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347 rows where experiment.library_selection = "cDNA", technology = "celseq" and tissue_curation_coarse = "All anatomical structures"

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devstage_curation 8

devstage_curation_coarse 3

tissue_curation 2

experiment.library_layout 2

tissue_curation_coarse 1

  • All anatomical structures · 347 ✖

technology 1

  • celseq · 347 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • cDNA · 347 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
30508 30508 SRR27764648 SRX23429609 SRS20284060 SRP486518 PRJNA1070582 Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition GSE254439 Transcriptome Analysis Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However developing tissues also undergo dynamic morphogenesis which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/ß catenin signalling gradient which acts as a morphogen to establish embryonic anterior posterior patterning revealed that unfit cells with abnormal Wnt/ß catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/ß catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues this system may support tissue robustness and disease prevention. Overall design: ß catCA constitutive active form of ß catenin expressing GFP+ cells or ßcatCA unexpressing GFP cells from ß catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.   pubmed:39546611   Mosaic GFP control GFP min lot2 GSM8042248   source name:early embryonic cell|strain:AB|tissue:early embryonic cell|developmental stage:9 hpf loc name:missing|collection date:missing Mosaic GFP control GFP min lot2 Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Assembly: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm. early embryonic cell   Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.   strain:AB|tissue:early embryonic cell|developmental stage:9 hpf GSM8042248 GSM8042248: Mosaic GFP control GFP min lot2; Danio rerio; RNA Seq GSM8042248 r1 GSM8042248 1 Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 1500   SRP486518     Mosaic_GFP_control_GFP_min_lot2.fastq.gz fastq 7474464.0 207624.0 GSM8042248 r1 0:36 A:1796571;C:1274347;G:1548876;T:2854637;N:33 36       1796571 1274347 1548876 2854637 33 SRX23429609 SRS20284060 SRA1793856 Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University 1 0.82922   0.20207   0.86143   0.54661   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Japan 2024-01-29 Gastrula Embryo Embryo Imprecise All anatomical structures
30509 30509 SRR27764649 SRX23429608 SRS20284059 SRP486518 PRJNA1070582 Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition GSE254439 Transcriptome Analysis Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However developing tissues also undergo dynamic morphogenesis which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/ß catenin signalling gradient which acts as a morphogen to establish embryonic anterior posterior patterning revealed that unfit cells with abnormal Wnt/ß catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/ß catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues this system may support tissue robustness and disease prevention. Overall design: ß catCA constitutive active form of ß catenin expressing GFP+ cells or ßcatCA unexpressing GFP cells from ß catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.   pubmed:39546611   Mosaic GFP control GFP min lot1 GSM8042247   source name:early embryonic cell|strain:AB|tissue:early embryonic cell|developmental stage:9 hpf loc name:missing|collection date:missing Mosaic GFP control GFP min lot1 Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Assembly: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm. early embryonic cell   Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.   strain:AB|tissue:early embryonic cell|developmental stage:9 hpf GSM8042247 GSM8042247: Mosaic GFP control GFP min lot1; Danio rerio; RNA Seq GSM8042247 r1 GSM8042247 1 Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 1500   SRP486518     Mosaic_GFP_control_GFP_min_lot1.fastq.gz fastq 8256240.0 229340.0 GSM8042247 r1 0:36 A:1947003;C:1345938;G:1692065;T:3271133;N:101 36       1947003 1345938 1692065 3271133 101 SRX23429608 SRS20284059 SRA1793856 Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University 1 0.83305   0.17754   0.8619   0.61474   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Japan 2024-01-29 Gastrula Embryo Embryo Imprecise All anatomical structures
30510 30510 SRR27764650 SRX23429607 SRS20284058 SRP486518 PRJNA1070582 Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition GSE254439 Transcriptome Analysis Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However developing tissues also undergo dynamic morphogenesis which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/ß catenin signalling gradient which acts as a morphogen to establish embryonic anterior posterior patterning revealed that unfit cells with abnormal Wnt/ß catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/ß catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues this system may support tissue robustness and disease prevention. Overall design: ß catCA constitutive active form of ß catenin expressing GFP+ cells or ßcatCA unexpressing GFP cells from ß catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.   pubmed:39546611   Mosaic beta catCA GFP min lot2 GSM8042246   source name:early embryonic cell|strain:AB|tissue:early embryonic cell|developmental stage:9 hpf loc name:missing|collection date:missing Mosaic beta catCA GFP min lot2 Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Assembly: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm. early embryonic cell   Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.   strain:AB|tissue:early embryonic cell|developmental stage:9 hpf GSM8042246 GSM8042246: Mosaic beta catCA GFP min lot2; Danio rerio; RNA Seq GSM8042246 r1 GSM8042246 1 Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 1500   SRP486518     Mosaic_beta-catCA_GFP_min_lot2.fastq.gz fastq 856836.0 23801.0 GSM8042246 r1 0:36 A:217589;C:147419;G:175612;T:316201;N:15 36       217589 147419 175612 316201 15 SRX23429607 SRS20284058 SRA1793856 Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University 1 0.82481   0.28434   0.95371   0.61551   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Japan 2024-01-29 Gastrula Embryo Embryo Imprecise All anatomical structures
30511 30511 SRR27764651 SRX23429606 SRS20284057 SRP486518 PRJNA1070582 Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition GSE254439 Transcriptome Analysis Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However developing tissues also undergo dynamic morphogenesis which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/ß catenin signalling gradient which acts as a morphogen to establish embryonic anterior posterior patterning revealed that unfit cells with abnormal Wnt/ß catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/ß catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues this system may support tissue robustness and disease prevention. Overall design: ß catCA constitutive active form of ß catenin expressing GFP+ cells or ßcatCA unexpressing GFP cells from ß catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.   pubmed:39546611   Mosaic beta catCA GFP min lot1 GSM8042245   source name:early embryonic cell|strain:AB|tissue:early embryonic cell|developmental stage:9 hpf loc name:missing|collection date:missing Mosaic beta catCA GFP min lot1 Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Assembly: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm. early embryonic cell   Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.   strain:AB|tissue:early embryonic cell|developmental stage:9 hpf GSM8042245 GSM8042245: Mosaic beta catCA GFP min lot1; Danio rerio; RNA Seq GSM8042245 r1 GSM8042245 1 Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 1500   SRP486518     Mosaic_beta-catCA_GFP_min_lot1.fastq.gz fastq 7181388.0 199483.0 GSM8042245 r1 0:36 A:1744919;C:1207643;G:1456829;T:2771919;N:78 36       1744919 1207643 1456829 2771919 78 SRX23429606 SRS20284057 SRA1793856 Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University 1 0.83629   0.16823   0.84774   0.64548   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Japan 2024-01-29 Gastrula Embryo Embryo Imprecise All anatomical structures
38073 38073 SRR1531483 SRX665263 SRS670077 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   18 somites stage straightened secti1d tail to head GSM1448820   tissue:deyolked embryo head removed|Stage:18 somites|sectioning direction:tail to head|section thickness:24 µm|embedding strategy:deyolked and straightened embryo 18 somites stage straightened secti1d tail to head Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections deyolked embryo head removed Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:18 somites|sectioning direction:tail to head|section thickness:24 µm|embedding strategy:deyolked and straightened embryo GSM1448820 GSM1448820: 18 somites stage straightened secti1d tail to head; Danio rerio; RNA Seq GSM1448820   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448820 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_18ss_TH_R2.fastq.gz dr_18ss_TH_R1.fastq.gz fastq fastq 15779230884.0 154698342.0 GSM1448820 r1 0:51 1:51 A:3451000604;C:2392800593;G:2522666152;T:7412137093;N:626442 51 51     3451000604 2392800593 2522666152 7412137093 626442 SRX665263 SRS670077 SRA177126 GEO Hubrecht Institute 2 0.11555 0.70031 0.08647 0.12212 0.98238 0.78946 0.48905 0.5514 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Embryo Imprecise All anatomical structures
38074 38074 SRR1531482 SRX665262 SRS670076 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somites stage straightened secti1d tail to head replicate GSM1448819   tissue:deyolked embryo|Stage:15 somites|sectioning direction:tail to head|section thickness:18 µm|embedding strategy:deyolked and straightened embryo 15 somites stage straightened secti1d tail to head replicate Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections deyolked embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:tail to head|section thickness:18 µm|embedding strategy:deyolked and straightened embryo GSM1448819 GSM1448819: 15 somites stage straightened secti1d tail to head replicate; Danio rerio; RNA Seq GSM1448819   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448819 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_15ss_TH2_R2.fastq.gz dr_15ss_TH2_R1.fastq.gz fastq fastq 4502603442.0 44143171.0 GSM1448819 r1 0:51 1:51 A:1010801791;C:688133305;G:712006267;T:2047960758;N:43701321 51 51     1010801791 688133305 712006267 2047960758 43701321 SRX665262 SRS670076 SRA177126 GEO Hubrecht Institute 2 0.0903 0.78618 0.08054 0.12953 0.98703 0.78046 0.53574 0.52775 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Embryo Imprecise All anatomical structures
