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 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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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 48248,SRR7119805,SRX4041448,SRS3258926,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively,,pubmed:30867528,,Danio rerio RNAseq 3dpf mut8,GSM3131196,,tissue:whole embryo|strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / ,Danio rerio RNAseq 3dpf mut8,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,whole embryo,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.,strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / ,GSM3131196,GSM3131196: Danio rerio RNAseq 3dpf mut8; Danio rerio; RNA Seq,GSM3131196,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,GEO Accession:GSM3131196,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP144601,,,NDC-ring1b-3dpf-repl8-13282_R1.fastq.gz NDC-ring1b-3dpf-repl8-13282_R2.fastq.gz,fastq fastq,2586301116.0,30789299.0,GSM3131196 r1,0:42 1:42,A:689082798;C:590336938;G:600860389;T:705094245;N:926746,42,42,,,689082798,590336938,600860389,705094245,926746,SRX4041448,SRS3258926,SRA699717,GEO,"Molecular Biology, Radboud University",2,0.87813,0.89136,0.27656,0.27012,0.67351,0.6745,0.44828,0.44382,42,42,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Whole Organism,All anatomical structures 48249,SRR7119804,SRX4041447,SRS3258925,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively,,pubmed:30867528,,Danio rerio RNAseq 3dpf mut7,GSM3131195,,tissue:whole embryo|strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / ,Danio rerio RNAseq 3dpf mut7,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,whole embryo,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.,strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / ,GSM3131195,GSM3131195: Danio rerio RNAseq 3dpf mut7; Danio rerio; RNA Seq,GSM3131195,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,GEO Accession:GSM3131195,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP144601,,,NDC-ring1b-3dpf-repl7-13281_R2.fastq.gz NDC-ring1b-3dpf-repl7-13281_R1.fastq.gz,fastq fastq,1514220876.0,18026439.0,GSM3131195 r1,0:42 1:42,A:409686548;C:340910820;G:347249065;T:415826325;N:548118,42,42,,,409686548,340910820,347249065,415826325,548118,SRX4041447,SRS3258925,SRA699717,GEO,"Molecular Biology, Radboud University",2,0.88991,0.90191,0.30704,0.30119,0.66695,0.66922,0.45618,0.46008,42,42,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Whole Organism,All anatomical structures 48250,SRR7119802,SRX4041446,SRS3258924,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively,,pubmed:30867528,,Danio rerio RNAseq 3dpf mut6,GSM3131194,,tissue:whole embryo|strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / ,Danio rerio RNAseq 3dpf mut6,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,whole embryo,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.,strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / ,GSM3131194,GSM3131194: Danio rerio RNAseq 3dpf mut6; Danio rerio; RNA Seq,GSM3131194,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,GEO Accession:GSM3131194,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP144601,,,NDC-ring1b-3dpf-repl6-13280_R1.fastq.gz NDC-ring1b-3dpf-repl6-13280_R2.fastq.gz,fastq fastq,2265837168.0,26974252.0,GSM3131194 r1,0:42 1:42,A:528919905;C:579225021;G:616897328;T:539985252;N:809662,42,42,,,528919905,579225021,616897328,539985252,809662,SRX4041446,SRS3258924,SRA699717,GEO,"Molecular Biology, Radboud University",2,0.73468,0.76482,0.24568,0.25398,0.70516,0.70414,0.44042,0.43826,42,42,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Whole Organism,All anatomical structures 48251,SRR7119801,SRX4041445,SRS3258923,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively,,pubmed:30867528,,Danio rerio RNAseq 3dpf mut5,GSM3131193,,tissue:whole embryo|strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / ,Danio rerio RNAseq 3dpf mut5,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,whole embryo,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.,strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / ,GSM3131193,GSM3131193: Danio rerio RNAseq 3dpf mut5; Danio rerio; RNA Seq,GSM3131193,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,GEO Accession:GSM3131193,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP144601,,,NDC-ring1b-3dpf-repl5-13279_R1.fastq.gz NDC-ring1b-3dpf-repl5-13279_R2.fastq.gz,fastq fastq,2434539072.0,28982608.0,GSM3131193 r1,0:42 1:42,A:657750716;C:546331298;G:559727917;T:669858999;N:870142,42,42,,,657750716,546331298,559727917,669858999,870142,SRX4041445,SRS3258923,SRA699717,GEO,"Molecular Biology, Radboud University",2,0.88994,0.9052,0.31921,0.31753,0.67105,0.67245,0.43524,0.44685,42,42,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Whole Organism,All anatomical structures 