metadata: run_metadata: 106 rows where devstage_curation = "Zygote" and technology = "celseq"

106 rows where devstage_curation = "Zygote" and technology = "celseq"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	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.study_ref	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
38122	38122	SRR1555598	SRX684706	SRS687823	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0106	GSM1483841	tissue:single embryo	Metazome ZF timecourse sample 0106	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:4240	GSM1483841	GSM1483841: Metazome ZF timecourse sample 0106; Danio rerio; RNA Seq	GSM1483841	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483841	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0106.fastq.gz	fastq	3911705.0	111763.0	GSM1483841 r1	0:35	A:1100064;C:790487;G:836206;T:1169251;N:15697	35	1100064	790487	836206	1169251	15697	SRX684706	SRS687823	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.72414	0.09461	0.96725	0.4942	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38123	38123	SRR1555597	SRX684705	SRS687821	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0105	GSM1483840	tissue:single embryo	Metazome ZF timecourse sample 0105	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:4200	GSM1483840	GSM1483840: Metazome ZF timecourse sample 0105; Danio rerio; RNA Seq	GSM1483840	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483840	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0105.fastq.gz	fastq	32877145.0	939347.0	GSM1483840 r1	0:35	A:9524894;C:6625944;G:6696548;T:9953576;N:76183	35	9524894	6625944	6696548	9953576	76183	SRX684705	SRS687821	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.74436	0.07095	0.88201	0.47612	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38124	38124	SRR1555596	SRX684704	SRS687822	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0104	GSM1483839	tissue:single embryo	Metazome ZF timecourse sample 0104	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:4160	GSM1483839	GSM1483839: Metazome ZF timecourse sample 0104; Danio rerio; RNA Seq	GSM1483839	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483839	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0104.fastq.gz	fastq	83810020.0	2394572.0	GSM1483839 r1	0:35	A:24075610;C:16799998;G:16694424;T:25967423;N:272565	35	24075610	16799998	16694424	25967423	272565	SRX684704	SRS687822	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.7588	0.07993	0.84449	0.49785	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38125	38125	SRR1555595	SRX684703	SRS687820	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0103	GSM1483838	tissue:single embryo	Metazome ZF timecourse sample 0103	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:4120	GSM1483838	GSM1483838: Metazome ZF timecourse sample 0103; Danio rerio; RNA Seq	GSM1483838	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483838	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0103.fastq.gz	fastq	98206150.0	2805890.0	GSM1483838 r1	0:35	A:28361916;C:19232789;G:19589483;T:30798968;N:222994	35	28361916	19232789	19589483	30798968	222994	SRX684703	SRS687820	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.75509	0.13429	0.81117	0.49102	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38126	38126	SRR1555594	SRX684702	SRS687819	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0102	GSM1483837	tissue:single embryo	Metazome ZF timecourse sample 0102	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:4080	GSM1483837	GSM1483837: Metazome ZF timecourse sample 0102; Danio rerio; RNA Seq	GSM1483837	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483837	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0102.fastq.gz	fastq	192817835.0	5509081.0	GSM1483837 r1	0:35	A:55969077;C:36880901;G:37835921;T:61101558;N:1030378	35	55969077	36880901	37835921	61101558	1030378	SRX684702	SRS687819	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.73387	0.17245	0.80164	0.48657	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38127	38127	SRR1555593	SRX684701	SRS687818	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0101	GSM1483836	tissue:single embryo	Metazome ZF timecourse sample 0101	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:4040	GSM1483836	GSM1483836: Metazome ZF timecourse sample 0101; Danio rerio; RNA Seq	GSM1483836	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483836	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0101.fastq.gz	fastq	374339455.0	10695413.0	GSM1483836 r1	0:35	A:112191846;C:73679996;G:73185024;T:114766825;N:515764	35	112191846	73679996	73185024	114766825	515764	SRX684701	SRS687818	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.83131	0.16618	0.77812	0.49895	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38128	38128	SRR1555592	SRX684700	SRS687816	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0100	GSM1483835	tissue:single embryo	Metazome ZF timecourse sample 0100	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:4000	GSM1483835	GSM1483835: Metazome ZF timecourse sample 0100; Danio rerio; RNA Seq	GSM1483835	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483835	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0100.fastq.gz	fastq	15239420.0	435412.0	GSM1483835 r1	0:35	A:4361241;C:3088134;G:3269084;T:4498093;N:22868	35	4361241	3088134	3269084	4498093	22868	SRX684700	SRS687816	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.7702	0.17879	0.92904	0.505	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38129	38129	SRR1555591	SRX684699	SRS687817	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0099	GSM1483834	tissue:single embryo	Metazome ZF timecourse sample 0099	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3960	GSM1483834	GSM1483834: Metazome ZF timecourse sample 0099; Danio rerio; RNA Seq	GSM1483834	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483834	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0099.fastq.gz	fastq	284196500.0	8119900.0	GSM1483834 r1	0:35	A:81991733;C:57440756;G:58362818;T:86010858;N:390335	35	81991733	57440756	58362818	86010858	390335	SRX684699	SRS687817	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.81284	0.1715	0.78468	0.49472	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38130	38130	SRR1555590	SRX684698	SRS687815	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0098	GSM1483833	tissue:single embryo	Metazome ZF timecourse sample 0098	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3920	GSM1483833	GSM1483833: Metazome ZF timecourse sample 0098; Danio rerio; RNA Seq	GSM1483833	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483833	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0098.fastq.gz	fastq	244245015.0	6978429.0	GSM1483833 r1	0:35	A:70141725;C:48500061;G:50748992;T:74478239;N:375998	35	70141725	48500061	50748992	74478239	375998	SRX684698	SRS687815	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.79668	0.17718	0.79271	0.45966	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38131	38131	SRR1555589	SRX684697	SRS687814	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0097	GSM1483832	tissue:single embryo	Metazome ZF timecourse