29356068,42485478,609124,SRX684690,SRS687807,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.71151,,0.17711,,0.82789,,0.52369,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38139,SRR1555581,SRX684689,SRS687806,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0089,GSM1483824,,tissue:single embryo,Metazome ZF timecourse sample 0089,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3560,GSM1483824,GSM1483824: Metazome ZF timecourse sample 0089; Danio rerio; RNA Seq,GSM1483824,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483824,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0089.fastq.gz,fastq,99569015.0,2844829.0,GSM1483824 r1,0:35,A:28763571;C:20065085;G:19332839;T:31088193;N:319327,35,,,,28763571,20065085,19332839,31088193,319327,SRX684689,SRS687806,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.74177,,0.13103,,0.81854,,0.51184,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38140,SRR1555580,SRX684688,SRS687805,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0088,GSM1483823,,tissue:single embryo,Metazome ZF timecourse sample 0088,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3520,GSM1483823,GSM1483823: Metazome ZF timecourse sample 0088; Danio rerio; RNA Seq,GSM1483823,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483823,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0088.fastq.gz,fastq,168790055.0,4822573.0,GSM1483823 r1,0:35,A:49034449;C:32785565;G:33439918;T:52997820;N:532303,35,,,,49034449,32785565,33439918,52997820,532303,SRX684688,SRS687805,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.73454,,0.15775,,0.8047,,0.50587,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38141,SRR1555579,SRX684687,SRS687803,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0087,GSM1483822,,tissue:single embryo,Metazome ZF timecourse sample 0087,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3480,GSM1483822,GSM1483822: Metazome ZF timecourse sample 0087; Danio rerio; RNA Seq,GSM1483822,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483822,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0087.fastq.gz,fastq,83155975.0,2375885.0,GSM1483822 r1,0:35,A:23985678;C:16871573;G:17048421;T:25086100;N:164203,35,,,,23985678,16871573,17048421,25086100,164203,SRX684687,SRS687803,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75055,,0.10258,,0.83952,,0.49914,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38142,SRR1555578,SRX684686,SRS687804,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0086,GSM1483821,,tissue:single embryo,Metazome ZF timecourse sample 0086,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3440,GSM1483821,GSM1483821: Metazome ZF timecourse sample 0086; Danio rerio; RNA Seq,GSM1483821,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483821,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0086.fastq.gz,fastq,36772155.0,1050633.0,GSM1483821 r1,0:35,A:10536765;C:7377251;G:7701105;T:11014088;N:142946,35,,,,10536765,7377251,7701105,11014088,142946,SRX684686,SRS687804,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.745,,0.08312,,0.88209,,0.52632,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38143,SRR1555577,SRX684685,SRS687802,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0085,GSM1483820,,tissue:single embryo,Metazome ZF timecourse sample 0085,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3400,GSM1483820,GSM1483820: Metazome ZF timecourse sample 0085; Danio rerio; RNA Seq,GSM1483820,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483820,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0085.fastq.gz,fastq,142281650.0,4065190.0,GSM1483820 r1,0:35,A:41238155;C:28228882;G:28727190;T:43901346;N:186077,35,,,,41238155,28228882,28727190,43901346,186077,SRX684685,SRS687802,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80695,,0.14045,,0.80361,,0.5,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38144,SRR1555576,SRX684684,SRS687800,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0084,GSM1483819,,tissue:single embryo,Metazome ZF timecourse sample 0084,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3360,GSM1483819,GSM1483819: Metazome ZF timecourse sample 0084; Danio rerio; RNA Seq,GSM1483819,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483819,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0084.fastq.gz,fastq,147589295.0,4216837.0,GSM1483819 r1,0:35,A:42100013;C:30125860;G:31767504;T:43391728;N:204190,35,,,,42100013,30125860,31767504,43391728,204190,SRX684684,SRS687800,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80373,,0.08661,,0.83157,,0.51923,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38145,SRR1555575,SRX684683,SRS687801,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0083,GSM1483818,,tissue:single embryo,Metazome ZF timecourse sample 0083,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3320,GSM1483818,GSM1483818: Metazome ZF timecourse sample 0083; Danio rerio; RNA Seq,GSM1483818,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483818,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0083.fastq.gz,fastq,147243985.0,4206971.0,GSM1483818 r1,0:35,A:42533757;C:29874233;G:30500611;T:44132167;N:203217,35,,,,42533757,29874233,30500611,44132167,203217,SRX684683,SRS687801,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80738,,0.08642,,0.82219,,0.49396,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38146,SRR1555574,SRX684682,SRS687799,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0082,GSM1483817,,tissue:single embryo,Metazome ZF timecourse sample 0082,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3280,GSM1483817,GSM1483817: Metazome ZF timecourse sample 0082; Danio rerio; RNA Seq,GSM1483817,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483817,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0082.fastq.gz,fastq,96747735.0,2764221.0,GSM1483817 r1,0:35,A:26768730;C:19578598;G:21713242;T:28549716;N:137449,35,,,,26768730,19578598,21713242,28549716,137449,SRX684682,SRS687799,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80738,,0.09417,,0.85167,,0.50713,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38147,SRR1555573,SRX684681,SRS687798,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0081,GSM1483816,,tissue:single embryo,Metazome ZF timecourse sample 0081,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3240,GSM1483816,GSM1483816: Metazome ZF timecourse sample 0081; Danio rerio; RNA Seq,GSM1483816,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483816,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0081.fastq.gz,fastq,158402895.0,4525797.0,GSM1483816 r1,0:35,A:46939694;C:31610300;G:32050592;T:47571349;N:230960,35,,,,46939694,31610300,32050592,47571349,230960,SRX684681,SRS687798,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.78709,,0.11916,,0.82351,,0.48714,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38148,SRR1555572,SRX684680,SRS687797,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0080,GSM1483815,,tissue:single embryo,Metazome ZF timecourse sample 0080,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3200,GSM1483815,GSM1483815: Metazome ZF timecourse sample 0080; Danio rerio; RNA Seq,GSM1483815,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483815,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0080.fastq.gz,fastq,1432375.0,40925.0,GSM1483815 r1,0:35,A:422951;C:297837;G:308257;T:400778;N:2552,35,,,,422951,297837,308257,400778,2552,SRX684680,SRS687797,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.7103,,0.12471,,0.9811,,0.57619,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38149,SRR1555571,SRX684679,SRS687796,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0079,GSM1483814,,tissue:single