48252,SRR7119800,SRX4041444,SRS3258922,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively,,pubmed:30867528,,Danio rerio RNAseq 3dpf mut3,GSM3131192,,tissue:whole embryo|strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / ,Danio rerio RNAseq 3dpf mut3,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,whole embryo,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.,strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / ,GSM3131192,GSM3131192: Danio rerio RNAseq 3dpf mut3; Danio rerio; RNA Seq,GSM3131192,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,GEO Accession:GSM3131192,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP144601,,,Ring1b-3dpf-replicate3-12247_R1.fastq.gz Ring1b-3dpf-replicate3-12247_R2.fastq.gz,fastq fastq,932865948.0,11105547.0,GSM3131192 r1,0:42 1:42,A:254207252;C:191875016;G:235114678;T:251619175;N:49827,42,42,,,254207252,191875016,235114678,251619175,49827,SRX4041444,SRS3258922,SRA699717,GEO,"Molecular Biology, Radboud University",2,0.83623,0.84228,0.56402,0.55503,0.69193,0.69045,0.46635,0.47045,42,42,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Whole Organism,All anatomical structures 48253,SRR7119799,SRX4041443,SRS3258933,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively,,pubmed:30867528,,Danio rerio RNAseq 3dpf mut2,GSM3131191,,tissue:whole embryo|strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / ,Danio rerio RNAseq 3dpf mut2,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,whole embryo,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.,strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / ,GSM3131191,GSM3131191: Danio rerio RNAseq 3dpf mut2; Danio rerio; RNA Seq,GSM3131191,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,GEO Accession:GSM3131191,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP144601,,,Ring1b-3dpf-replicate2-12246_R1.fastq.gz Ring1b-3dpf-replicate2-12246_R2.fastq.gz,fastq fastq,1428569856.0,17006784.0,GSM3131191 r1,0:42 1:42,A:375553518;C:323985274;G:352887011;T:376064416;N:79637,42,42,,,375553518,323985274,352887011,376064416,79637,SRX4041443,SRS3258933,SRA699717,GEO,"Molecular Biology, Radboud University",2,0.80267,0.81635,0.42059,0.41851,0.67598,0.67564,0.46878,0.47374,42,42,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Whole Organism,All anatomical structures 48254,SRR7119798,SRX4041442,SRS3258921,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively,,pubmed:30867528,,Danio rerio RNAseq 3dpf mut1,GSM3131190,,tissue:whole embryo|strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / ,Danio rerio RNAseq 3dpf mut1,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,whole embryo,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.,strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / ,GSM3131190,GSM3131190: Danio rerio RNAseq 3dpf mut1; Danio rerio; RNA Seq,GSM3131190,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,GEO Accession:GSM3131190,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP144601,,,Ring1b-3dpf-replicate1-12245_R1.fastq.gz Ring1b-3dpf-replicate1-12245_R2.fastq.gz,fastq fastq,1619814000.0,19283500.0,GSM3131190 r1,0:42 1:42,A:434648048;C:363147668;G:388048793;T:433881736;N:87755,42,42,,,434648048,363147668,388048793,433881736,87755,SRX4041442,SRS3258921,SRA699717,GEO,"Molecular Biology, Radboud University",2,0.79912,0.81304,0.45971,0.46081,0.67556,0.6759,0.46577,0.46988,42,42,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Whole Organism,All anatomical structures 48255,SRR7119797,SRX4041441,SRS3258932,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively,,pubmed:30867528,,Danio rerio RNAseq 3dpf wt13,GSM3131189,,tissue:whole embryo|strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type,Danio rerio RNAseq 3dpf wt13,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,whole embryo,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.,strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type,GSM3131189,GSM3131189: Danio rerio RNAseq 3dpf wt13; Danio rerio; RNA Seq,GSM3131189,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,GEO Accession:GSM3131189,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP144601,,,NDC-TLF-3dpf-repl13-13287_R1.fastq.gz NDC-TLF-3dpf-repl13-13287_R2.fastq.gz,fastq fastq,1535721936.0,18282404.0,GSM3131189 r1,0:42 1:42,A:403114263;C:355464889;G:362868285;T:413725995;N:548504,42,42,,,403114263,355464889,362868285,413725995,548504,SRX4041441,SRS3258932,SRA699717,GEO,"Molecular Biology, Radboud University",2,0.89271,0.90739,0.24124,0.23374,0.67292,0.67349,0.45333,0.45657,42,42,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Whole Organism,All anatomical structures 48256,SRR7119796,SRX4041440,SRS3258920,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively,,pubmed:30867528,,Danio rerio RNAseq 3dpf wt12,GSM3131188,,tissue:whole embryo|strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type,Danio