sample 0097	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3880	GSM1483832	GSM1483832: Metazome ZF timecourse sample 0097; Danio rerio; RNA Seq	GSM1483832	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483832	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0097.fastq.gz	fastq	215347510.0	6152786.0	GSM1483832 r1	0:35	A:62928172;C:42420829;G:43902946;T:65803342;N:292221	35	62928172	42420829	43902946	65803342	292221	SRX684697	SRS687814	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.80605	0.17396	0.78873	0.50241	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38132	38132	SRR1555588	SRX684696	SRS687813	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0096	GSM1483831	tissue:single embryo	Metazome ZF timecourse sample 0096	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3840	GSM1483831	GSM1483831: Metazome ZF timecourse sample 0096; Danio rerio; RNA Seq	GSM1483831	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483831	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0096.fastq.gz	fastq	13992230.0	399778.0	GSM1483831 r1	0:35	A:4077402;C:2837417;G:2856511;T:4200750;N:20150	35	4077402	2837417	2856511	4200750	20150	SRX684696	SRS687813	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.77543	0.14778	0.93288	0.48967	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38133	38133	SRR1555587	SRX684695	SRS687811	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0095	GSM1483830	tissue:single embryo	Metazome ZF timecourse sample 0095	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3800	GSM1483830	GSM1483830: Metazome ZF timecourse sample 0095; Danio rerio; RNA Seq	GSM1483830	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483830	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0095.fastq.gz	fastq	290151435.0	8290041.0	GSM1483830 r1	0:35	A:86694666;C:56953853;G:57315219;T:88811589;N:376108	35	86694666	56953853	57315219	88811589	376108	SRX684695	SRS687811	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.79098	0.18155	0.79034	0.51338	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38134	38134	SRR1555586	SRX684694	SRS687810	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0094	GSM1483829	tissue:single embryo	Metazome ZF timecourse sample 0094	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3760	GSM1483829	GSM1483829: Metazome ZF timecourse sample 0094; Danio rerio; RNA Seq	GSM1483829	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483829	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0094.fastq.gz	fastq	645422925.0	18440655.0	GSM1483829 r1	0:35	A:186408265;C:127218686;G:131406509;T:199399112;N:990353	35	186408265	127218686	131406509	199399112	990353	SRX684694	SRS687810	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.81184	0.15572	0.78496	0.48733	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38135	38135	SRR1555585	SRX684693	SRS687812	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0093	GSM1483828	tissue:single embryo	Metazome ZF timecourse sample 0093	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3720	GSM1483828	GSM1483828: Metazome ZF timecourse sample 0093; Danio rerio; RNA Seq	GSM1483828	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483828	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0093.fastq.gz	fastq	82574205.0	2359263.0	GSM1483828 r1	0:35	A:24239984;C:16625180;G:16309055;T:25123568;N:276418	35	24239984	16625180	16309055	25123568	276418	SRX684693	SRS687812	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.75557	0.14554	0.82205	0.49736	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38136	38136	SRR1555584	SRX684692	SRS687809	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0092	GSM1483827	tissue:single embryo	Metazome ZF timecourse sample 0092	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3680	GSM1483827	GSM1483827: Metazome ZF timecourse sample 0092; Danio rerio; RNA Seq	GSM1483827	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483827	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0092.fastq.gz	fastq	72186905.0	2062483.0	GSM1483827 r1	0:35	A:21349438;C:14361391;G:14472348;T:21766197;N:237531	35	21349438	14361391	14472348	21766197	237531	SRX684692	SRS687809	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.74348	0.13614	0.8309	0.51328	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38137	38137	SRR1555583	SRX684691	SRS687808	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0091	GSM1483826	tissue:single embryo	Metazome ZF timecourse sample 0091	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3640	GSM1483826	GSM1483826: Metazome ZF timecourse sample 0091; Danio rerio; RNA Seq	GSM1483826	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483826	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0091.fastq.gz	fastq	18405940.0	525884.0	GSM1483826 r1	0:35	A:5374937;C:3766785;G:3774551;T:5451369;N:38298	35	5374937	3766785	3774551	5451369	38298	SRX684691	SRS687808	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.74005	0.11089	0.91494	0.49823	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38138	38138	SRR1555582	SRX684690	SRS687807	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0090	GSM1483825	tissue:single embryo	Metazome ZF timecourse sample 0090	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3600	GSM1483825	GSM1483825: Metazome ZF timecourse sample 0090; Danio rerio; RNA Seq	GSM1483825	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483825	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0090.fastq.gz	fastq	141938265.0	4055379.0	GSM1483825 r1	0:35	A:41371650;C:28115945;G:29356068;T:42485478;N:609124	35	41371650	28115945	29356068	42485478	609124	SRX684690	SRS687807	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.71151	0.17711	0.82789	0.52369	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38139	38139	SRR1555581	SRX684689	SRS687806	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0089	GSM1483824	tissue:single embryo	Metazome ZF timecourse sample 0089	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3560	GSM1483824	GSM1483824: Metazome ZF timecourse sample 0089; Danio rerio; RNA Seq	GSM1483824	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483824	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0089.fastq.gz	fastq	99569015.0	2844829.0	GSM1483824 r1	0:35	A:28763571;C:20065085;G:19332839;T:31088193;N:319327	35	28763571	20065085	19332839	31088193	319327	SRX684689	SRS687806	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.74177	0.13103	0.81854	0.51184	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38140	38140	SRR1555580	SRX684688	SRS687805	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0088	GSM1483823	tissue:single embryo	Metazome ZF timecourse sample 0088	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3520	GSM1483823	GSM1483823: Metazome ZF timecourse sample 0088; Danio rerio; RNA Seq	GSM1483823	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483823	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0088.fastq.gz	fastq	168790055.0	4822573.0	GSM1483823 r1	0:35	A:49034449;C:32785565;G:33439918;T:52997820;N:532303	35	49034449	32785565	33439918	52997820	532303	SRX684688	SRS687805	