38075 38075 SRR1531481 SRX665261 SRS670075 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   sections 97 108 for samples dr 15ss TH and dr 15ss HT GSM1448818   tissue:deyolked embryo|Stage:15 somites|sectioning direction:head to tail and tail to head|section thickness:18 µm|embedding strategy:deyolked and straightened embryo sections 97 108 for samples dr 15ss TH and dr 15ss HT Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections deyolked embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:head to tail and tail to head|section thickness:18 µm|embedding strategy:deyolked and straightened embryo GSM1448818 GSM1448818: sections 97 108 for samples dr 15ss TH and dr 15ss HT; Danio rerio; RNA Seq GSM1448818   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448818 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_15ss_TH97-108_HT97-108_R2.fastq.gz dr_15ss_TH97-108_HT97-108_R1.fastq.gz fastq fastq 472071606.0 4628153.0 GSM1448818 r1 0:51 1:51 A:108013079;C:76852222;G:73612321;T:208300498;N:5293486 51 51     108013079 76852222 73612321 208300498 5293486 SRX665261 SRS670075 SRA177126 GEO Hubrecht Institute 2 0.06997 0.71056 0.06103 0.12966 0.9865 0.79446 0.53118 0.53673 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Embryo Imprecise All anatomical structures
38076 38076 SRR1531480 SRX665260 SRS670074 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somites stage straightened secti1d tail to head GSM1448817   tissue:deyolked embryo|Stage:15 somites|sectioning direction:tail to head|section thickness:18 µm|embedding strategy:deyolked and straightened embryo 15 somites stage straightened secti1d tail to head Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections deyolked embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:tail to head|section thickness:18 µm|embedding strategy:deyolked and straightened embryo GSM1448817 GSM1448817: 15 somites stage straightened secti1d tail to head; Danio rerio; RNA Seq GSM1448817   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448817 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_15ss_TH_R1.fastq.gz dr_15ss_TH_R2.fastq.gz fastq fastq 3381229314.0 33149307.0 GSM1448817 r1 0:51 1:51 A:806003850;C:517726785;G:527487361;T:1491678004;N:38333314 51 51     806003850 517726785 527487361 1491678004 38333314 SRX665260 SRS670074 SRA177126 GEO Hubrecht Institute 2 0.06812 0.69273 0.05849 0.1511 0.98502 0.7834 0.47808 0.53868 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Embryo Imprecise All anatomical structures
38077 38077 SRR1531479 SRX665259 SRS670073 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somites stage straightened secti1d head to tail GSM1448816   tissue:deyolked embryo|Stage:15 somites|sectioning direction:head to tail|section thickness:18 µm|embedding strategy:deyolked and straightened embryo 15 somites stage straightened secti1d head to tail Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections deyolked embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:head to tail|section thickness:18 µm|embedding strategy:deyolked and straightened embryo GSM1448816 GSM1448816: 15 somites stage straightened secti1d head to tail; Danio rerio; RNA Seq GSM1448816   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448816 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_15ss_HT_R1.fastq.gz dr_15ss_HT_R2.fastq.gz fastq fastq 3476174076.0 34080138.0 GSM1448816 r1 0:51 1:51 A:800519794;C:540890287;G:554165272;T:1542680760;N:37917963 51 51     800519794 540890287 554165272 1542680760 37917963 SRX665259 SRS670073 SRA177126 GEO Hubrecht Institute 2 0.06769 0.70036 0.05945 0.13184 0.98849 0.79026 0.50058 0.57003 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Embryo Imprecise All anatomical structures
38078 38078 SRR1531477 SRX665258 SRS670072 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somite stage secti1d from right to left GSM1448815   tissue:whole embryo|Stage:15 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo 15 somite stage secti1d from right to left Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo GSM1448815 GSM1448815: 15 somite stage secti1d from right to left; Danio rerio; RNA Seq GSM1448815   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448815 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_15ss_RL_R1.fastq.gz dr_15ss_RL_R2.fastq.gz fastq fastq 3840123336.0 37648268.0 GSM1448815 r1 0:51 1:51 A:915153174;C:577478134;G:648196113;T:1695635476;N:3660439 51 51     915153174 577478134 648196113 1695635476 3660439 SRX665258 SRS670072 SRA177126 GEO Hubrecht Institute 2 0.05313 0.71589 0.0419 0.15174 0.97717 0.77484 0.5218 0.45828 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38079 38079 SRR1531478 SRX665258 SRS670072 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somite stage secti1d from right to left GSM1448815   tissue:whole embryo|Stage:15 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo 15 somite stage secti1d from right to left Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo GSM1448815 GSM1448815: 15 somite stage secti1d from right to left; Danio rerio; RNA Seq GSM1448815   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448815 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_15ss_RL_R1.fastq.gz miseq_dr_15ss_RL_R2.fastq.gz fastq fastq 619303490.0 1235999.0 GSM1448815 r2 0:251 1:250.06 A:196814024;C:126079066;G:111585151;T:184825248;N:1 251 250     196814024 126079066 111585151 184825248 1 SRX665258 SRS670072 SRA177126 GEO Hubrecht Institute 2 0.37674 0.6743 0.06734 0.08523 0.92516 0.86196 0.56151 0.54745 251 251 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38080 38080 SRR1531475 SRX665257 SRS670070 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somite stage secti1d from left to right GSM1448814   tissue:whole embryo|Stage:15 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo 15 somite stage secti1d from left to right Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo GSM1448814 GSM1448814: 15 somite stage secti1d from left to right; Danio rerio; RNA Seq GSM1448814   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448814 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_15ss_LR_R2.fastq.gz dr_15ss_LR_R1.fastq.gz fastq fastq 2077803342.0 20370621.0 GSM1448814 r1 0:51 1:51 A:487276259;C:320933398;G:342175116;T:925418636;N:1999933 51 51     487276259 320933398 342175116 925418636 1999933 SRX665257 SRS670070 SRA177126 GEO Hubrecht Institute 2 0.04544 0.77533 0.03741 0.15439 0.98435 0.77662 0.56397 0.57005 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38081 38081 SRR1531476 SRX665257 SRS670070 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somite stage secti1d from left to right GSM1448814   tissue:whole embryo|Stage:15 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo 15 somite stage secti1d from left to right Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo GSM1448814 GSM1448814: 15 somite stage secti1d from left to right; Danio rerio; RNA Seq GSM1448814   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448814 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_15ss_LR_R1.fastq.gz miseq_dr_15ss_LR_R2.fastq.gz fastq fastq 648479770.0 1294232.0 GSM1448814 r2 0:251 1:250.05 A:208271519;C:133135452;G:114142609;T:192930139;N:51 251 250     208271519 133135452 114142609 192930139 51 SRX665257 SRS670070 SRA177126 GEO Hubrecht Institute 2 0.34992 0.64011 0.08713 0.16967 0.92103 0.83853 0.54292 0.52547 251 250 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38082 38082 SRR1531473 SRX665256 SRS670071 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somite stage secti1d from dorsal to ventral end GSM1448813   tissue:whole embryo|Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo 15 somite stage secti1d from dorsal to ventral end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo GSM1448813 GSM1448813: 15 somite stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq GSM1448813   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448813 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_15ss_DV_R1.fastq.gz dr_15ss_DV_R2.fastq.gz fastq fastq 2516804610.0 24674555.0 GSM1448813 r1 0:51 1:51 A:579818006;C:406550753;G:379205422;T:1129932140;N:21298289 51 51     579818006 406550753 379205422 1129932140 21298289 SRX665256 SRS670071 SRA177126 GEO Hubrecht Institute 2 0.04189 0.74891 0.03368 0.12625 0.98695 0.78423 0.46823 0.53429 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38083 38083 SRR1531474 SRX665256 SRS670071 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somite stage secti1d from dorsal to ventral end GSM1448813   tissue:whole embryo|Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo 15 somite stage secti1d from dorsal to ventral end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo GSM1448813 GSM1448813: 15 somite stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq GSM1448813   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448813 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_15ss_DV_R1.fastq.gz miseq_dr_15ss_DV_R2.fastq.gz fastq fastq 1831352383.0 3654695.0 GSM1448813 r2 0:251 1:250.10 A:593055798;C:392880040;G:312965357;T:532451118;N:70 251 250     593055798 392880040 312965357 532451118 70 SRX665256 SRS670071 SRA177126 GEO Hubrecht Institute 2 0.27976 0.58087 0.05423 0.08127 0.93943 0.88868 0.51246 0.50653 251 251 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38084 38084 SRR1531471 SRX665255 SRS670069 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somite stage secti1d from ventral to dorsal end GSM1448812   tissue:whole embryo|Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo 15 somite stage secti1d from ventral to dorsal end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo GSM1448812 GSM1448812: 15 somite stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq GSM1448812   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448812 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_15ss_VD_R1.fastq.gz dr_15ss_VD_R2.fastq.gz fastq fastq 1673808678.0 16409889.0 GSM1448812 r1 0:51 1:51 A:397744759;C:269067687;G:250815180;T:740808813;N:15372239 51 51     397744759 269067687 250815180 740808813 15372239 SRX665255 SRS670069 SRA177126 GEO Hubrecht Institute 2 0.05917 0.69313 0.0499 0.19364 0.98364 0.78232 0.54626 0.5434 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38085 38085 SRR1531472 SRX665255 SRS670069 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somite stage secti1d from ventral to dorsal end GSM1448812   tissue:whole embryo|Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo 15 somite stage secti1d from ventral to dorsal end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo GSM1448812 GSM1448812: 15 somite stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq GSM1448812   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448812 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_15ss_VD_R2.fastq.gz miseq_dr_15ss_VD_R1.fastq.gz fastq fastq 587520609.0 1172567.0 GSM1448812 r2 0:251 1:250.06 A:194391951;C:123162952;G:98682047;T:171283648;N:11 251 250     194391951 123162952 98682047 171283648 11 SRX665255 SRS670069 SRA177126 GEO Hubrecht Institute 2 0.25906 0.51091 0.10052 0.13544 0.94274 0.90015 0.54255 0.53365 251 251 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38086 38086 SRR1531470 SRX665254 SRS670068 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somite stage secti1d from posterior to anterior end GSM1448811   tissue:whole embryo|Stage:15 somites|sectioning direction:posterior anterior|section thickness:18 µm|embedding strategy:intact embryo 15 somite stage secti1d from posterior to anterior end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:posterior