rerio RNAseq 3dpf wt12,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,whole embryo,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.,strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type,GSM3131188,GSM3131188: Danio rerio RNAseq 3dpf wt12; Danio rerio; RNA Seq,GSM3131188,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,GEO Accession:GSM3131188,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP144601,,,NDC-TLF-3dpf-repl12-13286_R1.fastq.gz NDC-TLF-3dpf-repl12-13286_R2.fastq.gz,fastq fastq,1296768900.0,15437725.0,GSM3131188 r1,0:42 1:42,A:342053865;C:298842079;G:305530839;T:349875429;N:466688,42,42,,,342053865,298842079,305530839,349875429,466688,SRX4041440,SRS3258920,SRA699717,GEO,"Molecular Biology, Radboud University",2,0.88405,0.90076,0.25686,0.24808,0.67365,0.67156,0.44757,0.45604,42,42,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Whole Organism,All anatomical structures 48257,SRR7119795,SRX4041439,SRS3258919,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively,,pubmed:30867528,,Danio rerio RNAseq 3dpf wt11,GSM3131187,,tissue:whole embryo|strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type,Danio rerio RNAseq 3dpf wt11,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,whole embryo,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.,strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type,GSM3131187,GSM3131187: Danio rerio RNAseq 3dpf wt11; Danio rerio; RNA Seq,GSM3131187,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,GEO Accession:GSM3131187,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP144601,,,NDC-TLF-3dpf-repl11-13285_R1.fastq.gz NDC-TLF-3dpf-repl11-13285_R2.fastq.gz,fastq fastq,2485819560.0,29593090.0,GSM3131187 r1,0:42 1:42,A:637012348;C:587468873;G:621718352;T:638709810;N:910177,42,42,,,637012348,587468873,621718352,638709810,910177,SRX4041439,SRS3258919,SRA699717,GEO,"Molecular Biology, Radboud University",2,0.81173,0.83081,0.26441,0.27241,0.69572,0.69863,0.46814,0.46844,42,42,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Whole Organism,All anatomical structures 48258,SRR7119794,SRX4041438,SRS3258918,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively,,pubmed:30867528,,Danio rerio RNAseq 3dpf wt5,GSM3131186,,tissue:whole embryo|strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type,Danio rerio RNAseq 3dpf wt5,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,whole embryo,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.,strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type,GSM3131186,GSM3131186: Danio rerio RNAseq 3dpf wt5; Danio rerio; RNA Seq,GSM3131186,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,GEO Accession:GSM3131186,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP144601,,,NDC-TLF-3dpf-repl5-13284_R1.fastq.gz NDC-TLF-3dpf-repl5-13284_R2.fastq.gz,fastq fastq,854422548.0,10171697.0,GSM3131186 r1,0:42 1:42,A:227799696;C:189132544;G:207116976;T:230065989;N:307343,42,42,,,227799696,189132544,207116976,230065989,307343,SRX4041438,SRS3258918,SRA699717,GEO,"Molecular Biology, Radboud University",2,0.8869,0.89921,0.29991,0.30201,0.67259,0.67466,0.43395,0.45782,42,42,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Whole Organism,All anatomical structures 48259,SRR7119793,SRX4041437,SRS3258917,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively,,pubmed:30867528,,Danio rerio RNAseq 3dpf wt4,GSM3131185,,tissue:whole embryo|strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type,Danio rerio RNAseq 3dpf wt4,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,whole embryo,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.,strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type,GSM3131185,GSM3131185: Danio rerio RNAseq 3dpf wt4; Danio rerio; RNA Seq,GSM3131185,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,GEO Accession:GSM3131185,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP144601,,,NDC-TLF-3dpf-repl4-13283_R1.fastq.gz NDC-TLF-3dpf-repl4-13283_R2.fastq.gz,fastq fastq,1884789312.0,22437968.0,GSM3131185 r1,0:42 1:42,A:516338681;C:420191388;G:421311695;T:526266145;N:681403,42,42,,,516338681,420191388,421311695,526266145,681403,SRX4041437,SRS3258917,SRA699717,GEO,"Molecular Biology, Radboud University",2,0.89533,0.90768,0.30891,0.30384,0.66492,0.66636,0.44687,0.45358,42,42,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Whole Organism,All anatomical structures 48260,SRR7119792,SRX4041436,SRS3258916,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively,,pubmed:30867528,,Danio rerio RNAseq 3dpf wt3,GSM3131184,,tissue:whole embryo|strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type,Danio rerio RNAseq 3dpf wt3,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,whole embryo,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.,strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type,GSM3131184,GSM3131184: Danio rerio RNAseq 3dpf wt3; Danio rerio; RNA Seq,GSM3131184,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,GEO Accession:GSM3131184,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP144601,,,TLF-3dpf-replicate3-12250_R1.fastq.gz TLF-3dpf-replicate3-12250_R2.fastq.gz,fastq fastq,1781685444.0,21210541.0,GSM3131184 r1,0:42 1:42,A:454462414;C:421206578;G:449348079;T:456572027;N:96346,42,42,,,454462414,421206578,449348079,456572027,96346,SRX4041436,SRS3258916,SRA699717,GEO,"Molecular Biology, Radboud University",2,0.77224,0.79091,0.333,0.33343,0.67229,0.67265,0.46461,0.47357,42,42,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Whole Organism,All anatomical structures 48261,SRR7119790,SRX4041435,SRS3258915,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively,,pubmed:30867528,,Danio rerio RNAseq 3dpf wt2,GSM3131183,,tissue:whole embryo|strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type,Danio rerio RNAseq 3dpf wt2,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,whole embryo,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.,strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type,GSM3131183,GSM3131183: Danio rerio RNAseq 3dpf wt2; Danio rerio; RNA Seq,GSM3131183,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,GEO Accession:GSM3131183,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP144601,,,TLF-3dpf-replicate2-12249_R1.fastq.gz TLF-3dpf-replicate2-12249_R2.fastq.gz,fastq fastq,1548027852.0,18428903.0,GSM3131183 r1,0:42 1:42,A:396847823;C:364731299;G:388571797;T:397788001;N:88932,42,42,,,396847823,364731299,388571797,397788001,88932,SRX4041435,SRS3258915,SRA699717,GEO,"Molecular Biology, Radboud University",2,0.79516,0.81734,0.30973,0.3124,0.67095,0.67381,0.45609,0.4615,42,42,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Whole Organism,All anatomical structures 48262,SRR7119789,SRX4041434,SRS3258914,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively,,pubmed:30867528,,Danio rerio RNAseq 3dpf wt1,GSM3131182,,tissue:whole embryo|strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type,Danio rerio RNAseq 3dpf wt1,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,whole embryo,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.,strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type,GSM3131182,GSM3131182: Danio rerio RNAseq 3dpf wt1; Danio rerio; RNA Seq,GSM3131182,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation,GEO Accession:GSM3131182,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP144601,,,TLF-3dpf-replicate1-12248_R1.fastq.gz TLF-3dpf-replicate1-12248_R2.fastq.gz,fastq fastq,1443284556.0,17181959.0,GSM3131182 r1,0:42 1:42,A:371226822;C:343019970;G:358627075;T:370330892;N:79797,42,42,,,371226822,343019970,358627075,370330892,79797,SRX4041434,SRS3258914,SRA699717,GEO,"Molecular Biology, Radboud University",2,0.82734,0.83906,0.35561,0.35376,0.68816,0.69112,0.53167,0.53342,42,42,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Whole Organism,All anatomical structures 60041,SRR12125406,SRX8646725,SRS6930268,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb6 5.25hpf,GSM4648254,,source name:Whole embryo|strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb6 5.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648254,GSM4648254: TL emb6 5.25hpf; Danio rerio; RNA Seq,GSM4648254,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648254,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb6_5_25hpf.fastq,fastq,629273169.0,9988463.0,GSM4648254 r1,0:63,A:187901113;C:108762017;G:141486490;T:190996993;N:126556,63,,,,187901113,108762017,141486490,190996993,126556,SRX8646725,SRS6930268,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83255,,0.08071,,0.78056,,0.60842,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures 60042,SRR12125405,SRX8646724,SRS6930266,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb5 5.25hpf,GSM4648253,,source name:Whole embryo|strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb5 5.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648253,GSM4648253: TL emb5 5.25hpf; Danio rerio; RNA Seq,GSM4648253,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648253,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb5_5_25hpf.fastq,fastq,628500159.0,9976193.0,GSM4648253 r1,0:63,A:185452655;C:102493031;G:141851568;T:198575851;N:127054,63,,,,185452655,102493031,141851568,198575851,127054,SRX8646724,SRS6930266,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.81984,,0.07983,,0.77232,,0.54808,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures 60043,SRR12125404,SRX8646723,SRS6930265,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb4 5.25hpf,GSM4648252,,source name:Whole embryo|strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb4 5.