embryo,Metazome ZF timecourse sample 0079,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3160,GSM1483814,GSM1483814: Metazome ZF timecourse sample 0079; Danio rerio; RNA Seq,GSM1483814,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483814,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0079.fastq.gz,fastq,171937640.0,4912504.0,GSM1483814 r1,0:35,A:49235964;C:34067309;G:35846095;T:52553397;N:234875,35,,,,49235964,34067309,35846095,52553397,234875,SRX684679,SRS687796,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.79389,,0.14252,,0.81107,,0.50474,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38150,SRR1555570,SRX684678,SRS687795,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0078,GSM1483813,,tissue:single embryo,Metazome ZF timecourse sample 0078,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3120,GSM1483813,GSM1483813: Metazome ZF timecourse sample 0078; Danio rerio; RNA Seq,GSM1483813,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483813,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0078.fastq.gz,fastq,220246950.0,6292770.0,GSM1483813 r1,0:35,A:63723749;C:43666354;G:45504302;T:67009596;N:342949,35,,,,63723749,43666354,45504302,67009596,342949,SRX684678,SRS687795,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80813,,0.1512,,0.80174,,0.49937,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38151,SRR1555569,SRX684677,SRS687794,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0077,GSM1483812,,tissue:single embryo,Metazome ZF timecourse sample 0077,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3080,GSM1483812,GSM1483812: Metazome ZF timecourse sample 0077; Danio rerio; RNA Seq,GSM1483812,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483812,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0077.fastq.gz,fastq,93138675.0,2661105.0,GSM1483812 r1,0:35,A:27102533;C:18314712;G:18498218;T:29006764;N:216448,35,,,,27102533,18314712,18498218,29006764,216448,SRX684677,SRS687794,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75818,,0.11499,,0.81572,,0.50169,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38152,SRR1555568,SRX684676,SRS687793,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0076,GSM1483811,,tissue:single embryo,Metazome ZF timecourse sample 0076,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3040,GSM1483811,GSM1483811: Metazome ZF timecourse sample 0076; Danio rerio; RNA Seq,GSM1483811,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483811,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0076.fastq.gz,fastq,118512415.0,3386069.0,GSM1483811 r1,0:35,A:33806370;C:23395934;G:24547522;T:36374942;N:387647,35,,,,33806370,23395934,24547522,36374942,387647,SRX684676,SRS687793,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75326,,0.1088,,0.81667,,0.49341,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38153,SRR1555567,SRX684675,SRS687792,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0075,GSM1483810,,tissue:single embryo,Metazome ZF timecourse sample 0075,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:3000,GSM1483810,GSM1483810: Metazome ZF timecourse sample 0075; Danio rerio; RNA Seq,GSM1483810,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483810,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0075.fastq.gz,fastq,2520525.0,72015.0,GSM1483810 r1,0:35,A:818327;C:420638;G:441967;T:833315;N:6278,35,,,,818327,420638,441967,833315,6278,SRX684675,SRS687792,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.7119,,0.22445,,0.97368,,0.51561,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38154,SRR1555566,SRX684674,SRS687791,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0074,GSM1483809,,tissue:single embryo,Metazome ZF timecourse sample 0074,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2960,GSM1483809,GSM1483809: Metazome ZF timecourse sample 0074; Danio rerio; RNA Seq,GSM1483809,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483809,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0074.fastq.gz,fastq,95385710.0,2725306.0,GSM1483809 r1,0:35,A:27032549;C:18681500;G:19490852;T:29708978;N:471831,35,,,,27032549,18681500,19490852,29708978,471831,SRX684674,SRS687791,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75216,,0.09004,,0.83469,,0.48768,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38155,SRR1555565,SRX684673,SRS687790,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0073,GSM1483808,,tissue:single embryo,Metazome ZF timecourse sample 0073,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2920,GSM1483808,GSM1483808: Metazome ZF timecourse sample 0073; Danio rerio; RNA Seq,GSM1483808,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483808,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0073.fastq.gz,fastq,149165835.0,4261881.0,GSM1483808 r1,0:35,A:42991931;C:29913953;G:30117935;T:45803552;N:338464,35,,,,42991931,29913953,30117935,45803552,338464,SRX684673,SRS687790,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.76488,,0.10545,,0.80586,,0.5046,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38156,SRR1555564,SRX684672,SRS687789,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0072,GSM1483807,,tissue:single embryo,Metazome ZF timecourse sample 0072,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2880,GSM1483807,GSM1483807: Metazome ZF timecourse sample 0072; Danio rerio; RNA Seq,GSM1483807,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483807,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0072.fastq.gz,fastq,203829675.0,5823705.0,GSM1483807 r1,0:35,A:61171233;C:40047517;G:44515900;T:57461403;N:633622,35,,,,61171233,40047517,44515900,57461403,633622,SRX684672,SRS687789,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.65225,,0.10254,,0.82014,,0.50437,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38157,SRR1555563,SRX684671,SRS687788,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0071,GSM1483806,,tissue:single embryo,Metazome ZF timecourse sample 0071,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2840,GSM1483806,GSM1483806: Metazome ZF timecourse sample 0071; Danio rerio; RNA Seq,GSM1483806,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483806,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0071.fastq.gz,fastq,107894360.0,3082696.0,GSM1483806 r1,0:35,A:30475809;C:22092085;G:22685204;T:32400616;N:240646,35,,,,30475809,22092085,22685204,32400616,240646,SRX684671,SRS687788,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.77637,,0.10375,,0.81574,,0.50918,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38158,SRR1555562,SRX684670,SRS687787,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0070,GSM1483805,,tissue:single embryo,Metazome ZF timecourse sample 0070,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2800,GSM1483805,GSM1483805: Metazome ZF timecourse sample 0070; Danio rerio; RNA Seq,GSM1483805,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483805,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0070.fastq.gz,fastq,102775820.0,2936452.0,GSM1483805 r1,0:35,A:29014067;C:20865233;G:21656956;T:30738746;N:500818,35,,,,29014067,20865233,21656956,30738746,500818,SRX684670,SRS687787,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.7643,,0.09535,,0.8325,,0.51201,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38159,SRR1555561,SRX684669,SRS687786,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0069,GSM1483804,,tissue:single embryo,Metazome ZF timecourse sample 0069,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2760,GSM1483804,GSM1483804: Metazome ZF timecourse sample 0069; Danio rerio; RNA