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.73454	0.15775	0.8047	0.50587	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38141	38141	SRR1555579	SRX684687	SRS687803	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0087	GSM1483822	tissue:single embryo	Metazome ZF timecourse sample 0087	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3480	GSM1483822	GSM1483822: Metazome ZF timecourse sample 0087; Danio rerio; RNA Seq	GSM1483822	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483822	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0087.fastq.gz	fastq	83155975.0	2375885.0	GSM1483822 r1	0:35	A:23985678;C:16871573;G:17048421;T:25086100;N:164203	35	23985678	16871573	17048421	25086100	164203	SRX684687	SRS687803	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.75055	0.10258	0.83952	0.49914	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38142	38142	SRR1555578	SRX684686	SRS687804	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0086	GSM1483821	tissue:single embryo	Metazome ZF timecourse sample 0086	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3440	GSM1483821	GSM1483821: Metazome ZF timecourse sample 0086; Danio rerio; RNA Seq	GSM1483821	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483821	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0086.fastq.gz	fastq	36772155.0	1050633.0	GSM1483821 r1	0:35	A:10536765;C:7377251;G:7701105;T:11014088;N:142946	35	10536765	7377251	7701105	11014088	142946	SRX684686	SRS687804	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.745	0.08312	0.88209	0.52632	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38143	38143	SRR1555577	SRX684685	SRS687802	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0085	GSM1483820	tissue:single embryo	Metazome ZF timecourse sample 0085	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3400	GSM1483820	GSM1483820: Metazome ZF timecourse sample 0085; Danio rerio; RNA Seq	GSM1483820	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483820	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0085.fastq.gz	fastq	142281650.0	4065190.0	GSM1483820 r1	0:35	A:41238155;C:28228882;G:28727190;T:43901346;N:186077	35	41238155	28228882	28727190	43901346	186077	SRX684685	SRS687802	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.80695	0.14045	0.80361	0.5	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38144	38144	SRR1555576	SRX684684	SRS687800	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0084	GSM1483819	tissue:single embryo	Metazome ZF timecourse sample 0084	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3360	GSM1483819	GSM1483819: Metazome ZF timecourse sample 0084; Danio rerio; RNA Seq	GSM1483819	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483819	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0084.fastq.gz	fastq	147589295.0	4216837.0	GSM1483819 r1	0:35	A:42100013;C:30125860;G:31767504;T:43391728;N:204190	35	42100013	30125860	31767504	43391728	204190	SRX684684	SRS687800	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.80373	0.08661	0.83157	0.51923	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38145	38145	SRR1555575	SRX684683	SRS687801	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0083	GSM1483818	tissue:single embryo	Metazome ZF timecourse sample 0083	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3320	GSM1483818	GSM1483818: Metazome ZF timecourse sample 0083; Danio rerio; RNA Seq	GSM1483818	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483818	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0083.fastq.gz	fastq	147243985.0	4206971.0	GSM1483818 r1	0:35	A:42533757;C:29874233;G:30500611;T:44132167;N:203217	35	42533757	29874233	30500611	44132167	203217	SRX684683	SRS687801	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.80738	0.08642	0.82219	0.49396	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38146	38146	SRR1555574	SRX684682	SRS687799	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0082	GSM1483817	tissue:single embryo	Metazome ZF timecourse sample 0082	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3280	GSM1483817	GSM1483817: Metazome ZF timecourse sample 0082; Danio rerio; RNA Seq	GSM1483817	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483817	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0082.fastq.gz	fastq	96747735.0	2764221.0	GSM1483817 r1	0:35	A:26768730;C:19578598;G:21713242;T:28549716;N:137449	35	26768730	19578598	21713242	28549716	137449	SRX684682	SRS687799	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.80738	0.09417	0.85167	0.50713	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38147	38147	SRR1555573	SRX684681	SRS687798	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0081	GSM1483816	tissue:single embryo	Metazome ZF timecourse sample 0081	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3240	GSM1483816	GSM1483816: Metazome ZF timecourse sample 0081; Danio rerio; RNA Seq	GSM1483816	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483816	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0081.fastq.gz	fastq	158402895.0	4525797.0	GSM1483816 r1	0:35	A:46939694;C:31610300;G:32050592;T:47571349;N:230960	35	46939694	31610300	32050592	47571349	230960	SRX684681	SRS687798	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.78709	0.11916	0.82351	0.48714	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38148	38148	SRR1555572	SRX684680	SRS687797	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0080	GSM1483815	tissue:single embryo	Metazome ZF timecourse sample 0080	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3200	GSM1483815	GSM1483815: Metazome ZF timecourse sample 0080; Danio rerio; RNA Seq	GSM1483815	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483815	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0080.fastq.gz	fastq	1432375.0	40925.0	GSM1483815 r1	0:35	A:422951;C:297837;G:308257;T:400778;N:2552	35	422951	297837	308257	400778	2552	SRX684680	SRS687797	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.7103	0.12471	0.9811	0.57619	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38149	38149	SRR1555571	SRX684679	SRS687796	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0079	GSM1483814	tissue:single embryo	Metazome ZF timecourse sample 0079	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3160	GSM1483814	GSM1483814: Metazome ZF timecourse sample 0079; Danio rerio; RNA Seq	GSM1483814	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483814	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0079.fastq.gz	fastq	171937640.0	4912504.0	GSM1483814 r1	0:35	A:49235964;C:34067309;G:35846095;T:52553397;N:234875	35	49235964	34067309	35846095	52553397	234875	SRX684679	SRS687796	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.79389	0.14252	0.81107	0.50474	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38150	38150	SRR1555570	SRX684678	SRS687795	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0078	GSM1483813	tissue:single embryo	Metazome ZF timecourse sample 0078	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3120	GSM1483813	GSM1483813: Metazome ZF timecourse sample 0078; Danio rerio; RNA Seq	GSM1483813	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483813	