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648252,GSM4648252: TL emb4 5.25hpf; Danio rerio; RNA Seq,GSM4648252,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648252,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb4_5_25hpf.fastq,fastq,418163886.0,6637522.0,GSM4648252 r1,0:63,A:126255886;C:72281485;G:95392900;T:124146654;N:86961,63,,,,126255886,72281485,95392900,124146654,86961,SRX8646723,SRS6930265,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.82908,,0.07514,,0.78025,,0.63356,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures 60044,SRR12125403,SRX8646722,SRS6930267,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb6 5.25hpf,GSM4648251,,source name:Whole embryo|strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb6 5.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648251,GSM4648251: AB emb6 5.25hpf; Danio rerio; RNA Seq,GSM4648251,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648251,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb6_5_25hpf.fastq,fastq,853663797.0,13550219.0,GSM4648251 r1,0:63,A:255371849;C:147150704;G:193587744;T:257383442;N:170058,63,,,,255371849,147150704,193587744,257383442,170058,SRX8646722,SRS6930267,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83677,,0.09016,,0.77445,,0.60529,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures 60045,SRR12125402,SRX8646721,SRS6930264,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb5 5.25hpf,GSM4648250,,source name:Whole embryo|strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb5 5.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648250,GSM4648250: AB emb5 5.25hpf; Danio rerio; RNA Seq,GSM4648250,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648250,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb5_5_25hpf.fastq,fastq,1197811755.0,19012885.0,GSM4648250 r1,0:63,A:366408232;C:210221584;G:280850075;T:340089873;N:241991,63,,,,366408232,210221584,280850075,340089873,241991,SRX8646721,SRS6930264,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.86965,,0.06886,,0.79364,,0.73599,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures 60046,SRR12125401,SRX8646720,SRS6930263,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb4 5.25hpf,GSM4648249,,source name:Whole embryo|strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb4 5.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648249,GSM4648249: AB emb4 5.25hpf; Danio rerio; RNA Seq,GSM4648249,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648249,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb4_5_25hpf.fastq,fastq,629932527.0,9998929.0,GSM4648249 r1,0:63,A:193361276;C:107009709;G:146668961;T:182764345;N:128236,63,,,,193361276,107009709,146668961,182764345,128236,SRX8646720,SRS6930263,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.85596,,0.07156,,0.78731,,0.71237,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures 60047,SRR12125400,SRX8646719,SRS6930262,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb3 5.25hpf,GSM4648248,,source name:Whole embryo|strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb3 5.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648248,GSM4648248: TL emb3 5.25hpf; Danio rerio; RNA Seq,GSM4648248,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648248,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb3_5_25hpf.fastq,fastq,1069366364.0,15960692.0,GSM4648248 r1,0:67,A:323825047;C:184028766;G:241899926;T:319408897;N:203728,67,,,,323825047,184028766,241899926,319408897,203728,SRX8646719,SRS6930262,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83558,,0.07461,,0.78476,,0.63113,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures 60048,SRR12125399,SRX8646718,SRS6930261,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb2 5.25hpf,GSM4648247,,source name:Whole embryo|strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb2 5.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648247,GSM4648247: TL emb2 5.25hpf; Danio rerio; RNA Seq,GSM4648247,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648247,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb2_5_25hpf.fastq,fastq,899735898.0,13428894.0,GSM4648247 r1,0:67,A:271859449;C:157711028;G:206650787;T:263341201;N:173433,67,,,,271859449,157711028,206650787,263341201,173433,SRX8646718,SRS6930261,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84037,,0.07528,,0.78498,,0.66749,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures 60049,SRR12125398,SRX8646717,SRS6930260,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb1 5.25hpf,GSM4648246,,source name:Whole embryo|strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb1 5.