anterior|section thickness:18 µm|embedding strategy:intact embryo GSM1448811 GSM1448811: 15 somite stage secti1d from posterior to anterior end; Danio rerio; RNA Seq GSM1448811   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448811 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_15ss_PA_R2.fastq.gz dr_15ss_PA_R1.fastq.gz fastq fastq 2483143794.0 24344547.0 GSM1448811 r1 0:51 1:51 A:563038776;C:400378151;G:372280878;T:1126633332;N:20812657 51 51     563038776 400378151 372280878 1126633332 20812657 SRX665254 SRS670068 SRA177126 GEO Hubrecht Institute 2 0.04278 0.78001 0.03367 0.11539 0.98727 0.77865 0.49734 0.53041 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38087 38087 SRR1531469 SRX665253 SRS670067 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somite stage secti1d from anterior to posterior end GSM1448810   tissue:whole embryo|Stage:15 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo 15 somite stage secti1d from anterior to posterior end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo GSM1448810 GSM1448810: 15 somite stage secti1d from anterior to posterior end; Danio rerio; RNA Seq GSM1448810   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448810 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_15ss_AP_R2.fastq.gz dr_15ss_AP_R1.fastq.gz fastq fastq 3436281570.0 33689035.0 GSM1448810 r1 0:51 1:51 A:794842891;C:552474558;G:514289189;T:1545720661;N:28954271 51 51     794842891 552474558 514289189 1545720661 28954271 SRX665253 SRS670067 SRA177126 GEO Hubrecht Institute 2 0.04616 0.72787 0.03714 0.11902 0.98636 0.78372 0.50428 0.54252 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38088 38088 SRR1531468 SRX665252 SRS670066 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   10 somite stage secti1d from right to left GSM1448809   tissue:whole embryo|Stage:10 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo 10 somite stage secti1d from right to left Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:10 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo GSM1448809 GSM1448809: 10 somite stage secti1d from right to left; Danio rerio; RNA Seq GSM1448809   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448809 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_10ss_RL_R2.fastq.gz dr_10ss_RL_R1.fastq.gz fastq fastq 2058025848.0 20176724.0 GSM1448809 r1 0:51 1:51 A:466388690;C:327195544;G:324646168;T:921984274;N:17811172 51 51     466388690 327195544 324646168 921984274 17811172 SRX665252 SRS670066 SRA177126 GEO Hubrecht Institute 2 0.03352 0.82842 0.02775 0.10176 0.99019 0.7878 0.56827 0.53664 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38089 38089 SRR1531467 SRX665251 SRS670065 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   10 somite stage secti1d from left to right GSM1448808   tissue:whole embryo|Stage:10 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo 10 somite stage secti1d from left to right Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:10 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo GSM1448808 GSM1448808: 10 somite stage secti1d from left to right; Danio rerio; RNA Seq GSM1448808   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448808 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_10ss_LR_R1.fastq.gz dr_10ss_LR_R2.fastq.gz fastq fastq 2372600886.0 23260793.0 GSM1448808 r1 0:51 1:51 A:539978604;C:369014393;G:373430985;T:1069557826;N:20619078 51 51     539978604 369014393 373430985 1069557826 20619078 SRX665251 SRS670065 SRA177126 GEO Hubrecht Institute 2 0.04947 0.82594 0.04114 0.11817 0.98703 0.77727 0.5181 0.46105 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38090 38090 SRR1531465 SRX665250 SRS670064 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   10 somite stage secti1d from dorsal to ventral end GSM1448807   tissue:whole embryo|Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo 10 somite stage secti1d from dorsal to ventral end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo GSM1448807 GSM1448807: 10 somite stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq GSM1448807   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448807 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_10ss_DV_R1.fastq.gz dr_10ss_DV_R2.fastq.gz fastq fastq 4808137200.0 47138600.0 GSM1448807 r1 0:51 1:51 A:1069537756;C:773357615;G:788490520;T:2131916220;N:44835089 51 51     1069537756 773357615 788490520 2131916220 44835089 SRX665250 SRS670064 SRA177126 GEO Hubrecht Institute 2 0.05336 0.7348 0.04376 0.11098 0.98311 0.78829 0.55869 0.5169 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38091 38091 SRR1531466 SRX665250 SRS670064 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   10 somite stage secti1d from dorsal to ventral end GSM1448807   tissue:whole embryo|Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo 10 somite stage secti1d from dorsal to ventral end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo GSM1448807 GSM1448807: 10 somite stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq GSM1448807   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448807 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_10ss_DV_R1.fastq.gz miseq_dr_10ss_DV_R2.fastq.gz fastq fastq 981031778.0 1957880.0 GSM1448807 r2 0:251 1:250.07 A:318017696;C:204637111;G:170546834;T:287830124;N:13 251 250     318017696 204637111 170546834 287830124 13 SRX665250 SRS670064 SRA177126 GEO Hubrecht Institute 2 0.28421 0.5957 0.04748 0.07361 0.93917 0.88298 0.53618 0.53493 251 251 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38092 38092 SRR1531463 SRX665249 SRS670063 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   10 somite stage secti1d from ventral to dorsal end GSM1448806   tissue:whole embryo|Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo 10 somite stage secti1d from ventral to dorsal end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo GSM1448806 GSM1448806: 10 somite stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq GSM1448806   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448806 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_10ss_VD_R1.fastq.gz dr_10ss_VD_R2.fastq.gz fastq fastq 4042242048.0 39629824.0 GSM1448806 r1 0:51 1:51 A:880941046;C:636899286;G:642176352;T:1845085169;N:37140195 51 51     880941046 636899286 642176352 1845085169 37140195 SRX665249 SRS670063 SRA177126 GEO Hubrecht Institute 2 0.04898 0.80518 0.04234 0.10309 0.99044 0.78437 0.4974 0.53264 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38093 38093 SRR1531464 SRX665249 SRS670063 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   10 somite stage secti1d from ventral to dorsal end GSM1448806   tissue:whole embryo|Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo 10 somite stage secti1d from ventral to dorsal end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo GSM1448806 GSM1448806: 10 somite stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq GSM1448806   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448806 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_10ss_VD_R1.fastq.gz miseq_dr_10ss_VD_R2.fastq.gz fastq fastq 738071470.0 1473056.0 GSM1448806 r2 0:251 1:250.05 A:241662059;C:148514183;G:127467910;T:220427298;N:20 251 250     241662059 148514183 127467910 220427298 20 SRX665249 SRS670063 SRA177126 GEO Hubrecht Institute 2 0.33554 0.65168 0.04798 0.07375 0.93334 0.87121 0.53425 0.51721 251 251 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38094 38094 SRR1531461 SRX665248 SRS670062 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   10 somite stage secti1d from posterior to anterior end GSM1448805   tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo 10 somite stage secti1d from posterior to anterior end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo GSM1448805 GSM1448805: 10 somite stage secti1d from posterior to anterior end; Danio rerio; RNA Seq GSM1448805   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448805 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_10ss_PA_R1.fastq.gz dr_10ss_PA_R2.fastq.gz fastq fastq 4759203720.0 46658860.0 GSM1448805 r1 0:51 1:51 A:1044025561;C:745846492;G:761494052;T:2164007108;N:43830507 51 51     1044025561 745846492 761494052 2164007108 43830507 SRX665248 SRS670062 SRA177126 GEO Hubrecht Institute 2 0.04594 0.81204 0.0388 0.10992 0.98938 0.78244 0.51272 0.52639 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38095 38095 SRR1531462 SRX665248 SRS670062 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   10 somite stage secti1d from posterior to anterior end GSM1448805   tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo 10 somite stage secti1d from posterior to anterior end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo GSM1448805 GSM1448805: 10 somite stage secti1d from posterior to anterior end; Danio rerio; RNA Seq GSM1448805   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448805 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_10ss_PA_R2.fastq.gz miseq_dr_10ss_PA_R1.fastq.gz fastq fastq 923948352.0 1843960.0 GSM1448805 r2 0:251 1:250.07 A:301981474;C:189568545;G:157916393;T:274481921;N:19 251 250     301981474 189568545 157916393 274481921 19 SRX665248 SRS670062 SRA177126 GEO Hubrecht Institute 2 0.33803 0.65569 0.05131 0.07917 0.93419 0.87355 0.4399 0.52526 251 251 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38096 38096 SRR1531460 SRX665247 SRS670061 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   10 somite stage secti1d from anterior to posterior end replicate GSM1448804   tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo 10 somite stage secti1d from anterior to posterior end replicate Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo GSM1448804 GSM1448804: 10 somite stage secti1d from anterior to posterior end replicate; Danio rerio; RNA Seq GSM1448804   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448804 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_10ss_AP2_R1.fastq.gz dr_10ss_AP2_R2.fastq.gz fastq fastq 2096761878.0 20556489.0 GSM1448804 r1 0:51 1:51 A:486131317;C:330426143;G:323887100;T:938024368;N:18292950 51 51     486131317 330426143 323887100 938024368 18292950 SRX665247 SRS670061 SRA177126 GEO Hubrecht Institute 2 0.0484 0.78914 0.0396 0.12303 0.9866 0.78234 0.53395 0.53422 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38097 38097 SRR1531458 SRX665246 SRS670060 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   10 somite stage secti1d from anterior to posterior end GSM1448803   tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo 10 somite stage secti1d from anterior to posterior end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo GSM1448803 GSM1448803: 10 somite stage secti1d from anterior to posterior end; Danio rerio; RNA Seq GSM1448803   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448803 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_10ss_AP_R2.fastq.gz dr_10ss_AP_R1.fastq.gz fastq fastq 3873169500.0 37972250.0 GSM1448803 r1 0:51 1:51 A:844434990;C:614503150;G:615061181;T:1763736099;N:35434080 51 51     844434990 614503150 615061181 1763736099 35434080 SRX665246 SRS670060 SRA177126 GEO Hubrecht Institute 2 0.0354 0.81065 0.02893 0.12263 0.98944 0.77386 0.52631 0.52007 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38098 38098 