Seq,GSM1483804,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483804,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0069.fastq.gz,fastq,178882445.0,5110927.0,GSM1483804 r1,0:35,A:51610621;C:35847602;G:36898756;T:54275519;N:249947,35,,,,51610621,35847602,36898756,54275519,249947,SRX684669,SRS687786,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.81481,,0.1212,,0.80338,,0.48647,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38160,SRR1555560,SRX684668,SRS687784,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0068,GSM1483803,,tissue:single embryo,Metazome ZF timecourse sample 0068,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2720,GSM1483803,GSM1483803: Metazome ZF timecourse sample 0068; Danio rerio; RNA Seq,GSM1483803,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483803,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0068.fastq.gz,fastq,289924775.0,8283565.0,GSM1483803 r1,0:35,A:85968202;C:57218562;G:58533597;T:87797178;N:407236,35,,,,85968202,57218562,58533597,87797178,407236,SRX684668,SRS687784,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.78411,,0.12015,,0.80736,,0.5018,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38161,SRR1555559,SRX684667,SRS687785,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0067,GSM1483802,,tissue:single embryo,Metazome ZF timecourse sample 0067,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2680,GSM1483802,GSM1483802: Metazome ZF timecourse sample 0067; Danio rerio; RNA Seq,GSM1483802,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483802,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0067.fastq.gz,fastq,12717355.0,363353.0,GSM1483802 r1,0:35,A:3757539;C:2504848;G:2608725;T:3830804;N:15439,35,,,,3757539,2504848,2608725,3830804,15439,SRX684667,SRS687785,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.77835,,0.12605,,0.92604,,0.45926,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38162,SRR1555558,SRX684666,SRS687783,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0066,GSM1483801,,tissue:single embryo,Metazome ZF timecourse sample 0066,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2640,GSM1483801,GSM1483801: Metazome ZF timecourse sample 0066; Danio rerio; RNA Seq,GSM1483801,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483801,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0066.fastq.gz,fastq,5206040.0,148744.0,GSM1483801 r1,0:35,A:1490985;C:1039675;G:1088231;T:1579040;N:8109,35,,,,1490985,1039675,1088231,1579040,8109,SRX684666,SRS687783,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.77355,,0.11605,,0.96587,,0.48121,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38163,SRR1555557,SRX684665,SRS687782,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0065,GSM1483800,,tissue:single embryo,Metazome ZF timecourse sample 0065,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2600,GSM1483800,GSM1483800: Metazome ZF timecourse sample 0065; Danio rerio; RNA Seq,GSM1483800,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483800,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0065.fastq.gz,fastq,49543620.0,1415532.0,GSM1483800 r1,0:35,A:13699613;C:9907599;G:10751987;T:15115154;N:69267,35,,,,13699613,9907599,10751987,15115154,69267,SRX684665,SRS687782,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.81049,,0.12615,,0.86367,,0.51632,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38164,SRR1555556,SRX684664,SRS687781,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0064,GSM1483799,,tissue:single embryo,Metazome ZF timecourse sample 0064,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2560,GSM1483799,GSM1483799: Metazome ZF timecourse sample 0064; Danio rerio; RNA Seq,GSM1483799,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483799,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0064.fastq.gz,fastq,247601200.0,7074320.0,GSM1483799 r1,0:35,A:70332996;C:49278360;G:54252598;T:73390003;N:347243,35,,,,70332996,49278360,54252598,73390003,347243,SRX684664,SRS687781,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80448,,0.14935,,0.80975,,0.54749,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38165,SRR1555555,SRX684663,SRS687779,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0063,GSM1483798,,tissue:single embryo,Metazome ZF timecourse sample 0063,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2520,GSM1483798,GSM1483798: Metazome ZF timecourse sample 0063; Danio rerio; RNA Seq,GSM1483798,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483798,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0063.fastq.gz,fastq,139474895.0,3984997.0,GSM1483798 r1,0:35,A:39999821;C:27945450;G:29190975;T:42159133;N:179516,35,,,,39999821,27945450,29190975,42159133,179516,SRX684663,SRS687779,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80752,,0.14329,,0.81645,,0.50673,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38166,SRR1555554,SRX684662,SRS687780,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0062,GSM1483797,,tissue:single embryo,Metazome ZF timecourse sample 0062,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2480,GSM1483797,GSM1483797: Metazome ZF timecourse sample 0062; Danio rerio; RNA Seq,GSM1483797,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483797,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0062.fastq.gz,fastq,177095730.0,5059878.0,GSM1483797 r1,0:35,A:50196021;C:35043121;G:37861516;T:53732194;N:262878,35,,,,50196021,35043121,37861516,53732194,262878,SRX684662,SRS687780,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.81092,,0.13179,,0.8199,,0.49636,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38167,SRR1555553,SRX684661,SRS687778,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0061,GSM1483796,,tissue:single embryo,Metazome ZF timecourse sample 0061,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2440,GSM1483796,GSM1483796: Metazome ZF timecourse sample 0061; Danio rerio; RNA Seq,GSM1483796,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483796,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0061.fastq.gz,fastq,117262810.0,3350366.0,GSM1483796 r1,0:35,A:33678050;C:23425078;G:24368870;T:35496994;N:293818,35,,,,33678050,23425078,24368870,35496994,293818,SRX684661,SRS687778,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.71242,,0.11354,,0.83514,,0.51134,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38168,SRR1555552,SRX684660,SRS687777,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0060,GSM1483795,,tissue:single embryo,Metazome ZF timecourse sample 0060,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2400,GSM1483795,GSM1483795: Metazome ZF timecourse sample 0060; Danio rerio; RNA Seq,GSM1483795,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483795,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0060.fastq.gz,fastq,50485225.0,1442435.0,GSM1483795 r1,0:35,A:14629070;C:9936986;G:10066758;T:15611930;N:240481,35,,,,14629070,9936986,10066758,15611930,240481,SRX684660,SRS687777,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.74045,,0.14214,,0.84703,,0.50639,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38169,SRR1555551,SRX684659,SRS687776,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0059,GSM1483794,,tissue:single embryo,Metazome ZF timecourse sample 0059,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2360,GSM1483794,GSM1483794: Metazome ZF timecourse sample 0059; Danio rerio; RNA Seq,GSM1483794,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483794,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0059.fastq.gz,fastq,129110905.0,3688883.0,GSM1483794 