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648246,GSM4648246: TL emb1 5.25hpf; Danio rerio; RNA Seq,GSM4648246,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648246,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb1_5_25hpf.fastq,fastq,539868982.0,8057746.0,GSM4648246 r1,0:67,A:164876385;C:95791327;G:123943212;T:155156126;N:101932,67,,,,164876385,95791327,123943212,155156126,101932,SRX8646717,SRS6930260,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83865,,0.06636,,0.78953,,0.69934,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures 60050,SRR12125397,SRX8646716,SRS6930259,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb3 5.25hpf,GSM4648245,,source name:Whole embryo|strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb3 5.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648245,GSM4648245: AB emb3 5.25hpf; Danio rerio; RNA Seq,GSM4648245,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648245,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb3_5_25hpf.fastq,fastq,493512486.0,7365858.0,GSM4648245 r1,0:67,A:151344823;C:86707549;G:113245311;T:142120578;N:94225,67,,,,151344823,86707549,113245311,142120578,94225,SRX8646716,SRS6930259,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84007,,0.0974,,0.77979,,0.68149,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures 60051,SRR12125396,SRX8646715,SRS6930258,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb2 5.25hpf,GSM4648244,,source name:Whole embryo|strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb2 5.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648244,GSM4648244: AB emb2 5.25hpf; Danio rerio; RNA Seq,GSM4648244,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648244,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb2_5_25hpf.fastq,fastq,1157452269.0,17275407.0,GSM4648244 r1,0:67,A:355287094;C:204659659;G:273293682;T:323995566;N:216268,67,,,,355287094,204659659,273293682,323995566,216268,SRX8646715,SRS6930258,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.87638,,0.06853,,0.80426,,0.77626,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures 60052,SRR12125395,SRX8646714,SRS6930257,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb1 5.25hpf,GSM4648243,,source name:Whole embryo|strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb1 5.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648243,GSM4648243: AB emb1 5.25hpf; Danio rerio; RNA Seq,GSM4648243,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648243,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb1_5_25hpf.fastq,fastq,1327040056.0,19806568.0,GSM4648243 r1,0:67,A:409987389;C:235374040;G:312942941;T:368491782;N:243904,67,,,,409987389,235374040,312942941,368491782,243904,SRX8646714,SRS6930257,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.8667,,0.06371,,0.80588,,0.77484,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures 60053,SRR12125394,SRX8646713,SRS6930256,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb6 4.25hpf,GSM4648242,,source name:Whole embryo|strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb6 4.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648242,GSM4648242: TL emb6 4.25hpf; Danio rerio; RNA Seq,GSM4648242,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648242,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb6_4_25hpf.fastq,fastq,648226908.0,10289316.0,GSM4648242 r1,0:63,A:186626188;C:108596134;G:148654113;T:204221173;N:129300,63,,,,186626188,108596134,148654113,204221173,129300,SRX8646713,SRS6930256,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84314,,0.06862,,0.77398,,0.56825,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60054,SRR12125393,SRX8646712,SRS6930255,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb5 4.25hpf,GSM4648241,,source name:Whole embryo|strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb5 4.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648241,GSM4648241: TL emb5 4.25hpf; Danio rerio; RNA Seq,GSM4648241,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648241,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb5_4_25hpf.fastq,fastq,734406057.0,11657239.0,GSM4648241 r1,0:63,A:210803716;C:130159870;G:171759422;T:221537069;N:145980,63,,,,210803716,130159870,171759422,221537069,145980,SRX8646712,SRS6930255,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.85492,,0.06162,,0.78212,,0.38833,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60055,SRR12125392,SRX8646711,SRS6930254,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb4 4.25hpf,GSM4648240,,source name:Whole embryo|strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb4 4.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648240,GSM4648240: TL emb4 4.25hpf; Danio rerio; RNA Seq,GSM4648240,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648240,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb4_4_25hpf.fastq,fastq,848080548.0,13461596.0,GSM4648240 r1,0:63,A:244171248;C:146950905;G:197166889;T:259622371;N:169135,63,,,,244171248,146950905,197166889,259622371,169135,SRX8646711,SRS6930254,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.85266,,0.06536,,0.78356,,0.61672,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60056,SRR12125391,SRX8646710,SRS6930253,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb6 4.25hpf,GSM4648239,,source name:Whole embryo|strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb6 4.