SRR1531459 SRX665246 SRS670060 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   10 somite stage secti1d from anterior to posterior end GSM1448803   tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo 10 somite stage secti1d from anterior to posterior end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo GSM1448803 GSM1448803: 10 somite stage secti1d from anterior to posterior end; Danio rerio; RNA Seq GSM1448803   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448803 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_10ss_AP_R1.fastq.gz miseq_dr_10ss_AP_R2.fastq.gz fastq fastq 496084013.0 990096.0 GSM1448803 r2 0:251 1:250.05 A:161790706;C:99237964;G:85634725;T:149420610;N:8 251 250     161790706 99237964 85634725 149420610 8 SRX665246 SRS670060 SRA177126 GEO Hubrecht Institute 2 0.35483 0.66804 0.06659 0.09269 0.92699 0.86113 0.53381 0.51797 251 251 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38099 38099 SRR1531457 SRX665245 SRS670059 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from dorsal to ventral end replicate GSM1448802   tissue:whole embryo|Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from dorsal to ventral end replicate Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo GSM1448802 GSM1448802: shield stage secti1d from dorsal to ventral end replicate; Danio rerio; RNA Seq GSM1448802   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448802 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_shield_DV2_R2.fastq.gz dr_shield_DV2_R1.fastq.gz fastq fastq 2735350014.0 26817157.0 GSM1448802 r1 0:51 1:51 A:650077339;C:412458828;G:411687121;T:1237686190;N:23440536 51 51     650077339 412458828 411687121 1237686190 23440536 SRX665245 SRS670059 SRA177126 GEO Hubrecht Institute 2 0.02556 0.75175 0.01912 0.10697 0.99076 0.79819 0.54093 0.55229 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38100 38100 SRR1531455 SRX665244 SRS670058 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from dorsal to ventral end GSM1448801   tissue:whole embryo|Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from dorsal to ventral end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo GSM1448801 GSM1448801: shield stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq GSM1448801   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448801 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_shield_DV_R1.fastq.gz dr_shield_DV_R2.fastq.gz fastq fastq 1605318738.0 15738419.0 GSM1448801 r1 0:51 1:51 A:361176217;C:248822696;G:253372108;T:726629351;N:15318366 51 51     361176217 248822696 253372108 726629351 15318366 SRX665244 SRS670058 SRA177126 GEO Hubrecht Institute 2 0.02633 0.68496 0.02344 0.10104 0.99638 0.80006 0.46031 0.57655 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38101 38101 SRR1531456 SRX665244 SRS670058 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from dorsal to ventral end GSM1448801   tissue:whole embryo|Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from dorsal to ventral end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo GSM1448801 GSM1448801: shield stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq GSM1448801   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448801 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_shield_DV_R1.fastq.gz miseq_dr_shield_DV_R2.fastq.gz fastq fastq 114907294.0 229320.0 GSM1448801 r2 0:251 1:250.08 A:37813553;C:24168661;G:19441624;T:33483456;N:0 251 250     37813553 24168661 19441624 33483456 0 SRX665244 SRS670058 SRA177126 GEO Hubrecht Institute 2 0.26022 0.46204 0.03083 0.05933 0.94627 0.89301 0.56728 0.55478 251 250 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38102 38102 SRR1531453 SRX665243 SRS670056 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from ventral to dorsal end GSM1448800   tissue:whole embryo|Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from ventral to dorsal end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo GSM1448800 GSM1448800: shield stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq GSM1448800   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448800 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_shield_VD_R1.fastq.gz dr_shield_VD_R2.fastq.gz fastq fastq 1840839492.0 18047446.0 GSM1448800 r1 0:51 1:51 A:421253850;C:292045914;G:295175858;T:814744774;N:17619096 51 51     421253850 292045914 295175858 814744774 17619096 SRX665243 SRS670056 SRA177126 GEO Hubrecht Institute 2 0.01815 0.6287 0.01468 0.09567 0.99452 0.80975 0.5259 0.58926 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38103 38103 SRR1531454 SRX665243 SRS670056 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from ventral to dorsal end GSM1448800   tissue:whole embryo|Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from ventral to dorsal end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo GSM1448800 GSM1448800: shield stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq GSM1448800   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448800 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_shield_VD_R2.fastq.gz miseq_dr_shield_VD_R1.fastq.gz fastq fastq 158531701.0 316379.0 GSM1448800 r2                       SRX665243 SRS670056 SRA177126 GEO Hubrecht Institute 2 0.06803 0.1733 0.00916 0.026 0.94085 0.88899 0.58254 0.5723 251 251 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38104 38104 SRR1531451 SRX665242 SRS670055 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from right to left GSM1448799   tissue:whole embryo|Stage:shield stage|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from right to left Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo GSM1448799 GSM1448799: shield stage secti1d from right to left; Danio rerio; RNA Seq GSM1448799   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448799 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_shield_RL_R1.fastq.gz dr_shield_RL_R2.fastq.gz fastq fastq 2003076918.0 19638009.0 GSM1448799 r1 0:51 1:51 A:457537608;C:308292947;G:312973612;T:905317961;N:18954790 51 51     457537608 308292947 312973612 905317961 18954790 SRX665242 SRS670055 SRA177126 GEO Hubrecht Institute 2 0.02111 0.7573 0.01656 0.11316 0.99364 0.8005 0.4501 0.59142 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38105 38105 SRR1531452 SRX665242 SRS670055 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from right to left GSM1448799   tissue:whole embryo|Stage:shield stage|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from right to left Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo GSM1448799 GSM1448799: shield stage secti1d from right to left; Danio rerio; RNA Seq GSM1448799   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448799 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_shield_RL_R1.fastq.gz miseq_dr_shield_RL_R2.fastq.gz fastq fastq 154180181.0 307695.0 GSM1448799 r2 0:251 1:250.08 A:50801230;C:32293099;G:25917988;T:45167860;N:4 251 250     50801230 32293099 25917988 45167860 4 SRX665242 SRS670055 SRA177126 GEO Hubrecht Institute 2 0.31553 0.64085 0.03613 0.06829 0.94101 0.8938 0.60272 0.58117 251 251 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38106 38106 SRR1531449 SRX665241 SRS670053 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from left to right GSM1448798   tissue:whole embryo|Stage:shield stage|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from left to right Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo GSM1448798 GSM1448798: shield stage secti1d from left to right; Danio rerio; RNA Seq GSM1448798   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448798 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_shield_LR_R1.fastq.gz dr_shield_LR_R2.fastq.gz fastq fastq 1755442542.0 17210221.0 GSM1448798 r1 0:51 1:51 A:401133098;C:265688355;G:264899378;T:807011867;N:16709844 51 51     401133098 265688355 264899378 807011867 16709844 SRX665241 SRS670053 SRA177126 GEO Hubrecht Institute 2 0.02829 0.71918 0.02455 0.14486 0.99484 0.79866 0.50383 0.57925 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38107 38107 SRR1531450 SRX665241 SRS670053 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from left to right GSM1448798   tissue:whole embryo|Stage:shield stage|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from left to right Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo GSM1448798 GSM1448798: shield stage secti1d from left to right; Danio rerio; RNA Seq GSM1448798   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448798 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_shield_LR_R1.fastq.gz miseq_dr_shield_LR_R2.fastq.gz fastq fastq 139755993.0 278913.0 GSM1448798 r2 0:251 1:250.07 A:46536591;C:28346077;G:23036783;T:41836538;N:4 251 250     46536591 28346077 23036783 41836538 4 SRX665241 SRS670053 SRA177126 GEO Hubrecht Institute 2 0.27443 0.57858 0.06346 0.09954 0.94194 0.89522 0.55896 0.56169 251 251 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38108 38108 SRR1531448 SRX665240 SRS670054 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from vegetal to animal pole replicate GSM1448797   tissue:whole embryo|Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from vegetal to animal pole replicate Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo GSM1448797 GSM1448797: shield stage secti1d from vegetal to animal pole replicate; Danio rerio; RNA Seq GSM1448797   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448797 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_shield_VA2_R1.fastq.gz dr_shield_VA2_R2.fastq.gz fastq fastq 1962884532.0 19243966.0 GSM1448797 r1 0:51 1:51 A:449529690;C:292065368;G:287973067;T:916330652;N:16985755 51 51     449529690 292065368 287973067 916330652 16985755 SRX665240 SRS670054 SRA177126 GEO Hubrecht Institute 2 0.04512 0.77455 0.03997 0.11233 0.99293 0.78488 0.50931 0.5171 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38109 38109 SRR1531446 SRX665239 SRS670057 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from vegetal to animal pole GSM1448796   tissue:whole embryo|Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from vegetal to animal pole Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo GSM1448796 GSM1448796: shield stage secti1d from vegetal to animal pole; Danio rerio; RNA Seq GSM1448796   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448796 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_shield_VA_R2.fastq.gz dr_shield_VA_R1.fastq.gz fastq fastq 2367839934.0 23214117.0 GSM1448796 r1 0:51 1:51 A:544061124;C:369321045;G:383489434;T:1047897582;N:23070749 51 51     544061124 369321045 383489434 1047897582 23070749 SRX665239 SRS670057 SRA177126 GEO Hubrecht Institute 2 0.02284 0.57831 0.0199 0.08251 0.99579 0.81653 0.4451 0.5792 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38110 38110 SRR1531447 SRX665239 SRS670057 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from vegetal to animal pole GSM1448796   tissue:whole embryo|Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from vegetal to animal pole Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo GSM1448796 GSM1448796: shield stage secti1d from vegetal to animal pole; Danio rerio; RNA Seq GSM1448796   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448796 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_shield_VA_R1.fastq.gz