r1,0:35,A:37661404;C:25258511;G:25987964;T:39941302;N:261724,35,,,,37661404,25258511,25987964,39941302,261724,SRX684659,SRS687776,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.74152,,0.13117,,0.81749,,0.51022,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38170,SRR1555550,SRX684658,SRS687775,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0058,GSM1483793,,tissue:single embryo,Metazome ZF timecourse sample 0058,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2320,GSM1483793,GSM1483793: Metazome ZF timecourse sample 0058; Danio rerio; RNA Seq,GSM1483793,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483793,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0058.fastq.gz,fastq,91514045.0,2614687.0,GSM1483793 r1,0:35,A:26231450;C:17984688;G:18624952;T:28210031;N:462924,35,,,,26231450,17984688,18624952,28210031,462924,SRX684658,SRS687775,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75933,,0.13326,,0.8294,,0.50639,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38171,SRR1555549,SRX684657,SRS687774,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0057,GSM1483792,,tissue:single embryo,Metazome ZF timecourse sample 0057,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2280,GSM1483792,GSM1483792: Metazome ZF timecourse sample 0057; Danio rerio; RNA Seq,GSM1483792,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483792,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0057.fastq.gz,fastq,254944305.0,7284123.0,GSM1483792 r1,0:35,A:73169774;C:51240668;G:52956333;T:76957748;N:619782,35,,,,73169774,51240668,52956333,76957748,619782,SRX684657,SRS687774,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75832,,0.11669,,0.80937,,0.50798,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38172,SRR1555548,SRX684656,SRS687773,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0056,GSM1483791,,tissue:single embryo,Metazome ZF timecourse sample 0056,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2240,GSM1483791,GSM1483791: Metazome ZF timecourse sample 0056; Danio rerio; RNA Seq,GSM1483791,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483791,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0056.fastq.gz,fastq,99176700.0,2833620.0,GSM1483791 r1,0:35,A:28266891;C:20096113;G:20730721;T:29621152;N:461823,35,,,,28266891,20096113,20730721,29621152,461823,SRX684656,SRS687773,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75342,,0.1218,,0.82982,,0.52199,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38173,SRR1555547,SRX684655,SRS687772,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0055,GSM1483790,,tissue:single embryo,Metazome ZF timecourse sample 0055,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2200,GSM1483790,GSM1483790: Metazome ZF timecourse sample 0055; Danio rerio; RNA Seq,GSM1483790,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483790,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0055.fastq.gz,fastq,151127480.0,4317928.0,GSM1483790 r1,0:35,A:43591040;C:30002113;G:30975524;T:46254070;N:304733,35,,,,43591040,30002113,30975524,46254070,304733,SRX684655,SRS687772,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75764,,0.12465,,0.81249,,0.51762,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38174,SRR1555546,SRX684654,SRS687771,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0054,GSM1483789,,tissue:single embryo,Metazome ZF timecourse sample 0054,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2160,GSM1483789,GSM1483789: Metazome ZF timecourse sample 0054; Danio rerio; RNA Seq,GSM1483789,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483789,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0054.fastq.gz,fastq,69059795.0,1973137.0,GSM1483789 r1,0:35,A:19683826;C:13807471;G:14484211;T:20733707;N:350580,35,,,,19683826,13807471,14484211,20733707,350580,SRX684654,SRS687771,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.68459,,0.10792,,0.85865,,0.53677,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38175,SRR1555545,SRX684653,SRS687770,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0053,GSM1483788,,tissue:single embryo,Metazome ZF timecourse sample 0053,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2120,GSM1483788,GSM1483788: Metazome ZF timecourse sample 0053; Danio rerio; RNA Seq,GSM1483788,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483788,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0053.fastq.gz,fastq,191369430.0,5467698.0,GSM1483788 r1,0:35,A:53654936;C:37894425;G:41404133;T:58136035;N:279901,35,,,,53654936,37894425,41404133,58136035,279901,SRX684653,SRS687770,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80463,,0.1324,,0.81489,,0.49,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38176,SRR1555544,SRX684652,SRS687768,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0052,GSM1483787,,tissue:single embryo,Metazome ZF timecourse sample 0052,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2080,GSM1483787,GSM1483787: Metazome ZF timecourse sample 0052; Danio rerio; RNA Seq,GSM1483787,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483787,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0052.fastq.gz,fastq,215564930.0,6158998.0,GSM1483787 r1,0:35,A:63312652;C:41647031;G:43302090;T:66999251;N:303906,35,,,,63312652,41647031,43302090,66999251,303906,SRX684652,SRS687768,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.79312,,0.14581,,0.80748,,0.4943,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38177,SRR1555543,SRX684651,SRS687769,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0051,GSM1483786,,tissue:single embryo,Metazome ZF timecourse sample 0051,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2040,GSM1483786,GSM1483786: Metazome ZF timecourse sample 0051; Danio rerio; RNA Seq,GSM1483786,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483786,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0051.fastq.gz,fastq,290737720.0,8306792.0,GSM1483786 r1,0:35,A:85354255;C:55749822;G:57830877;T:91385535;N:417231,35,,,,85354255,55749822,57830877,91385535,417231,SRX684651,SRS687769,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.79714,,0.14915,,0.80351,,0.48212,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38178,SRR1555542,SRX684650,SRS687767,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0050,GSM1483785,,tissue:single embryo,Metazome ZF timecourse sample 0050,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:2000,GSM1483785,GSM1483785: Metazome ZF timecourse sample 0050; Danio rerio; RNA Seq,GSM1483785,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483785,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0050.fastq.gz,fastq,127885835.0,3653881.0,GSM1483785 r1,0:35,A:36640576;C:24900786;G:26610416;T:39561545;N:172512,35,,,,36640576,24900786,26610416,39561545,172512,SRX684650,SRS687767,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80166,,0.14944,,0.81122,,0.46057,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38179,SRR1555541,SRX684649,SRS687766,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0049,GSM1483784,,tissue:single embryo,Metazome ZF timecourse sample 0049,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1960,GSM1483784,GSM1483784: Metazome ZF timecourse sample 0049; Danio rerio; RNA Seq,GSM1483784,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483784,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0049.fastq.gz,fastq,288732220.0,8249492.0,GSM1483784 r1,0:35,A:82273862;C:55791356;G:60225084;T:90004597;N:437321,35,,,,82273862,55791356,60225084,90004597,437321,SRX684649,SRS687766,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80699,,0.14603,,0.80119,,0.50186,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38180,SRR1555540,SRX684648,SRS687765,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0048,GSM1483783,,tissue:single embryo,Metazome ZF timecourse sample 