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648239,GSM4648239: AB emb6 4.25hpf; Danio rerio; RNA Seq,GSM4648239,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648239,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb6_4_25hpf.fastq,fastq,801023769.0,12714663.0,GSM4648239 r1,0:63,A:229516390;C:133164924;G:183459290;T:254724395;N:158770,63,,,,229516390,133164924,183459290,254724395,158770,SRX8646710,SRS6930253,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84498,,0.08229,,0.76516,,0.54649,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60057,SRR12125390,SRX8646709,SRS6930252,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb5 4.25hpf,GSM4648238,,source name:Whole embryo|strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb5 4.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648238,GSM4648238: AB emb5 4.25hpf; Danio rerio; RNA Seq,GSM4648238,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648238,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb5_4_25hpf.fastq,fastq,916020630.0,14540010.0,GSM4648238 r1,0:63,A:265921679;C:156404174;G:214021996;T:279489346;N:183435,63,,,,265921679,156404174,214021996,279489346,183435,SRX8646709,SRS6930252,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.86891,,0.06574,,0.78332,,0.64733,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60058,SRR12125389,SRX8646708,SRS6930251,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb4 4.25hpf,GSM4648237,,source name:Whole embryo|strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb4 4.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648237,GSM4648237: AB emb4 4.25hpf; Danio rerio; RNA Seq,GSM4648237,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648237,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb4_4_25hpf.fastq,fastq,648949077.0,10300779.0,GSM4648237 r1,0:63,A:189284026;C:107954215;G:152710596;T:198865842;N:134398,63,,,,189284026,107954215,152710596,198865842,134398,SRX8646708,SRS6930251,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.86363,,0.07026,,0.77701,,0.64544,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60059,SRR12125388,SRX8646707,SRS6930250,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb3 4.25hpf,GSM4648236,,source name:Whole embryo|strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb3 4.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648236,GSM4648236: TL emb3 4.25hpf; Danio rerio; RNA Seq,GSM4648236,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648236,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb3_4_25hpf.fastq,fastq,516466016.0,7708448.0,GSM4648236 r1,0:67,A:159159432;C:88645898;G:115271897;T:153289294;N:99495,67,,,,159159432,88645898,115271897,153289294,99495,SRX8646707,SRS6930250,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83753,,0.06603,,0.78255,,0.63318,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60060,SRR12125387,SRX8646706,SRS6930249,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb2 4.25hpf,GSM4648235,,source name:Whole embryo|strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb2 4.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648235,GSM4648235: TL emb2 4.25hpf; Danio rerio; RNA Seq,GSM4648235,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648235,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb2_4_25hpf.fastq,fastq,733560086.0,10948658.0,GSM4648235 r1,0:67,A:223892555;C:125768367;G:165649772;T:218113018;N:136374,67,,,,223892555,125768367,165649772,218113018,136374,SRX8646706,SRS6930249,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83779,,0.067,,0.77987,,0.63741,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60061,SRR12125386,SRX8646705,SRS6930248,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb1 4.25hpf,GSM4648234,,source name:Whole embryo|strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb1 4.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648234,GSM4648234: TL emb1 4.25hpf; Danio rerio; RNA Seq,GSM4648234,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648234,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb1_4_25hpf.fastq,fastq,996559273.0,14874019.0,GSM4648234 r1,0:67,A:306056021;C:172219093;G:225165148;T:292935389;N:183622,67,,,,306056021,172219093,225165148,292935389,183622,SRX8646705,SRS6930248,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83661,,0.06598,,0.78042,,0.64801,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60062,SRR12125385,SRX8646704,SRS6930247,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb3 4.25hpf,GSM4648233,,source name:Whole embryo|strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb3 4.