miseq_dr_shield_VA_R2.fastq.gz fastq fastq 139677889.0 278764.0 GSM1448796 r2 0:251 1:250.06 A:45877333;C:29821713;G:24032460;T:39946380;N:3 251 250     45877333 29821713 24032460 39946380 3 SRX665239 SRS670057 SRA177126 GEO Hubrecht Institute 2 0.21444 0.33364 0.02489 0.04529 0.95156 0.901 0.56549 0.55749 251 251 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38111 38111 SRR1531444 SRX665238 SRS670052 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from animal to vegetal pole GSM1448795   tissue:whole embryo|Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from animal to vegetal pole Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 µm|embedding strategy:intact embryo GSM1448795 GSM1448795: shield stage secti1d from animal to vegetal pole; Danio rerio; RNA Seq GSM1448795   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448795 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_shield_AV_R1.fastq.gz dr_shield_AV_R2.fastq.gz fastq fastq 2059615110.0 20192305.0 GSM1448795 r1 0:51 1:51 A:487942041;C:328047311;G:336282927;T:886836259;N:20506572 51 51     487942041 328047311 336282927 886836259 20506572 SRX665238 SRS670052 SRA177126 GEO Hubrecht Institute 2 0.01633 0.50842 0.0136 0.07269 0.99541 0.82183 0.51242 0.59281 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38112 38112 SRR1531445 SRX665238 SRS670052 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from animal to vegetal pole GSM1448795   tissue:whole embryo|Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from animal to vegetal pole Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 µm|embedding strategy:intact embryo GSM1448795 GSM1448795: shield stage secti1d from animal to vegetal pole; Danio rerio; RNA Seq GSM1448795   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448795 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_shield_AV_R1.fastq.gz miseq_dr_shield_AV_R2.fastq.gz fastq fastq 176530873.0 352271.0 GSM1448795 r2 0:251 1:250.12 A:57029265;C:38838035;G:30065677;T:50597891;N:5 251 250     57029265 38838035 30065677 50597891 5 SRX665238 SRS670052 SRA177126 GEO Hubrecht Institute 2 0.20318 0.26844 0.02342 0.03751 0.95499 0.9069 0.4325 0.57102 251 251 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38122 38122 SRR1555598 SRX684706 SRS687823 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0106 GSM1483841   tissue:single embryo Metazome ZF timecourse sample 0106 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:4240 GSM1483841 GSM1483841: Metazome ZF timecourse sample 0106; Danio rerio; RNA Seq GSM1483841   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483841 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0106.fastq.gz fastq 3911705.0 111763.0 GSM1483841 r1 0:35 A:1100064;C:790487;G:836206;T:1169251;N:15697 35       1100064 790487 836206 1169251 15697 SRX684706 SRS687823 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.72414   0.09461   0.96725   0.4942   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38123 38123 SRR1555597 SRX684705 SRS687821 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0105 GSM1483840   tissue:single embryo Metazome ZF timecourse sample 0105 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:4200 GSM1483840 GSM1483840: Metazome ZF timecourse sample 0105; Danio rerio; RNA Seq GSM1483840   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483840 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0105.fastq.gz fastq 32877145.0 939347.0 GSM1483840 r1 0:35 A:9524894;C:6625944;G:6696548;T:9953576;N:76183 35       9524894 6625944 6696548 9953576 76183 SRX684705 SRS687821 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.74436   0.07095   0.88201   0.47612   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38124 38124 SRR1555596 SRX684704 SRS687822 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0104 GSM1483839   tissue:single embryo Metazome ZF timecourse sample 0104 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:4160 GSM1483839 GSM1483839: Metazome ZF timecourse sample 0104; Danio rerio; RNA Seq GSM1483839   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483839 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0104.fastq.gz fastq 83810020.0 2394572.0 GSM1483839 r1 0:35 A:24075610;C:16799998;G:16694424;T:25967423;N:272565 35       24075610 16799998 16694424 25967423 272565 SRX684704 SRS687822 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.7588   0.07993   0.84449   0.49785   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38125 38125 SRR1555595 SRX684703 SRS687820 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0103 GSM1483838   tissue:single embryo Metazome ZF timecourse sample 0103 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:4120 GSM1483838 GSM1483838: Metazome ZF timecourse sample 0103; Danio rerio; RNA Seq GSM1483838   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483838 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0103.fastq.gz fastq 98206150.0 2805890.0 GSM1483838 r1 0:35 A:28361916;C:19232789;G:19589483;T:30798968;N:222994 35       28361916 19232789 19589483 30798968 222994 SRX684703 SRS687820 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.75509   0.13429   0.81117   0.49102   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38126 38126 SRR1555594 SRX684702 SRS687819 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0102 GSM1483837   tissue:single embryo Metazome ZF timecourse sample 0102 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:4080 GSM1483837 GSM1483837: Metazome ZF timecourse sample 0102; Danio rerio; RNA Seq GSM1483837   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483837 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0102.fastq.gz fastq 192817835.0 5509081.0 GSM1483837 r1 0:35 A:55969077;C:36880901;G:37835921;T:61101558;N:1030378 35       55969077 36880901 37835921 61101558 1030378 SRX684702 SRS687819 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.73387   0.17245   0.80164   0.48657   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38127 38127 SRR1555593 SRX684701 SRS687818 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0101 GSM1483836   tissue:single embryo Metazome ZF timecourse sample 0101 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:4040 GSM1483836 GSM1483836: Metazome ZF timecourse sample 0101; Danio rerio; RNA Seq GSM1483836   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483836 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0101.fastq.gz fastq 374339455.0 10695413.0 GSM1483836 r1 0:35 A:112191846;C:73679996;G:73185024;T:114766825;N:515764 35       112191846 73679996 73185024 114766825 515764 SRX684701 SRS687818 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.83131   0.16618   0.77812   0.49895   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38128 38128 SRR1555592 SRX684700 SRS687816 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0100 GSM1483835   tissue:single embryo Metazome ZF timecourse sample 0100 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:4000 GSM1483835 GSM1483835: Metazome ZF timecourse sample 0100; Danio rerio; RNA Seq GSM1483835   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483835 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0100.fastq.gz fastq 15239420.0 435412.0 GSM1483835 r1 0:35 A:4361241;C:3088134;G:3269084;T:4498093;N:22868 35       4361241 3088134 3269084 4498093 22868 SRX684700 SRS687816 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.7702   0.17879   0.92904   0.505   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38129 38129 SRR1555591 SRX684699 SRS687817 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0099 GSM1483834   tissue:single embryo Metazome ZF timecourse sample 0099 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3960 GSM1483834 GSM1483834: Metazome ZF timecourse sample 0099; Danio rerio; RNA Seq GSM1483834   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483834 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0099.fastq.gz fastq 284196500.0 8119900.0 GSM1483834 r1 0:35 A:81991733;C:57440756;G:58362818;T:86010858;N:390335 35       81991733 57440756 58362818 86010858 390335 SRX684699 SRS687817 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.81284   0.1715   0.78468   0.49472   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38130 38130 SRR1555590 SRX684698 SRS687815 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0098 GSM1483833   tissue:single embryo Metazome ZF timecourse sample 0098 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3920 GSM1483833 GSM1483833: Metazome ZF timecourse sample 0098; Danio rerio; RNA Seq GSM1483833   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483833 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0098.fastq.gz fastq 244245015.0 6978429.0 GSM1483833 r1 0:35 A:70141725;C:48500061;G:50748992;T:74478239;N:375998 35       70141725 48500061 50748992 74478239 375998 SRX684698 SRS687815 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.79668   0.17718   0.79271   0.45966   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38131 38131 SRR1555589 SRX684697 SRS687814 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0097 GSM1483832   tissue:single embryo Metazome ZF timecourse sample 0097 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3880 GSM1483832 GSM1483832: Metazome ZF timecourse sample 0097; Danio rerio; RNA Seq GSM1483832   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483832 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0097.fastq.gz fastq 215347510.0 6152786.0 GSM1483832 r1 0:35 A:62928172;C:42420829;G:43902946;T:65803342;N:292221 35       62928172 42420829 43902946 65803342 292221 SRX684697 SRS687814 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.80605   0.17396   0.78873   0.50241   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38132 38132 SRR1555588 SRX684696 SRS687813 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0096 GSM1483831   tissue:single embryo Metazome ZF timecourse sample 0096 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3840 GSM1483831 GSM1483831: Metazome ZF timecourse sample 0096; Danio rerio; RNA Seq GSM1483831   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483831 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0096.fastq.gz fastq 13992230.0 399778.0 GSM1483831 r1 0:35 A:4077402;C:2837417;G:2856511;T:4200750;N:20150 35       4077402 2837417 2856511 4200750 20150 SRX684696 SRS687813 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.77543   0.14778   0.93288   0.48967   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38133 38133 SRR1555587 SRX684695 SRS687811 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0095 GSM1483830   tissue:single embryo Metazome ZF timecourse sample 0095 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3800 GSM1483830 GSM1483830: Metazome ZF timecourse sample 0095; Danio rerio; RNA Seq GSM1483830   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483830 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0095.fastq.gz fastq 290151435.0 8290041.0 GSM1483830 r1 0:35 A:86694666;C:56953853;G:57315219;T:88811589;N:376108 35       86694666 56953853 57315219 88811589 376108 SRX684695 SRS687811 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.79098   0.18155   0.79034   0.51338   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38134 