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0078.fastq.gz	fastq	220246950.0	6292770.0	GSM1483813 r1	0:35	A:63723749;C:43666354;G:45504302;T:67009596;N:342949	35	63723749	43666354	45504302	67009596	342949	SRX684678	SRS687795	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.80813	0.1512	0.80174	0.49937	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38151	38151	SRR1555569	SRX684677	SRS687794	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0077	GSM1483812	tissue:single embryo	Metazome ZF timecourse sample 0077	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3080	GSM1483812	GSM1483812: Metazome ZF timecourse sample 0077; Danio rerio; RNA Seq	GSM1483812	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483812	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0077.fastq.gz	fastq	93138675.0	2661105.0	GSM1483812 r1	0:35	A:27102533;C:18314712;G:18498218;T:29006764;N:216448	35	27102533	18314712	18498218	29006764	216448	SRX684677	SRS687794	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.75818	0.11499	0.81572	0.50169	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38152	38152	SRR1555568	SRX684676	SRS687793	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0076	GSM1483811	tissue:single embryo	Metazome ZF timecourse sample 0076	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3040	GSM1483811	GSM1483811: Metazome ZF timecourse sample 0076; Danio rerio; RNA Seq	GSM1483811	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483811	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0076.fastq.gz	fastq	118512415.0	3386069.0	GSM1483811 r1	0:35	A:33806370;C:23395934;G:24547522;T:36374942;N:387647	35	33806370	23395934	24547522	36374942	387647	SRX684676	SRS687793	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.75326	0.1088	0.81667	0.49341	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38153	38153	SRR1555567	SRX684675	SRS687792	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0075	GSM1483810	tissue:single embryo	Metazome ZF timecourse sample 0075	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:3000	GSM1483810	GSM1483810: Metazome ZF timecourse sample 0075; Danio rerio; RNA Seq	GSM1483810	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483810	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0075.fastq.gz	fastq	2520525.0	72015.0	GSM1483810 r1	0:35	A:818327;C:420638;G:441967;T:833315;N:6278	35	818327	420638	441967	833315	6278	SRX684675	SRS687792	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.7119	0.22445	0.97368	0.51561	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38154	38154	SRR1555566	SRX684674	SRS687791	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0074	GSM1483809	tissue:single embryo	Metazome ZF timecourse sample 0074	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2960	GSM1483809	GSM1483809: Metazome ZF timecourse sample 0074; Danio rerio; RNA Seq	GSM1483809	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483809	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0074.fastq.gz	fastq	95385710.0	2725306.0	GSM1483809 r1	0:35	A:27032549;C:18681500;G:19490852;T:29708978;N:471831	35	27032549	18681500	19490852	29708978	471831	SRX684674	SRS687791	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.75216	0.09004	0.83469	0.48768	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38155	38155	SRR1555565	SRX684673	SRS687790	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0073	GSM1483808	tissue:single embryo	Metazome ZF timecourse sample 0073	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2920	GSM1483808	GSM1483808: Metazome ZF timecourse sample 0073; Danio rerio; RNA Seq	GSM1483808	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483808	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0073.fastq.gz	fastq	149165835.0	4261881.0	GSM1483808 r1	0:35	A:42991931;C:29913953;G:30117935;T:45803552;N:338464	35	42991931	29913953	30117935	45803552	338464	SRX684673	SRS687790	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.76488	0.10545	0.80586	0.5046	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38156	38156	SRR1555564	SRX684672	SRS687789	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0072	GSM1483807	tissue:single embryo	Metazome ZF timecourse sample 0072	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2880	GSM1483807	GSM1483807: Metazome ZF timecourse sample 0072; Danio rerio; RNA Seq	GSM1483807	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483807	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0072.fastq.gz	fastq	203829675.0	5823705.0	GSM1483807 r1	0:35	A:61171233;C:40047517;G:44515900;T:57461403;N:633622	35	61171233	40047517	44515900	57461403	633622	SRX684672	SRS687789	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.65225	0.10254	0.82014	0.50437	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38157	38157	SRR1555563	SRX684671	SRS687788	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0071	GSM1483806	tissue:single embryo	Metazome ZF timecourse sample 0071	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2840	GSM1483806	GSM1483806: Metazome ZF timecourse sample 0071; Danio rerio; RNA Seq	GSM1483806	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483806	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0071.fastq.gz	fastq	107894360.0	3082696.0	GSM1483806 r1	0:35	A:30475809;C:22092085;G:22685204;T:32400616;N:240646	35	30475809	22092085	22685204	32400616	240646	SRX684671	SRS687788	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.77637	0.10375	0.81574	0.50918	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38158	38158	SRR1555562	SRX684670	SRS687787	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0070	GSM1483805	tissue:single embryo	Metazome ZF timecourse sample 0070	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2800	GSM1483805	GSM1483805: Metazome ZF timecourse sample 0070; Danio rerio; RNA Seq	GSM1483805	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483805	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0070.fastq.gz	fastq	102775820.0	2936452.0	GSM1483805 r1	0:35	A:29014067;C:20865233;G:21656956;T:30738746;N:500818	35	29014067	20865233	21656956	30738746	500818	SRX684670	SRS687787	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.7643	0.09535	0.8325	0.51201	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38159	38159	SRR1555561	SRX684669	SRS687786	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0069	GSM1483804	tissue:single embryo	Metazome ZF timecourse sample 0069	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2760	GSM1483804	GSM1483804: Metazome ZF timecourse sample 0069; Danio rerio; RNA Seq	GSM1483804	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483804	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0069.fastq.gz	fastq	178882445.0	5110927.0	GSM1483804 r1	0:35	A:51610621;C:35847602;G:36898756;T:54275519;N:249947	35	51610621	35847602	36898756	54275519	249947	SRX684669	SRS687786	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.81481	0.1212	0.80338	0.48647	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38160	38160	SRR1555560	SRX684668	SRS687784	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0068	GSM1483803	tissue:single