0048,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1920,GSM1483783,GSM1483783: Metazome ZF timecourse sample 0048; Danio rerio; RNA Seq,GSM1483783,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483783,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0048.fastq.gz,fastq,72029510.0,2057986.0,GSM1483783 r1,0:35,A:20988018;C:14353166;G:14709018;T:21808886;N:170422,35,,,,20988018,14353166,14709018,21808886,170422,SRX684648,SRS687765,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.7657,,0.12723,,0.82903,,0.51174,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38181,SRR1555539,SRX684647,SRS687764,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0047,GSM1483782,,tissue:single embryo,Metazome ZF timecourse sample 0047,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1880,GSM1483782,GSM1483782: Metazome ZF timecourse sample 0047; Danio rerio; RNA Seq,GSM1483782,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483782,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0047.fastq.gz,fastq,68139750.0,1946850.0,GSM1483782 r1,0:35,A:19374753;C:13653921;G:14376686;T:20519427;N:214963,35,,,,19374753,13653921,14376686,20519427,214963,SRX684647,SRS687764,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75951,,0.09929,,0.84372,,0.49457,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38182,SRR1555538,SRX684646,SRS687763,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0046,GSM1483781,,tissue:single embryo,Metazome ZF timecourse sample 0046,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1840,GSM1483781,GSM1483781: Metazome ZF timecourse sample 0046; Danio rerio; RNA Seq,GSM1483781,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483781,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0046.fastq.gz,fastq,77208705.0,2205963.0,GSM1483781 r1,0:35,A:22006761;C:15565401;G:16227173;T:23236147;N:173223,35,,,,22006761,15565401,16227173,23236147,173223,SRX684646,SRS687763,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.78187,,0.11068,,0.82408,,0.50229,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38183,SRR1555537,SRX684645,SRS687762,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0045,GSM1483780,,tissue:single embryo,Metazome ZF timecourse sample 0045,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1800,GSM1483780,GSM1483780: Metazome ZF timecourse sample 0045; Danio rerio; RNA Seq,GSM1483780,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483780,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0045.fastq.gz,fastq,137583040.0,3930944.0,GSM1483780 r1,0:35,A:39174780;C:27210755;G:28507642;T:41999686;N:690177,35,,,,39174780,27210755,28507642,41999686,690177,SRX684645,SRS687762,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75598,,0.12311,,0.81682,,0.5009,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38184,SRR1555536,SRX684644,SRS687761,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0044,GSM1483779,,tissue:single embryo,Metazome ZF timecourse sample 0044,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1760,GSM1483779,GSM1483779: Metazome ZF timecourse sample 0044; Danio rerio; RNA Seq,GSM1483779,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483779,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0044.fastq.gz,fastq,173596780.0,4959908.0,GSM1483779 r1,0:35,A:50342468;C:34071199;G:35445470;T:53307736;N:429907,35,,,,50342468,34071199,35445470,53307736,429907,SRX684644,SRS687761,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75753,,0.11777,,0.81055,,0.49526,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38185,SRR1555535,SRX684643,SRS687760,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0043,GSM1483778,,tissue:single embryo,Metazome ZF timecourse sample 0043,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1720,GSM1483778,GSM1483778: Metazome ZF timecourse sample 0043; Danio rerio; RNA Seq,GSM1483778,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483778,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0043.fastq.gz,fastq,86602355.0,2474353.0,GSM1483778 r1,0:35,A:24985086;C:17224343;G:17613830;T:26349902;N:429194,35,,,,24985086,17224343,17613830,26349902,429194,SRX684643,SRS687760,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75503,,0.11846,,0.82706,,0.50298,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38186,SRR1555534,SRX684642,SRS687759,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0042,GSM1483777,,tissue:single embryo,Metazome ZF timecourse sample 0042,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1680,GSM1483777,GSM1483777: Metazome ZF timecourse sample 0042; Danio rerio; RNA Seq,GSM1483777,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483777,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0042.fastq.gz,fastq,188917295.0,5397637.0,GSM1483777 r1,0:35,A:55128132;C:36753131;G:38260811;T:58386915;N:388306,35,,,,55128132,36753131,38260811,58386915,388306,SRX684642,SRS687759,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75676,,0.12061,,0.80442,,0.5035,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38187,SRR1555533,SRX684641,SRS687758,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0041,GSM1483776,,tissue:single embryo,Metazome ZF timecourse sample 0041,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1640,GSM1483776,GSM1483776: Metazome ZF timecourse sample 0041; Danio rerio; RNA Seq,GSM1483776,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483776,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0041.fastq.gz,fastq,99641815.0,2846909.0,GSM1483776 r1,0:35,A:28559457;C:19637558;G:20746011;T:30190358;N:508431,35,,,,28559457,19637558,20746011,30190358,508431,SRX684641,SRS687758,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.76108,,0.11637,,0.82751,,0.5096,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38188,SRR1555532,SRX684640,SRS687757,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0040,GSM1483775,,tissue:single embryo,Metazome ZF timecourse sample 0040,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1600,GSM1483775,GSM1483775: Metazome ZF timecourse sample 0040; Danio rerio; RNA Seq,GSM1483775,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483775,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0040.fastq.gz,fastq,66500840.0,1900024.0,GSM1483775 r1,0:35,A:19905778;C:13336991;G:13569868;T:19599979;N:88224,35,,,,19905778,13336991,13569868,19599979,88224,SRX684640,SRS687757,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.79612,,0.14476,,0.84421,,0.51356,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38189,SRR1555531,SRX684639,SRS687756,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0039,GSM1483774,,tissue:single embryo,Metazome ZF timecourse sample 0039,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1560,GSM1483774,GSM1483774: Metazome ZF timecourse sample 0039; Danio rerio; RNA Seq,GSM1483774,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483774,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0039.fastq.gz,fastq,91322490.0,2609214.0,GSM1483774 r1,0:35,A:26896148;C:18075620;G:18949224;T:27276263;N:125235,35,,,,26896148,18075620,18949224,27276263,125235,SRX684639,SRS687756,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80286,,0.15016,,0.83195,,0.52775,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38190,SRR1555530,SRX684638,SRS687755,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0038,GSM1483773,,tissue:single embryo,Metazome ZF timecourse sample 0038,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1520,GSM1483773,GSM1483773: Metazome ZF timecourse sample 0038; Danio rerio; RNA Seq,GSM1483773,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483773,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0038.fastq.gz,fastq,101902745.0,2911507.0,GSM1483773 