38134 SRR1555586 SRX684694 SRS687810 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0094 GSM1483829   tissue:single embryo Metazome ZF timecourse sample 0094 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3760 GSM1483829 GSM1483829: Metazome ZF timecourse sample 0094; Danio rerio; RNA Seq GSM1483829   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483829 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0094.fastq.gz fastq 645422925.0 18440655.0 GSM1483829 r1 0:35 A:186408265;C:127218686;G:131406509;T:199399112;N:990353 35       186408265 127218686 131406509 199399112 990353 SRX684694 SRS687810 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.81184   0.15572   0.78496   0.48733   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38135 38135 SRR1555585 SRX684693 SRS687812 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0093 GSM1483828   tissue:single embryo Metazome ZF timecourse sample 0093 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3720 GSM1483828 GSM1483828: Metazome ZF timecourse sample 0093; Danio rerio; RNA Seq GSM1483828   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483828 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0093.fastq.gz fastq 82574205.0 2359263.0 GSM1483828 r1 0:35 A:24239984;C:16625180;G:16309055;T:25123568;N:276418 35       24239984 16625180 16309055 25123568 276418 SRX684693 SRS687812 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.75557   0.14554   0.82205   0.49736   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38136 38136 SRR1555584 SRX684692 SRS687809 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0092 GSM1483827   tissue:single embryo Metazome ZF timecourse sample 0092 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3680 GSM1483827 GSM1483827: Metazome ZF timecourse sample 0092; Danio rerio; RNA Seq GSM1483827   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483827 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0092.fastq.gz fastq 72186905.0 2062483.0 GSM1483827 r1 0:35 A:21349438;C:14361391;G:14472348;T:21766197;N:237531 35       21349438 14361391 14472348 21766197 237531 SRX684692 SRS687809 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.74348   0.13614   0.8309   0.51328   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38137 38137 SRR1555583 SRX684691 SRS687808 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0091 GSM1483826   tissue:single embryo Metazome ZF timecourse sample 0091 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3640 GSM1483826 GSM1483826: Metazome ZF timecourse sample 0091; Danio rerio; RNA Seq GSM1483826   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483826 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0091.fastq.gz fastq 18405940.0 525884.0 GSM1483826 r1 0:35 A:5374937;C:3766785;G:3774551;T:5451369;N:38298 35       5374937 3766785 3774551 5451369 38298 SRX684691 SRS687808 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.74005   0.11089   0.91494   0.49823   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38138 38138 SRR1555582 SRX684690 SRS687807 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0090 GSM1483825   tissue:single embryo Metazome ZF timecourse sample 0090 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3600 GSM1483825 GSM1483825: Metazome ZF timecourse sample 0090; Danio rerio; RNA Seq GSM1483825   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483825 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0090.fastq.gz fastq 141938265.0 4055379.0 GSM1483825 r1 0:35 A:41371650;C:28115945;G:29356068;T:42485478;N:609124 35       41371650 28115945 29356068 42485478 609124 SRX684690 SRS687807 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.71151   0.17711   0.82789   0.52369   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38139 38139 SRR1555581 SRX684689 SRS687806 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0089 GSM1483824   tissue:single embryo Metazome ZF timecourse sample 0089 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3560 GSM1483824 GSM1483824: Metazome ZF timecourse sample 0089; Danio rerio; RNA Seq GSM1483824   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483824 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0089.fastq.gz fastq 99569015.0 2844829.0 GSM1483824 r1 0:35 A:28763571;C:20065085;G:19332839;T:31088193;N:319327 35       28763571 20065085 19332839 31088193 319327 SRX684689 SRS687806 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.74177   0.13103   0.81854   0.51184   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38140 38140 SRR1555580 SRX684688 SRS687805 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0088 GSM1483823   tissue:single embryo Metazome ZF timecourse sample 0088 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3520 GSM1483823 GSM1483823: Metazome ZF timecourse sample 0088; Danio rerio; RNA Seq GSM1483823   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483823 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0088.fastq.gz fastq 168790055.0 4822573.0 GSM1483823 r1 0:35 A:49034449;C:32785565;G:33439918;T:52997820;N:532303 35       49034449 32785565 33439918 52997820 532303 SRX684688 SRS687805 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.73454   0.15775   0.8047   0.50587   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38141 38141 SRR1555579 SRX684687 SRS687803 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0087 GSM1483822   tissue:single embryo Metazome ZF timecourse sample 0087 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3480 GSM1483822 GSM1483822: Metazome ZF timecourse sample 0087; Danio rerio; RNA Seq GSM1483822   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483822 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0087.fastq.gz fastq 83155975.0 2375885.0 GSM1483822 r1 0:35 A:23985678;C:16871573;G:17048421;T:25086100;N:164203 35       23985678 16871573 17048421 25086100 164203 SRX684687 SRS687803 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.75055   0.10258   0.83952   0.49914   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38142 38142 SRR1555578 SRX684686 SRS687804 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0086 GSM1483821   tissue:single embryo Metazome ZF timecourse sample 0086 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3440 GSM1483821 GSM1483821: Metazome ZF timecourse sample 0086; Danio rerio; RNA Seq GSM1483821   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483821 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0086.fastq.gz fastq 36772155.0 1050633.0 GSM1483821 r1 0:35 A:10536765;C:7377251;G:7701105;T:11014088;N:142946 35       10536765 7377251 7701105 11014088 142946 SRX684686 SRS687804 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.745   0.08312   0.88209   0.52632   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38143 38143 SRR1555577 SRX684685 SRS687802 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0085 GSM1483820   tissue:single embryo Metazome ZF timecourse sample 0085 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3400 GSM1483820 GSM1483820: Metazome ZF timecourse sample 0085; Danio rerio; RNA Seq GSM1483820   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483820 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0085.fastq.gz fastq 142281650.0 4065190.0 GSM1483820 r1 0:35 A:41238155;C:28228882;G:28727190;T:43901346;N:186077 35       41238155 28228882 28727190 43901346 186077 SRX684685 SRS687802 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.80695   0.14045   0.80361   0.5   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38144 38144 SRR1555576 SRX684684 SRS687800 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0084 GSM1483819   tissue:single embryo Metazome ZF timecourse sample 0084 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3360 GSM1483819 GSM1483819: Metazome ZF timecourse sample 0084; Danio rerio; RNA Seq GSM1483819   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483819 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0084.fastq.gz fastq 147589295.0 4216837.0 GSM1483819 r1 0:35 A:42100013;C:30125860;G:31767504;T:43391728;N:204190 35       42100013 30125860 31767504 43391728 204190 SRX684684 SRS687800 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.80373   0.08661   0.83157   0.51923   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38145 38145 SRR1555575 SRX684683 SRS687801 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0083 GSM1483818   tissue:single embryo Metazome ZF timecourse sample 0083 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3320 GSM1483818 GSM1483818: Metazome ZF timecourse sample 0083; Danio rerio; RNA Seq GSM1483818   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483818 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0083.fastq.gz fastq 147243985.0 4206971.0 GSM1483818 r1 0:35 A:42533757;C:29874233;G:30500611;T:44132167;N:203217 35       42533757 29874233 30500611 44132167 203217 SRX684683 SRS687801 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.80738   0.08642   0.82219   0.49396   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38146 38146 SRR1555574 SRX684682 SRS687799 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0082 GSM1483817   tissue:single embryo Metazome ZF timecourse sample 0082 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3280 GSM1483817 GSM1483817: Metazome ZF timecourse sample 0082; Danio rerio; RNA Seq GSM1483817   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483817 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0082.fastq.gz fastq 96747735.0 2764221.0 GSM1483817 r1 0:35 A:26768730;C:19578598;G:21713242;T:28549716;N:137449 35       26768730 19578598 21713242 28549716 137449 SRX684682 SRS687799 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.80738   0.09417   0.85167   0.50713   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38147 38147 SRR1555573 SRX684681 SRS687798 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0081 GSM1483816   tissue:single embryo Metazome ZF timecourse sample 0081 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3240 GSM1483816 GSM1483816: Metazome ZF timecourse sample 0081; Danio rerio; RNA Seq GSM1483816   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483816 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0081.fastq.gz fastq 158402895.0 4525797.0 GSM1483816 r1 0:35 A:46939694;C:31610300;G:32050592;T:47571349;N:230960 35       46939694 31610300 32050592 47571349 230960 SRX684681 SRS687798 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.78709   0.11916   0.82351   0.48714   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38148 38148 SRR1555572 SRX684680 SRS687797 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0080 GSM1483815   tissue:single embryo Metazome ZF timecourse sample 0080 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3200 GSM1483815 GSM1483815: Metazome ZF timecourse sample 0080; Danio rerio; RNA Seq GSM1483815   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483815 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0080.fastq.gz fastq 1432375.0 40925.0 GSM1483815 r1 0:35 A:422951;C:297837;G:308257;T:400778;N:2552 35       422951 297837 308257 400778 2552 SRX684680 SRS687797 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.7103   0.12471   0.9811   0.57619   