embryo	Metazome ZF timecourse sample 0068	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2720	GSM1483803	GSM1483803: Metazome ZF timecourse sample 0068; Danio rerio; RNA Seq	GSM1483803	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483803	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0068.fastq.gz	fastq	289924775.0	8283565.0	GSM1483803 r1	0:35	A:85968202;C:57218562;G:58533597;T:87797178;N:407236	35	85968202	57218562	58533597	87797178	407236	SRX684668	SRS687784	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.78411	0.12015	0.80736	0.5018	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38161	38161	SRR1555559	SRX684667	SRS687785	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0067	GSM1483802	tissue:single embryo	Metazome ZF timecourse sample 0067	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2680	GSM1483802	GSM1483802: Metazome ZF timecourse sample 0067; Danio rerio; RNA Seq	GSM1483802	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483802	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0067.fastq.gz	fastq	12717355.0	363353.0	GSM1483802 r1	0:35	A:3757539;C:2504848;G:2608725;T:3830804;N:15439	35	3757539	2504848	2608725	3830804	15439	SRX684667	SRS687785	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.77835	0.12605	0.92604	0.45926	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38162	38162	SRR1555558	SRX684666	SRS687783	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0066	GSM1483801	tissue:single embryo	Metazome ZF timecourse sample 0066	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2640	GSM1483801	GSM1483801: Metazome ZF timecourse sample 0066; Danio rerio; RNA Seq	GSM1483801	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483801	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0066.fastq.gz	fastq	5206040.0	148744.0	GSM1483801 r1	0:35	A:1490985;C:1039675;G:1088231;T:1579040;N:8109	35	1490985	1039675	1088231	1579040	8109	SRX684666	SRS687783	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.77355	0.11605	0.96587	0.48121	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38163	38163	SRR1555557	SRX684665	SRS687782	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0065	GSM1483800	tissue:single embryo	Metazome ZF timecourse sample 0065	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2600	GSM1483800	GSM1483800: Metazome ZF timecourse sample 0065; Danio rerio; RNA Seq	GSM1483800	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483800	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0065.fastq.gz	fastq	49543620.0	1415532.0	GSM1483800 r1	0:35	A:13699613;C:9907599;G:10751987;T:15115154;N:69267	35	13699613	9907599	10751987	15115154	69267	SRX684665	SRS687782	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.81049	0.12615	0.86367	0.51632	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38164	38164	SRR1555556	SRX684664	SRS687781	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0064	GSM1483799	tissue:single embryo	Metazome ZF timecourse sample 0064	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2560	GSM1483799	GSM1483799: Metazome ZF timecourse sample 0064; Danio rerio; RNA Seq	GSM1483799	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483799	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0064.fastq.gz	fastq	247601200.0	7074320.0	GSM1483799 r1	0:35	A:70332996;C:49278360;G:54252598;T:73390003;N:347243	35	70332996	49278360	54252598	73390003	347243	SRX684664	SRS687781	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.80448	0.14935	0.80975	0.54749	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38165	38165	SRR1555555	SRX684663	SRS687779	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0063	GSM1483798	tissue:single embryo	Metazome ZF timecourse sample 0063	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2520	GSM1483798	GSM1483798: Metazome ZF timecourse sample 0063; Danio rerio; RNA Seq	GSM1483798	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483798	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0063.fastq.gz	fastq	139474895.0	3984997.0	GSM1483798 r1	0:35	A:39999821;C:27945450;G:29190975;T:42159133;N:179516	35	39999821	27945450	29190975	42159133	179516	SRX684663	SRS687779	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.80752	0.14329	0.81645	0.50673	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38166	38166	SRR1555554	SRX684662	SRS687780	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0062	GSM1483797	tissue:single embryo	Metazome ZF timecourse sample 0062	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2480	GSM1483797	GSM1483797: Metazome ZF timecourse sample 0062; Danio rerio; RNA Seq	GSM1483797	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483797	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0062.fastq.gz	fastq	177095730.0	5059878.0	GSM1483797 r1	0:35	A:50196021;C:35043121;G:37861516;T:53732194;N:262878	35	50196021	35043121	37861516	53732194	262878	SRX684662	SRS687780	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.81092	0.13179	0.8199	0.49636	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38167	38167	SRR1555553	SRX684661	SRS687778	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0061	GSM1483796	tissue:single embryo	Metazome ZF timecourse sample 0061	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2440	GSM1483796	GSM1483796: Metazome ZF timecourse sample 0061; Danio rerio; RNA Seq	GSM1483796	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483796	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0061.fastq.gz	fastq	117262810.0	3350366.0	GSM1483796 r1	0:35	A:33678050;C:23425078;G:24368870;T:35496994;N:293818	35	33678050	23425078	24368870	35496994	293818	SRX684661	SRS687778	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.71242	0.11354	0.83514	0.51134	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38168	38168	SRR1555552	SRX684660	SRS687777	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0060	GSM1483795	tissue:single embryo	Metazome ZF timecourse sample 0060	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2400	GSM1483795	GSM1483795: Metazome ZF timecourse sample 0060; Danio rerio; RNA Seq	GSM1483795	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483795	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0060.fastq.gz	fastq	50485225.0	1442435.0	GSM1483795 r1	0:35	A:14629070;C:9936986;G:10066758;T:15611930;N:240481	35	14629070	9936986	10066758	15611930	240481	SRX684660	SRS687777	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.74045	0.14214	0.84703	0.50639	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38169	38169	SRR1555551	SRX684659	SRS687776	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0059	GSM1483794	tissue:single embryo	Metazome ZF timecourse sample 0059	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2360	GSM1483794	GSM1483794: Metazome ZF timecourse sample 0059; Danio rerio; RNA Seq	GSM1483794	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483794	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0059.fastq.gz	fastq	129110905.0	3688883.0	GSM1483794 r1	0:35	A:37661404;C:25258511;G:25987964;T:39941302;N:261724	35	37661404	25258511	25987964	39941302	261724	SRX684659	SRS687776	