r1,0:35,A:30262327;C:20264495;G:20848086;T:30389349;N:138488,35,,,,30262327,20264495,20848086,30389349,138488,SRX684638,SRS687755,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.79914,,0.14724,,0.83047,,0.51145,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38191,SRR1555529,SRX684637,SRS687754,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0037,GSM1483772,,tissue:single embryo,Metazome ZF timecourse sample 0037,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1480,GSM1483772,GSM1483772: Metazome ZF timecourse sample 0037; Danio rerio; RNA Seq,GSM1483772,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483772,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0037.fastq.gz,fastq,81416650.0,2326190.0,GSM1483772 r1,0:35,A:23902634;C:16036242;G:17201817;T:24155587;N:120370,35,,,,23902634,16036242,17201817,24155587,120370,SRX684637,SRS687754,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.78827,,0.18587,,0.84674,,0.44219,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38192,SRR1555528,SRX684636,SRS687752,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0036,GSM1483771,,tissue:single embryo,Metazome ZF timecourse sample 0036,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1440,GSM1483771,GSM1483771: Metazome ZF timecourse sample 0036; Danio rerio; RNA Seq,GSM1483771,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483771,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0036.fastq.gz,fastq,75971315.0,2170609.0,GSM1483771 r1,0:35,A:22267492;C:15517952;G:15279496;T:22807339;N:99036,35,,,,22267492,15517952,15279496,22807339,99036,SRX684636,SRS687752,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.74377,,0.14648,,0.84348,,0.53283,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38193,SRR1555527,SRX684635,SRS687753,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0035,GSM1483770,,tissue:single embryo,Metazome ZF timecourse sample 0035,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1400,GSM1483770,GSM1483770: Metazome ZF timecourse sample 0035; Danio rerio; RNA Seq,GSM1483770,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483770,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0035.fastq.gz,fastq,1394330.0,39838.0,GSM1483770 r1,0:35,A:402051;C:272276;G:287822;T:429952;N:2229,35,,,,402051,272276,287822,429952,2229,SRX684635,SRS687753,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.74877,,0.12157,,0.98646,,0.52724,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38194,SRR1555526,SRX684634,SRS687751,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0034,GSM1483769,,tissue:single embryo,Metazome ZF timecourse sample 0034,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1360,GSM1483769,GSM1483769: Metazome ZF timecourse sample 0034; Danio rerio; RNA Seq,GSM1483769,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483769,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0034.fastq.gz,fastq,35015155.0,1000433.0,GSM1483769 r1,0:35,A:10142602;C:6989087;G:7392583;T:10442983;N:47900,35,,,,10142602,6989087,7392583,10442983,47900,SRX684634,SRS687751,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80122,,0.12241,,0.88402,,0.53072,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38195,SRR1555525,SRX684633,SRS687749,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0033,GSM1483768,,tissue:single embryo,Metazome ZF timecourse sample 0033,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1320,GSM1483768,GSM1483768: Metazome ZF timecourse sample 0033; Danio rerio; RNA Seq,GSM1483768,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483768,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0033.fastq.gz,fastq,62990725.0,1799735.0,GSM1483768 r1,0:35,A:17788769;C:12319707;G:13858738;T:18933772;N:89739,35,,,,17788769,12319707,13858738,18933772,89739,SRX684633,SRS687749,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80408,,0.14198,,0.85802,,0.51504,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38196,SRR1555524,SRX684632,SRS687750,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0032,GSM1483767,,tissue:single embryo,Metazome ZF timecourse sample 0032,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1280,GSM1483767,GSM1483767: Metazome ZF timecourse sample 0032; Danio rerio; RNA Seq,GSM1483767,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483767,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0032.fastq.gz,fastq,55043730.0,1572678.0,GSM1483767 r1,0:35,A:15726201;C:10988676;G:11393651;T:16764103;N:171099,35,,,,15726201,10988676,11393651,16764103,171099,SRX684632,SRS687750,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75627,,0.11178,,0.84187,,0.51424,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38197,SRR1555523,SRX684631,SRS687748,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0031,GSM1483766,,tissue:single embryo,Metazome ZF timecourse sample 0031,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:1240,GSM1483766,GSM1483766: Metazome ZF timecourse sample 0031; Danio rerio; RNA Seq,GSM1483766,,1,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,GEO Accession:GSM1483766,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0031.fastq.gz,fastq,111829725.0,3195135.0,GSM1483766 r1,0:35,A:32037252;C:22024337;G:23195973;T:34219811;N:352352,35,,,,32037252,22024337,23195973,34219811,352352,SRX684631,SRS687748,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.76499,,0.1174,,0.81931,,0.48818,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 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 “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0030,GSM1483765,,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,,RNA was isolated using TRIzol as previously described 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,,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,,SRP045679,,,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,,,,24536411,16814066,17686889,25482053,167981,SRX684630,SRS687746,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75435,,0.12963,,0.8324,,0.50593,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 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 “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0029,GSM1483764,,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,,RNA was isolated using TRIzol as previously described 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,,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,,SRP045679,,,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,,,,14144967,10007963,10985572,15526449,195439,SRX684629,SRS687747,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75525,,0.10789,,0.85622,,0.50316,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 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 “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0028,GSM1483763,,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,,RNA was isolated using TRIzol as previously described 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,,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,,SRP045679,,,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,,,,16640840,11312049,11835693,17776215,136413,SRX684628,SRS687745,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.76575,,0.12571,,0.83782,,0.5033,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 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 “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0027,GSM1483762,,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,,RNA was isolated using TRIzol as previously described 