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38149 38149 SRR1555571 SRX684679 SRS687796 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0079 GSM1483814   tissue:single embryo Metazome ZF timecourse sample 0079 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3160 GSM1483814 GSM1483814: Metazome ZF timecourse sample 0079; Danio rerio; RNA Seq GSM1483814   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483814 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0079.fastq.gz fastq 171937640.0 4912504.0 GSM1483814 r1 0:35 A:49235964;C:34067309;G:35846095;T:52553397;N:234875 35       49235964 34067309 35846095 52553397 234875 SRX684679 SRS687796 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.79389   0.14252   0.81107   0.50474   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38150 38150 SRR1555570 SRX684678 SRS687795 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0078 GSM1483813   tissue:single embryo Metazome ZF timecourse sample 0078 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3120 GSM1483813 GSM1483813: Metazome ZF timecourse sample 0078; Danio rerio; RNA Seq GSM1483813   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483813 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0078.fastq.gz fastq 220246950.0 6292770.0 GSM1483813 r1 0:35 A:63723749;C:43666354;G:45504302;T:67009596;N:342949 35       63723749 43666354 45504302 67009596 342949 SRX684678 SRS687795 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.80813   0.1512   0.80174   0.49937   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38151 38151 SRR1555569 SRX684677 SRS687794 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0077 GSM1483812   tissue:single embryo Metazome ZF timecourse sample 0077 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3080 GSM1483812 GSM1483812: Metazome ZF timecourse sample 0077; Danio rerio; RNA Seq GSM1483812   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483812 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0077.fastq.gz fastq 93138675.0 2661105.0 GSM1483812 r1 0:35 A:27102533;C:18314712;G:18498218;T:29006764;N:216448 35       27102533 18314712 18498218 29006764 216448 SRX684677 SRS687794 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.75818   0.11499   0.81572   0.50169   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38152 38152 SRR1555568 SRX684676 SRS687793 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0076 GSM1483811   tissue:single embryo Metazome ZF timecourse sample 0076 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3040 GSM1483811 GSM1483811: Metazome ZF timecourse sample 0076; Danio rerio; RNA Seq GSM1483811   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483811 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0076.fastq.gz fastq 118512415.0 3386069.0 GSM1483811 r1 0:35 A:33806370;C:23395934;G:24547522;T:36374942;N:387647 35       33806370 23395934 24547522 36374942 387647 SRX684676 SRS687793 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.75326   0.1088   0.81667   0.49341   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38153 38153 SRR1555567 SRX684675 SRS687792 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0075 GSM1483810   tissue:single embryo Metazome ZF timecourse sample 0075 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:3000 GSM1483810 GSM1483810: Metazome ZF timecourse sample 0075; Danio rerio; RNA Seq GSM1483810   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483810 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0075.fastq.gz fastq 2520525.0 72015.0 GSM1483810 r1 0:35 A:818327;C:420638;G:441967;T:833315;N:6278 35       818327 420638 441967 833315 6278 SRX684675 SRS687792 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.7119   0.22445   0.97368   0.51561   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38154 38154 SRR1555566 SRX684674 SRS687791 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0074 GSM1483809   tissue:single embryo Metazome ZF timecourse sample 0074 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2960 GSM1483809 GSM1483809: Metazome ZF timecourse sample 0074; Danio rerio; RNA Seq GSM1483809   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483809 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0074.fastq.gz fastq 95385710.0 2725306.0 GSM1483809 r1 0:35 A:27032549;C:18681500;G:19490852;T:29708978;N:471831 35       27032549 18681500 19490852 29708978 471831 SRX684674 SRS687791 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.75216   0.09004   0.83469   0.48768   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38155 38155 SRR1555565 SRX684673 SRS687790 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0073 GSM1483808   tissue:single embryo Metazome ZF timecourse sample 0073 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2920 GSM1483808 GSM1483808: Metazome ZF timecourse sample 0073; Danio rerio; RNA Seq GSM1483808   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483808 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0073.fastq.gz fastq 149165835.0 4261881.0 GSM1483808 r1 0:35 A:42991931;C:29913953;G:30117935;T:45803552;N:338464 35       42991931 29913953 30117935 45803552 338464 SRX684673 SRS687790 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.76488   0.10545   0.80586   0.5046   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38156 38156 SRR1555564 SRX684672 SRS687789 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0072 GSM1483807   tissue:single embryo Metazome ZF timecourse sample 0072 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2880 GSM1483807 GSM1483807: Metazome ZF timecourse sample 0072; Danio rerio; RNA Seq GSM1483807   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483807 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0072.fastq.gz fastq 203829675.0 5823705.0 GSM1483807 r1 0:35 A:61171233;C:40047517;G:44515900;T:57461403;N:633622 35       61171233 40047517 44515900 57461403 633622 SRX684672 SRS687789 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.65225   0.10254   0.82014   0.50437   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38157 38157 SRR1555563 SRX684671 SRS687788 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0071 GSM1483806   tissue:single embryo Metazome ZF timecourse sample 0071 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2840 GSM1483806 GSM1483806: Metazome ZF timecourse sample 0071; Danio rerio; RNA Seq GSM1483806   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483806 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0071.fastq.gz fastq 107894360.0 3082696.0 GSM1483806 r1 0:35 A:30475809;C:22092085;G:22685204;T:32400616;N:240646 35       30475809 22092085 22685204 32400616 240646 SRX684671 SRS687788 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.77637   0.10375   0.81574   0.50918   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38158 38158 SRR1555562 SRX684670 SRS687787 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0070 GSM1483805   tissue:single embryo Metazome ZF timecourse sample 0070 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2800 GSM1483805 GSM1483805: Metazome ZF timecourse sample 0070; Danio rerio; RNA Seq GSM1483805   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483805 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0070.fastq.gz fastq 102775820.0 2936452.0 GSM1483805 r1 0:35 A:29014067;C:20865233;G:21656956;T:30738746;N:500818 35       29014067 20865233 21656956 30738746 500818 SRX684670 SRS687787 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.7643   0.09535   0.8325   0.51201   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38159 38159 SRR1555561 SRX684669 SRS687786 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0069 GSM1483804   tissue:single embryo Metazome ZF timecourse sample 0069 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2760 GSM1483804 GSM1483804: Metazome ZF timecourse sample 0069; Danio rerio; RNA Seq GSM1483804   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483804 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0069.fastq.gz fastq 178882445.0 5110927.0 GSM1483804 r1 0:35 A:51610621;C:35847602;G:36898756;T:54275519;N:249947 35       51610621 35847602 36898756 54275519 249947 SRX684669 SRS687786 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.81481   0.1212   0.80338   0.48647   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38160 38160 SRR1555560 SRX684668 SRS687784 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0068 GSM1483803   tissue:single embryo Metazome ZF timecourse sample 0068 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2720 GSM1483803 GSM1483803: Metazome ZF timecourse sample 0068; Danio rerio; RNA Seq GSM1483803   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483803 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0068.fastq.gz fastq 289924775.0 8283565.0 GSM1483803 r1 0:35 A:85968202;C:57218562;G:58533597;T:87797178;N:407236 35       85968202 57218562 58533597 87797178 407236 SRX684668 SRS687784 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.78411   0.12015   0.80736   0.5018   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38161 38161 SRR1555559 SRX684667 SRS687785 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0067 GSM1483802   tissue:single embryo Metazome ZF timecourse sample 0067 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2680 GSM1483802 GSM1483802: Metazome ZF timecourse sample 0067; Danio rerio; RNA Seq GSM1483802   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483802 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0067.fastq.gz fastq 12717355.0 363353.0 GSM1483802 r1 0:35 A:3757539;C:2504848;G:2608725;T:3830804;N:15439 35       3757539 2504848 2608725 3830804 15439 SRX684667 SRS687785 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.77835   0.12605   0.92604   0.45926   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38162 38162 SRR1555558 SRX684666 SRS687783 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0066 GSM1483801   tissue:single embryo Metazome ZF timecourse sample 0066 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2640 GSM1483801 GSM1483801: Metazome ZF timecourse sample 0066; Danio rerio; RNA Seq GSM1483801   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483801 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0066.fastq.gz fastq 5206040.0 148744.0 GSM1483801 r1 0:35 A:1490985;C:1039675;G:1088231;T:1579040;N:8109 35       1490985 1039675 1088231 1579040 8109 SRX684666 SRS687783 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.77355   0.11605   0.96587   0.48121   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38163 38163 SRR1555557 SRX684665 SRS687782 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0065 GSM1483800   tissue:single embryo Metazome ZF timecourse sample 0065 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2600 GSM1483800 GSM1483800: Metazome ZF timecourse sample 0065; Danio rerio; RNA Seq GSM1483800   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483800 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0065.fastq.gz fastq 49543620.0 1415532.0 GSM1483800 r1 0:35 A:13699613;C:9907599;G:10751987;T:15115154;N:69267 35       13699613 9907599 10751987 15115154 69267 SRX684665 SRS687782 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.81049   