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.74152	0.13117	0.81749	0.51022	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38170	38170	SRR1555550	SRX684658	SRS687775	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0058	GSM1483793	tissue:single embryo	Metazome ZF timecourse sample 0058	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2320	GSM1483793	GSM1483793: Metazome ZF timecourse sample 0058; Danio rerio; RNA Seq	GSM1483793	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483793	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0058.fastq.gz	fastq	91514045.0	2614687.0	GSM1483793 r1	0:35	A:26231450;C:17984688;G:18624952;T:28210031;N:462924	35	26231450	17984688	18624952	28210031	462924	SRX684658	SRS687775	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.75933	0.13326	0.8294	0.50639	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38171	38171	SRR1555549	SRX684657	SRS687774	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0057	GSM1483792	tissue:single embryo	Metazome ZF timecourse sample 0057	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2280	GSM1483792	GSM1483792: Metazome ZF timecourse sample 0057; Danio rerio; RNA Seq	GSM1483792	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483792	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0057.fastq.gz	fastq	254944305.0	7284123.0	GSM1483792 r1	0:35	A:73169774;C:51240668;G:52956333;T:76957748;N:619782	35	73169774	51240668	52956333	76957748	619782	SRX684657	SRS687774	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.75832	0.11669	0.80937	0.50798	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38172	38172	SRR1555548	SRX684656	SRS687773	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0056	GSM1483791	tissue:single embryo	Metazome ZF timecourse sample 0056	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2240	GSM1483791	GSM1483791: Metazome ZF timecourse sample 0056; Danio rerio; RNA Seq	GSM1483791	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483791	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0056.fastq.gz	fastq	99176700.0	2833620.0	GSM1483791 r1	0:35	A:28266891;C:20096113;G:20730721;T:29621152;N:461823	35	28266891	20096113	20730721	29621152	461823	SRX684656	SRS687773	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.75342	0.1218	0.82982	0.52199	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38173	38173	SRR1555547	SRX684655	SRS687772	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0055	GSM1483790	tissue:single embryo	Metazome ZF timecourse sample 0055	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2200	GSM1483790	GSM1483790: Metazome ZF timecourse sample 0055; Danio rerio; RNA Seq	GSM1483790	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483790	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0055.fastq.gz	fastq	151127480.0	4317928.0	GSM1483790 r1	0:35	A:43591040;C:30002113;G:30975524;T:46254070;N:304733	35	43591040	30002113	30975524	46254070	304733	SRX684655	SRS687772	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.75764	0.12465	0.81249	0.51762	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38174	38174	SRR1555546	SRX684654	SRS687771	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0054	GSM1483789	tissue:single embryo	Metazome ZF timecourse sample 0054	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2160	GSM1483789	GSM1483789: Metazome ZF timecourse sample 0054; Danio rerio; RNA Seq	GSM1483789	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483789	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0054.fastq.gz	fastq	69059795.0	1973137.0	GSM1483789 r1	0:35	A:19683826;C:13807471;G:14484211;T:20733707;N:350580	35	19683826	13807471	14484211	20733707	350580	SRX684654	SRS687771	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.68459	0.10792	0.85865	0.53677	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38175	38175	SRR1555545	SRX684653	SRS687770	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0053	GSM1483788	tissue:single embryo	Metazome ZF timecourse sample 0053	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2120	GSM1483788	GSM1483788: Metazome ZF timecourse sample 0053; Danio rerio; RNA Seq	GSM1483788	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483788	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0053.fastq.gz	fastq	191369430.0	5467698.0	GSM1483788 r1	0:35	A:53654936;C:37894425;G:41404133;T:58136035;N:279901	35	53654936	37894425	41404133	58136035	279901	SRX684653	SRS687770	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.80463	0.1324	0.81489	0.49	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38176	38176	SRR1555544	SRX684652	SRS687768	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0052	GSM1483787	tissue:single embryo	Metazome ZF timecourse sample 0052	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2080	GSM1483787	GSM1483787: Metazome ZF timecourse sample 0052; Danio rerio; RNA Seq	GSM1483787	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483787	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0052.fastq.gz	fastq	215564930.0	6158998.0	GSM1483787 r1	0:35	A:63312652;C:41647031;G:43302090;T:66999251;N:303906	35	63312652	41647031	43302090	66999251	303906	SRX684652	SRS687768	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.79312	0.14581	0.80748	0.4943	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38177	38177	SRR1555543	SRX684651	SRS687769	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0051	GSM1483786	tissue:single embryo	Metazome ZF timecourse sample 0051	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2040	GSM1483786	GSM1483786: Metazome ZF timecourse sample 0051; Danio rerio; RNA Seq	GSM1483786	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483786	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0051.fastq.gz	fastq	290737720.0	8306792.0	GSM1483786 r1	0:35	A:85354255;C:55749822;G:57830877;T:91385535;N:417231	35	85354255	55749822	57830877	91385535	417231	SRX684651	SRS687769	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.79714	0.14915	0.80351	0.48212	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38178	38178	SRR1555542	SRX684650	SRS687767	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0050	GSM1483785	tissue:single embryo	Metazome ZF timecourse sample 0050	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:2000	GSM1483785	GSM1483785: Metazome ZF timecourse sample 0050; Danio rerio; RNA Seq	GSM1483785	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483785	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0050.fastq.gz	fastq	127885835.0	3653881.0	GSM1483785 r1	0:35	A:36640576;C:24900786;G:26610416;T:39561545;N:172512	35	36640576	24900786	26610416	39561545	172512	SRX684650	SRS687767	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.80166	0.14944	0.81122	0.46057	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38179	38179	SRR1555541	SRX684649	SRS687766	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0049	GSM1483784	tissue:single embryo	Metazome ZF timecourse sample 0049	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:1960	GSM1483784	GSM1483784: Metazome ZF timecourse sample 0049; Danio rerio; RNA Seq	GSM1483784	