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,,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,,SRP045679,,,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,,,,26661426,17590689,18376834,28126871,297940,SRX684627,SRS687744,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.74007,,0.12423,,0.82935,,0.5148,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 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 “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0026,GSM1483761,,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,,RNA was isolated using TRIzol as previously described 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,,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,,SRP045679,,,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,,,,24959745,16874893,18128821,27123743,214838,SRX684626,SRS687743,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.74837,,0.12743,,0.83629,,0.50606,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 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 “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0025,GSM1483760,,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,,RNA was isolated using TRIzol as previously described 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,,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,,SRP045679,,,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,,,,16365571,11318721,11982274,17500837,304347,SRX684625,SRS687742,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.7636,,0.10031,,0.8507,,0.50098,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38204,SRR1555516,SRX684624,SRS687740,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0024,GSM1483759,,tissue:single embryo,Metazome ZF timecourse sample 0024,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:960,GSM1483759,GSM1483759: Metazome ZF timecourse sample 0024; Danio rerio; RNA Seq,GSM1483759,,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:GSM1483759,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0024.fastq.gz,fastq,85229060.0,2435116.0,GSM1483759 r1,0:35,A:24772925;C:16237353;G:16951106;T:27150797;N:116879,35,,,,24772925,16237353,16951106,27150797,116879,SRX684624,SRS687740,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80982,,0.1365,,0.8267,,0.5058,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38205,SRR1555515,SRX684623,SRS687741,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0023,GSM1483758,,tissue:single embryo,Metazome ZF timecourse sample 0023,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:920,GSM1483758,GSM1483758: Metazome ZF timecourse sample 0023; Danio rerio; RNA Seq,GSM1483758,,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:GSM1483758,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0023.fastq.gz,fastq,142493540.0,4071244.0,GSM1483758 r1,0:35,A:40601651;C:27501645;G:29719105;T:44467787;N:203352,35,,,,40601651,27501645,29719105,44467787,203352,SRX684623,SRS687741,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80616,,0.14305,,0.8213,,0.50924,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38206,SRR1555514,SRX684622,SRS687739,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0022,GSM1483757,,tissue:single embryo,Metazome ZF timecourse sample 0022,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:880,GSM1483757,GSM1483757: Metazome ZF timecourse sample 0022; Danio rerio; RNA Seq,GSM1483757,,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:GSM1483757,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0022.fastq.gz,fastq,56908320.0,1625952.0,GSM1483757 r1,0:35,A:15947917;C:11183121;G:11892006;T:17808919;N:76357,35,,,,15947917,11183121,11892006,17808919,76357,SRX684622,SRS687739,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.79224,,0.11615,,0.8561,,0.53437,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38207,SRR1555513,SRX684621,SRS687738,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0021,GSM1483756,,tissue:single embryo,Metazome ZF timecourse sample 0021,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:840,GSM1483756,GSM1483756: Metazome ZF timecourse sample 0021; Danio rerio; RNA Seq,GSM1483756,,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:GSM1483756,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0021.fastq.gz,fastq,24820950.0,709170.0,GSM1483756 r1,0:35,A:6713198;C:5063656;G:5459533;T:7546929;N:37634,35,,,,6713198,5063656,5459533,7546929,37634,SRX684621,SRS687738,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80904,,0.11316,,0.91762,,0.493,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38208,SRR1555512,SRX684620,SRS687737,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0020,GSM1483755,,tissue:single embryo,Metazome ZF timecourse sample 0020,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:800,GSM1483755,GSM1483755: Metazome ZF timecourse sample 0020; Danio rerio; RNA Seq,GSM1483755,,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:GSM1483755,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0020.fastq.gz,fastq,91343595.0,2609817.0,GSM1483755 r1,0:35,A:26206685;C:17802768;G:18482030;T:28730304;N:121808,35,,,,26206685,17802768,18482030,28730304,121808,SRX684620,SRS687737,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.81263,,0.11485,,0.83899,,0.52677,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38209,SRR1555511,SRX684619,SRS687736,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0019,GSM1483754,,tissue:single embryo,Metazome ZF timecourse sample 0019,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:760,GSM1483754,GSM1483754: Metazome ZF timecourse sample 0019; Danio rerio; RNA Seq,GSM1483754,,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:GSM1483754,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0019.fastq.gz,fastq,123260620.0,3521732.0,GSM1483754 r1,0:35,A:39401890;C:23075568;G:28389719;T:32221055;N:172388,35,,,,39401890,23075568,28389719,32221055,172388,SRX684619,SRS687736,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.58686,,0.09367,,0.85967,,0.51208,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38210,SRR1555510,SRX684618,SRS687735,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0018,GSM1483753,,tissue:single embryo,Metazome ZF timecourse sample 0018,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:720,GSM1483753,GSM1483753: Metazome ZF timecourse sample 0018; Danio rerio; RNA Seq,GSM1483753,,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:GSM1483753,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0018.fastq.gz,fastq,57966300.0,1656180.0,GSM1483753 r1,0:35,A:16492529;C:11304199;G:12109180;T:17982776;N:77616,35,,,,16492529,11304199,12109180,17982776,77616,SRX684618,SRS687735,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80616,,0.13361,,0.84912,,0.53137,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38211,SRR1555509,SRX684617,SRS687734,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0017,GSM1483752,,tissue:single embryo,Metazome ZF timecourse sample 0017,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:680,GSM1483752,GSM1483752: Metazome ZF timecourse sample 0017; Danio rerio; RNA Seq,GSM1483752,,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:GSM1483752,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0017.fastq.gz,fastq,132147295.0,3775637.0,GSM1483752 r1,0:35,A:36915214;C:25410425;G:28192958;T:41426664;N:202034,35,,,,36915214,25410425,28192958,41426664,202034,SRX684617,SRS687734,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.80857,,0.14396,,0.83692,,0.57958,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38212,SRR1555508,SRX684616,SRS687733,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0016,GSM1483751,,tissue:single embryo,Metazome ZF timecourse sample 0016,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:640,GSM1483751,GSM1483751: Metazome ZF timecourse sample 0016; Danio rerio; RNA Seq,GSM1483751,,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:GSM1483751,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0016.fastq.gz,fastq,32937275.0,941065.0,GSM1483751 r1,0:35,A:9312299;C:6391562;G:6744242;T:10414715;N:74457,35,,,,9312299,6391562,6744242,10414715,74457,SRX684616,SRS687733,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75923,,0.1172,,0.8686,,0.50849,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38213,SRR1555507,SRX684615,SRS687732,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0015,GSM1483750,,tissue:single embryo,Metazome ZF timecourse sample 0015,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:600,GSM1483750,GSM1483750: Metazome ZF timecourse sample 0015; Danio rerio; RNA Seq,GSM1483750,,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:GSM1483750,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0015.fastq.gz,fastq,64502620.0,1842932.0,GSM1483750 r1,0:35,A:19049723;C:12084471;G:12633732;T:20428159;N:306535,35,,,,19049723,12084471,12633732,20428159,306535,SRX684615,SRS687732,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.71007,,0.12094,,0.85251,,0.52468,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38214,SRR1555506,SRX684614,SRS687731,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0014,GSM1483749,,tissue:single embryo,Metazome ZF timecourse sample 0014,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:560,GSM1483749,GSM1483749: Metazome ZF timecourse sample 0014; Danio rerio; RNA Seq,GSM1483749,,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:GSM1483749,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0014.fastq.gz,fastq,10561040.0,301744.0,GSM1483749 r1,0:35,A:3044352;C:2031006;G:2160027;T:3304995;N:20660,35,,,,3044352,2031006,2160027,3304995,20660,SRX684614,SRS687731,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.69642,,0.13462,,0.92005,,0.57097,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38215,SRR1555505,SRX684613,SRS687730,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0013,GSM1483748,,tissue:single embryo,Metazome ZF timecourse sample 0013,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:520,GSM1483748,GSM1483748: Metazome ZF timecourse sample 0013; Danio rerio; RNA Seq,GSM1483748,,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:GSM1483748,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0013.fastq.gz,fastq,49145495.0,1404157.0,GSM1483748 r1,0:35,A:14056728;C:9335675;G:10026472;T:15466782;N:259838,35,,,,14056728,9335675,10026472,15466782,259838,SRX684613,SRS687730,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.75633,,0.15645,,0.85922,,0.54377,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38216,SRR1555504,SRX684612,SRS687729,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0012,GSM1483747,,tissue:single embryo,Metazome ZF timecourse sample 0012,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:480,GSM1483747,GSM1483747: Metazome ZF timecourse sample 0012; Danio rerio; RNA Seq,GSM1483747,,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:GSM1483747,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0012.fastq.gz,fastq,28826035.0,823601.0,GSM1483747 r1,0:35,A:7982688;C:5494145;G:6038827;T:9242290;N:68085,35,,,,7982688,5494145,6038827,9242290,68085,SRX684612,SRS687729,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.74394,,0.14799,,0.87574,,0.55095,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38217,SRR1555503,SRX684611,SRS687728,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0011,GSM1483746,,tissue:single embryo,Metazome ZF timecourse sample 0011,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:440,GSM1483746,GSM1483746: Metazome ZF timecourse sample 0011; Danio rerio; RNA Seq,GSM1483746,,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:GSM1483746,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0011.fastq.gz,fastq,17456880.0,498768.0,GSM1483746 r1,0:35,A:4797829;C:3387628;G:3753572;T:5439237;N:78614,35,,,,4797829,3387628,3753572,5439237,78614,SRX684611,SRS687728,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.74109,,0.14708,,0.88876,,0.58433,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38218,SRR1555502,SRX684610,SRS687727,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0010,GSM1483745,,tissue:single embryo,Metazome ZF timecourse sample 0010,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:400,GSM1483745,GSM1483745: Metazome ZF timecourse sample 0010; Danio rerio; RNA Seq,GSM1483745,,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:GSM1483745,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0010.fastq.gz,fastq,19589920.0,559712.0,GSM1483745 r1,0:35,A:5473764;C:3879069;G:4156596;T:6041022;N:39469,35,,,,5473764,3879069,4156596,6041022,39469,SRX684610,SRS687727,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.74169,,0.1527,,0.88532,,0.61597,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38219,SRR1555501,SRX684609,SRS687726,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0009,GSM1483744,,tissue:single embryo,Metazome ZF timecourse sample 0009,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:360,GSM1483744,GSM1483744: Metazome ZF timecourse sample 0009; Danio rerio; RNA Seq,GSM1483744,,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:GSM1483744,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0009.fastq.gz,fastq,15568315.0,444809.0,GSM1483744 r1,0:35,A:4372909;C:3010526;G:3254580;T:4855683;N:74617,35,,,,4372909,3010526,3254580,4855683,74617,SRX684609,SRS687726,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.73441,,0.15376,,0.89134,,0.59772,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38220,SRR1555500,SRX684608,SRS687725,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0008,GSM1483743,,tissue:single embryo,Metazome ZF timecourse sample 0008,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:320,GSM1483743,GSM1483743: Metazome ZF timecourse sample 0008; Danio rerio; RNA Seq,GSM1483743,,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:GSM1483743,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0008.fastq.gz,fastq,14135590.0,403874.0,GSM1483743 r1,0:35,A:3946109;C:2823508;G:3081822;T:4265555;N:18596,35,,,,3946109,2823508,3081822,4265555,18596,SRX684608,SRS687725,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.79663,,0.14994,,0.90964,,0.62753,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures 38221,SRR1555499,SRX684607,SRS687724,SRP045679,PRJNA258656,Danio rerio high resolution developmental transcriptomic time course,GSE60619,Transcriptome Analysis,Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples,parent bioproject:PRJNA287810,pubmed:26886793,,Metazome ZF timecourse sample 0007,GSM1483742,,tissue:single embryo,Metazome ZF timecourse sample 0007,Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix,single embryo,,RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.,zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.,time min post fertilization:280,GSM1483742,GSM1483742: Metazome ZF timecourse sample 0007; Danio rerio; RNA Seq,GSM1483742,,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:GSM1483742,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP045679,,,Metazome_ZF_timecourse_sample_0007.fastq.gz,fastq,44628115.0,1275089.0,GSM1483742 r1,0:35,A:12865499;C:8728555;G:9231806;T:13738642;N:63613,35,,,,12865499,8728555,9231806,13738642,63613,SRX684607,SRS687724,SRA179995,GEO,"Yanai, Biology, Technion - Israel Institute of Technology",1,0.78846,,0.12894,,0.85516,,0.58729,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Israel,2014-08-21,Zygote,Embryo,Embryo Imprecise,All anatomical structures