0.12615   0.86367   0.51632   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38164 38164 SRR1555556 SRX684664 SRS687781 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0064 GSM1483799   tissue:single embryo Metazome ZF timecourse sample 0064 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2560 GSM1483799 GSM1483799: Metazome ZF timecourse sample 0064; Danio rerio; RNA Seq GSM1483799   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483799 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0064.fastq.gz fastq 247601200.0 7074320.0 GSM1483799 r1 0:35 A:70332996;C:49278360;G:54252598;T:73390003;N:347243 35       70332996 49278360 54252598 73390003 347243 SRX684664 SRS687781 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.80448   0.14935   0.80975   0.54749   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38165 38165 SRR1555555 SRX684663 SRS687779 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0063 GSM1483798   tissue:single embryo Metazome ZF timecourse sample 0063 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2520 GSM1483798 GSM1483798: Metazome ZF timecourse sample 0063; Danio rerio; RNA Seq GSM1483798   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483798 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0063.fastq.gz fastq 139474895.0 3984997.0 GSM1483798 r1 0:35 A:39999821;C:27945450;G:29190975;T:42159133;N:179516 35       39999821 27945450 29190975 42159133 179516 SRX684663 SRS687779 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.80752   0.14329   0.81645   0.50673   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38166 38166 SRR1555554 SRX684662 SRS687780 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0062 GSM1483797   tissue:single embryo Metazome ZF timecourse sample 0062 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2480 GSM1483797 GSM1483797: Metazome ZF timecourse sample 0062; Danio rerio; RNA Seq GSM1483797   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483797 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0062.fastq.gz fastq 177095730.0 5059878.0 GSM1483797 r1 0:35 A:50196021;C:35043121;G:37861516;T:53732194;N:262878 35       50196021 35043121 37861516 53732194 262878 SRX684662 SRS687780 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.81092   0.13179   0.8199   0.49636   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38167 38167 SRR1555553 SRX684661 SRS687778 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0061 GSM1483796   tissue:single embryo Metazome ZF timecourse sample 0061 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2440 GSM1483796 GSM1483796: Metazome ZF timecourse sample 0061; Danio rerio; RNA Seq GSM1483796   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483796 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0061.fastq.gz fastq 117262810.0 3350366.0 GSM1483796 r1 0:35 A:33678050;C:23425078;G:24368870;T:35496994;N:293818 35       33678050 23425078 24368870 35496994 293818 SRX684661 SRS687778 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.71242   0.11354   0.83514   0.51134   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38168 38168 SRR1555552 SRX684660 SRS687777 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0060 GSM1483795   tissue:single embryo Metazome ZF timecourse sample 0060 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2400 GSM1483795 GSM1483795: Metazome ZF timecourse sample 0060; Danio rerio; RNA Seq GSM1483795   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483795 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0060.fastq.gz fastq 50485225.0 1442435.0 GSM1483795 r1 0:35 A:14629070;C:9936986;G:10066758;T:15611930;N:240481 35       14629070 9936986 10066758 15611930 240481 SRX684660 SRS687777 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.74045   0.14214   0.84703   0.50639   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38169 38169 SRR1555551 SRX684659 SRS687776 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0059 GSM1483794   tissue:single embryo Metazome ZF timecourse sample 0059 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2360 GSM1483794 GSM1483794: Metazome ZF timecourse sample 0059; Danio rerio; RNA Seq GSM1483794   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483794 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0059.fastq.gz fastq 129110905.0 3688883.0 GSM1483794 r1 0:35 A:37661404;C:25258511;G:25987964;T:39941302;N:261724 35       37661404 25258511 25987964 39941302 261724 SRX684659 SRS687776 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.74152   0.13117   0.81749   0.51022   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38170 38170 SRR1555550 SRX684658 SRS687775 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0058 GSM1483793   tissue:single embryo Metazome ZF timecourse sample 0058 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2320 GSM1483793 GSM1483793: Metazome ZF timecourse sample 0058; Danio rerio; RNA Seq GSM1483793   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483793 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0058.fastq.gz fastq 91514045.0 2614687.0 GSM1483793 r1 0:35 A:26231450;C:17984688;G:18624952;T:28210031;N:462924 35       26231450 17984688 18624952 28210031 462924 SRX684658 SRS687775 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.75933   0.13326   0.8294   0.50639   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38171 38171 SRR1555549 SRX684657 SRS687774 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0057 GSM1483792   tissue:single embryo Metazome ZF timecourse sample 0057 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2280 GSM1483792 GSM1483792: Metazome ZF timecourse sample 0057; Danio rerio; RNA Seq GSM1483792   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483792 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0057.fastq.gz fastq 254944305.0 7284123.0 GSM1483792 r1 0:35 A:73169774;C:51240668;G:52956333;T:76957748;N:619782 35       73169774 51240668 52956333 76957748 619782 SRX684657 SRS687774 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.75832   0.11669   0.80937   0.50798   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38172 38172 SRR1555548 SRX684656 SRS687773 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0056 GSM1483791   tissue:single embryo Metazome ZF timecourse sample 0056 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2240 GSM1483791 GSM1483791: Metazome ZF timecourse sample 0056; Danio rerio; RNA Seq GSM1483791   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483791 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0056.fastq.gz fastq 99176700.0 2833620.0 GSM1483791 r1 0:35 A:28266891;C:20096113;G:20730721;T:29621152;N:461823 35       28266891 20096113 20730721 29621152 461823 SRX684656 SRS687773 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.75342   0.1218   0.82982   0.52199   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38173 38173 SRR1555547 SRX684655 SRS687772 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0055 GSM1483790   tissue:single embryo Metazome ZF timecourse sample 0055 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2200 GSM1483790 GSM1483790: Metazome ZF timecourse sample 0055; Danio rerio; RNA Seq GSM1483790   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483790 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0055.fastq.gz fastq 151127480.0 4317928.0 GSM1483790 r1 0:35 A:43591040;C:30002113;G:30975524;T:46254070;N:304733 35       43591040 30002113 30975524 46254070 304733 SRX684655 SRS687772 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.75764   0.12465   0.81249   0.51762   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38174 38174 SRR1555546 SRX684654 SRS687771 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0054 GSM1483789   tissue:single embryo Metazome ZF timecourse sample 0054 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2160 GSM1483789 GSM1483789: Metazome ZF timecourse sample 0054; Danio rerio; RNA Seq GSM1483789   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483789 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0054.fastq.gz fastq 69059795.0 1973137.0 GSM1483789 r1 0:35 A:19683826;C:13807471;G:14484211;T:20733707;N:350580 35       19683826 13807471 14484211 20733707 350580 SRX684654 SRS687771 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.68459   0.10792   0.85865   0.53677   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38175 38175 SRR1555545 SRX684653 SRS687770 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0053 GSM1483788   tissue:single embryo Metazome ZF timecourse sample 0053 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2120 GSM1483788 GSM1483788: Metazome ZF timecourse sample 0053; Danio rerio; RNA Seq GSM1483788   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483788 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0053.fastq.gz fastq 191369430.0 5467698.0 GSM1483788 r1 0:35 A:53654936;C:37894425;G:41404133;T:58136035;N:279901 35       53654936 37894425 41404133 58136035 279901 SRX684653 SRS687770 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.80463   0.1324   0.81489   0.49   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38176 38176 SRR1555544 SRX684652 SRS687768 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0052 GSM1483787   tissue:single embryo Metazome ZF timecourse sample 0052 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2080 GSM1483787 GSM1483787: Metazome ZF timecourse sample 0052; Danio rerio; RNA Seq GSM1483787   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483787 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0052.fastq.gz fastq 215564930.0 6158998.0 GSM1483787 r1 0:35 A:63312652;C:41647031;G:43302090;T:66999251;N:303906 35       63312652 41647031 43302090 66999251 303906 SRX684652 SRS687768 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.79312   0.14581   0.80748   0.4943   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures
38177 38177 SRR1555543 SRX684651 SRS687769 SRP045679 PRJNA258656 Danio rerio high resolution developmental transcriptomic time course GSE60619 Transcriptome Analysis Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples parent bioproject:PRJNA287810 pubmed:26886793   Metazome ZF timecourse sample 0051 GSM1483786   tissue:single embryo Metazome ZF timecourse sample 0051 Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix single embryo   RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen. time min post fertilization:2040 GSM1483786 GSM1483786: Metazome ZF timecourse sample 0051; Danio rerio; RNA Seq GSM1483786   1 RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used. GEO Accession:GSM1483786 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP045679     Metazome_ZF_timecourse_sample_0051.fastq.gz fastq 290737720.0 8306792.0 GSM1483786 r1 0:35 A:85354255;C:55749822;G:57830877;T:91385535;N:417231 35       85354255 55749822 57830877 91385535 417231 SRX684651 SRS687769 SRA179995 GEO Yanai, Biology, Technion - Israel Institute of Technology 1 0.79714   0.14915   0.80351   0.48212   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2014-08-21 Zygote Embryo Embryo Imprecise All anatomical structures

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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");;