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483784	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0049.fastq.gz	fastq	288732220.0	8249492.0	GSM1483784 r1	0:35	A:82273862;C:55791356;G:60225084;T:90004597;N:437321	35	82273862	55791356	60225084	90004597	437321	SRX684649	SRS687766	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.80699	0.14603	0.80119	0.50186	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38180	38180	SRR1555540	SRX684648	SRS687765	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0048	GSM1483783	tissue:single embryo	Metazome ZF timecourse sample 0048	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:1920	GSM1483783	GSM1483783: Metazome ZF timecourse sample 0048; Danio rerio; RNA Seq	GSM1483783	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483783	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0048.fastq.gz	fastq	72029510.0	2057986.0	GSM1483783 r1	0:35	A:20988018;C:14353166;G:14709018;T:21808886;N:170422	35	20988018	14353166	14709018	21808886	170422	SRX684648	SRS687765	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.7657	0.12723	0.82903	0.51174	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38181	38181	SRR1555539	SRX684647	SRS687764	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0047	GSM1483782	tissue:single embryo	Metazome ZF timecourse sample 0047	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:1880	GSM1483782	GSM1483782: Metazome ZF timecourse sample 0047; Danio rerio; RNA Seq	GSM1483782	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483782	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0047.fastq.gz	fastq	68139750.0	1946850.0	GSM1483782 r1	0:35	A:19374753;C:13653921;G:14376686;T:20519427;N:214963	35	19374753	13653921	14376686	20519427	214963	SRX684647	SRS687764	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.75951	0.09929	0.84372	0.49457	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38182	38182	SRR1555538	SRX684646	SRS687763	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0046	GSM1483781	tissue:single embryo	Metazome ZF timecourse sample 0046	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:1840	GSM1483781	GSM1483781: Metazome ZF timecourse sample 0046; Danio rerio; RNA Seq	GSM1483781	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483781	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0046.fastq.gz	fastq	77208705.0	2205963.0	GSM1483781 r1	0:35	A:22006761;C:15565401;G:16227173;T:23236147;N:173223	35	22006761	15565401	16227173	23236147	173223	SRX684646	SRS687763	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.78187	0.11068	0.82408	0.50229	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38183	38183	SRR1555537	SRX684645	SRS687762	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0045	GSM1483780	tissue:single embryo	Metazome ZF timecourse sample 0045	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:1800	GSM1483780	GSM1483780: Metazome ZF timecourse sample 0045; Danio rerio; RNA Seq	GSM1483780	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483780	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0045.fastq.gz	fastq	137583040.0	3930944.0	GSM1483780 r1	0:35	A:39174780;C:27210755;G:28507642;T:41999686;N:690177	35	39174780	27210755	28507642	41999686	690177	SRX684645	SRS687762	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.75598	0.12311	0.81682	0.5009	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38184	38184	SRR1555536	SRX684644	SRS687761	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0044	GSM1483779	tissue:single embryo	Metazome ZF timecourse sample 0044	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:1760	GSM1483779	GSM1483779: Metazome ZF timecourse sample 0044; Danio rerio; RNA Seq	GSM1483779	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483779	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0044.fastq.gz	fastq	173596780.0	4959908.0	GSM1483779 r1	0:35	A:50342468;C:34071199;G:35445470;T:53307736;N:429907	35	50342468	34071199	35445470	53307736	429907	SRX684644	SRS687761	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.75753	0.11777	0.81055	0.49526	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38185	38185	SRR1555535	SRX684643	SRS687760	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0043	GSM1483778	tissue:single embryo	Metazome ZF timecourse sample 0043	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:1720	GSM1483778	GSM1483778: Metazome ZF timecourse sample 0043; Danio rerio; RNA Seq	GSM1483778	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483778	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0043.fastq.gz	fastq	86602355.0	2474353.0	GSM1483778 r1	0:35	A:24985086;C:17224343;G:17613830;T:26349902;N:429194	35	24985086	17224343	17613830	26349902	429194	SRX684643	SRS687760	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.75503	0.11846	0.82706	0.50298	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38186	38186	SRR1555534	SRX684642	SRS687759	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0042	GSM1483777	tissue:single embryo	Metazome ZF timecourse sample 0042	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:1680	GSM1483777	GSM1483777: Metazome ZF timecourse sample 0042; Danio rerio; RNA Seq	GSM1483777	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483777	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0042.fastq.gz	fastq	188917295.0	5397637.0	GSM1483777 r1	0:35	A:55128132;C:36753131;G:38260811;T:58386915;N:388306	35	55128132	36753131	38260811	58386915	388306	SRX684642	SRS687759	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.75676	0.12061	0.80442	0.5035	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38187	38187	SRR1555533	SRX684641	SRS687758	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0041	GSM1483776	tissue:single embryo	Metazome ZF timecourse sample 0041	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:1640	GSM1483776	GSM1483776: Metazome ZF timecourse sample 0041; Danio rerio; RNA Seq	GSM1483776	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483776	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0041.fastq.gz	fastq	99641815.0	2846909.0	GSM1483776 r1	0:35	A:28559457;C:19637558;G:20746011;T:30190358;N:508431	35	28559457	19637558	20746011	30190358	508431	SRX684641	SRS687758	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.76108	0.11637	0.82751	0.5096	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38188	38188	SRR1555532	SRX684640	SRS687757	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0040	GSM1483775	tissue:single embryo	Metazome ZF timecourse sample 0040	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:1600	GSM1483775	GSM1483775: Metazome ZF timecourse sample 0040; Danio rerio; RNA Seq	GSM1483775	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483775	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0040.fastq.gz	fastq	66500840.0	1900024.0	GSM1483775 r1	0:35	A:19905778;C:13336991;G:13569868;T:19599979;N:88224	35	19905778	13336991	13569868	19599979	88224	SRX684640	SRS687757	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.79612	0.14476	0.84421	0.51356	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38189	38189	SRR1555531	SRX684639	SRS687756	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0039	GSM1483774	tissue:single embryo	Metazome ZF timecourse sample 0039	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:1560	GSM1483774	GSM1483774: Metazome ZF timecourse sample 0039; Danio rerio; RNA Seq	GSM1483774	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483774	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0039.fastq.gz	fastq	91322490.0	2609214.0	GSM1483774 r1	0:35	A:26896148;C:18075620;G:18949224;T:27276263;N:125235	35	26896148	18075620	18949224	27276263	125235	SRX684639	SRS687756	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.80286	0.15016	0.83195	0.52775	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38190	38190	SRR1555530	SRX684638	SRS687755	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0038	GSM1483773	tissue:single embryo	Metazome ZF timecourse sample 0038	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:1520	GSM1483773	GSM1483773: Metazome ZF timecourse sample 0038; Danio rerio; RNA Seq	GSM1483773	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483773	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0038.fastq.gz	fastq	101902745.0	2911507.0	GSM1483773 r1	0:35	A:30262327;C:20264495;G:20848086;T:30389349;N:138488	35	30262327	20264495	20848086	30389349	138488	SRX684638	SRS687755	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.79914	0.14724	0.83047	0.51145	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38191	38191	SRR1555529	SRX684637	SRS687754	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0037	GSM1483772	tissue:single embryo	Metazome ZF timecourse sample 0037	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:1480	GSM1483772	GSM1483772: Metazome ZF timecourse sample 0037; Danio rerio; RNA Seq	GSM1483772	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483772	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0037.fastq.gz	fastq	81416650.0	2326190.0	GSM1483772 r1	0:35	A:23902634;C:16036242;G:17201817;T:24155587;N:120370	35	23902634	16036242	17201817	24155587	120370	SRX684637	SRS687754	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.78827	0.18587	0.84674	0.44219	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38192	38192	SRR1555528	SRX684636	SRS687752	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0036	GSM1483771	tissue:single embryo	Metazome ZF timecourse sample 0036	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:1440	GSM1483771	GSM1483771: Metazome ZF timecourse sample 0036; Danio rerio; RNA Seq	GSM1483771	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483771	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0036.fastq.gz	fastq	75971315.0	2170609.0	GSM1483771 r1	0:35	A:22267492;C:15517952;G:15279496;T:22807339;N:99036	35	22267492	15517952	15279496	22807339	99036	SRX684636	SRS687752	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.74377	0.14648	0.84348	0.53283	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38193	38193	SRR1555527	SRX684635	SRS687753	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0035	GSM1483770	tissue:single embryo	Metazome ZF timecourse sample 0035	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:1400	GSM1483770	GSM1483770: Metazome ZF timecourse sample 0035; Danio rerio; RNA Seq	GSM1483770	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483770	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0035.fastq.gz	fastq	1394330.0	39838.0	GSM1483770 r1	0:35	A:402051;C:272276;G:287822;T:429952;N:2229	35	402051	272276	287822	429952	2229	SRX684635	SRS687753	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.74877	0.12157	0.98646	0.52724	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38194	38194	SRR1555526	SRX684634	SRS687751	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0034	GSM1483769	tissue:single embryo	Metazome ZF timecourse sample 0034	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:1360	GSM1483769	GSM1483769: Metazome ZF timecourse sample 0034; Danio rerio; RNA Seq	GSM1483769	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483769	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0034.fastq.gz	fastq	35015155.0	1000433.0	GSM1483769 r1	0:35	A:10142602;C:6989087;G:7392583;T:10442983;N:47900	35	10142602	6989087	7392583	10442983	47900	SRX684634	SRS687751	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.80122	0.12241	0.88402	0.53072	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38195	38195	SRR1555525	SRX684633	SRS687749	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0033	GSM1483768	tissue:single embryo	Metazome ZF timecourse sample 0033	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:1320	GSM1483768	GSM1483768: Metazome ZF timecourse sample 0033; Danio rerio; RNA Seq	GSM1483768	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483768	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0033.fastq.gz	fastq	62990725.0	1799735.0	GSM1483768 r1	0:35	A:17788769;C:12319707;G:13858738;T:18933772;N:89739	35	17788769	12319707	13858738	18933772	89739	SRX684633	SRS687749	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.80408	0.14198	0.85802	0.51504	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38196	38196	SRR1555524	SRX684632	SRS687750	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0032	GSM1483767	tissue:single embryo	Metazome ZF timecourse sample 0032	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:1280	GSM1483767	GSM1483767: Metazome ZF timecourse sample 0032; Danio rerio; RNA Seq	GSM1483767	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483767	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0032.fastq.gz	fastq	55043730.0	1572678.0	GSM1483767 r1	0:35	A:15726201;C:10988676;G:11393651;T:16764103;N:171099	35	15726201	10988676	11393651	16764103	171099	SRX684632	SRS687750	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.75627	0.11178	0.84187	0.51424	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38197	38197	SRR1555523	SRX684631	SRS687748	SRP045679	PRJNA258656	Danio rerio high resolution developmental transcriptomic time course	GSE60619	Transcriptome Analysis	Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples	parent bioproject:PRJNA287810	pubmed:26886793	Metazome ZF timecourse sample 0031	GSM1483766	tissue:single embryo	Metazome ZF timecourse sample 0031	Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix	single embryo	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.	time min post fertilization:1240	GSM1483766	GSM1483766: Metazome ZF timecourse sample 0031; Danio rerio; RNA Seq	GSM1483766	1	RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.	GEO Accession:GSM1483766	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP045679	Metazome_ZF_timecourse_sample_0031.fastq.gz	fastq	111829725.0	3195135.0	GSM1483766 r1	0:35	A:32037252;C:22024337;G:23195973;T:34219811;N:352352	35	32037252	22024337	23195973	34219811	352352	SRX684631	SRS687748	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.76499	0.1174	0.81931	0.48818	35	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38198	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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

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