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648233,GSM4648233: AB emb3 4.25hpf; Danio rerio; RNA Seq,GSM4648233,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648233,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb3_4_25hpf.fastq,fastq,995183629.0,14853487.0,GSM4648233 r1,0:67,A:306982973;C:172407171;G:224381340;T:291223894;N:188251,67,,,,306982973,172407171,224381340,291223894,188251,SRX8646704,SRS6930247,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83741,,0.07596,,0.77484,,0.64838,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60063,SRR12125384,SRX8646703,SRS6930246,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb2 4.25hpf,GSM4648232,,source name:Whole embryo|strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb2 4.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648232,GSM4648232: AB emb2 4.25hpf; Danio rerio; RNA Seq,GSM4648232,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648232,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb2_4_25hpf.fastq,fastq,816027371.0,12179513.0,GSM4648232 r1,0:67,A:254674603;C:143689351;G:189951309;T:227560983;N:151125,67,,,,254674603,143689351,189951309,227560983,151125,SRX8646703,SRS6930246,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.87586,,0.0588,,0.79683,,0.77034,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60064,SRR12125383,SRX8646702,SRS6930245,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb1 4.25hpf,GSM4648231,,source name:Whole embryo|strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb1 4.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648231,GSM4648231: AB emb1 4.25hpf; Danio rerio; RNA Seq,GSM4648231,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648231,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb1_4_25hpf.fastq,fastq,908152237.0,13554511.0,GSM4648231 r1,0:67,A:285792221;C:161035180;G:211856601;T:249299580;N:168655,67,,,,285792221,161035180,211856601,249299580,168655,SRX8646702,SRS6930245,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.87466,,0.05237,,0.80671,,0.80003,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60065,SRR12125382,SRX8646701,SRS6930244,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb6 3.25hpf,GSM4648230,,source name:Whole embryo|strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb6 3.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648230,GSM4648230: TL emb6 3.25hpf; Danio rerio; RNA Seq,GSM4648230,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648230,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb6_3_25hpf.fastq,fastq,406690011.0,6455397.0,GSM4648230 r1,0:63,A:120677773;C:70454448;G:91897989;T:123574695;N:85106,63,,,,120677773,70454448,91897989,123574695,85106,SRX8646701,SRS6930244,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84562,,0.05274,,0.78709,,0.6243,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60066,SRR12125381,SRX8646700,SRS6930243,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb5 3.25hpf,GSM4648229,,source name:Whole embryo|strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb5 3.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648229,GSM4648229: TL emb5 3.25hpf; Danio rerio; RNA Seq,GSM4648229,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648229,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb5_3_25hpf.fastq,fastq,1342709172.0,21312844.0,GSM4648229 r1,0:63,A:393268889;C:230336007;G:306128117;T:412697568;N:278591,63,,,,393268889,230336007,306128117,412697568,278591,SRX8646700,SRS6930243,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84679,,0.05277,,0.78376,,0.61146,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60067,SRR12125380,SRX8646699,SRS6930241,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb4 3.25hpf,GSM4648228,,source name:Whole embryo|strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb4 3.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648228,GSM4648228: TL emb4 3.25hpf; Danio rerio; RNA Seq,GSM4648228,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648228,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb4_3_25hpf.fastq,fastq,679340970.0,10783190.0,GSM4648228 r1,0:63,A:202043678;C:117431893;G:154094046;T:205633514;N:137839,63,,,,202043678,117431893,154094046,205633514,137839,SRX8646699,SRS6930241,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84563,,0.05116,,0.78691,,0.63857,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60068,SRR12125379,SRX8646698,SRS6930240,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb6 3.25hpf,GSM4648227,,source name:Whole embryo|strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb6 3.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648227,GSM4648227: AB emb6 3.25hpf; Danio rerio; RNA Seq,GSM4648227,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648227,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb6_3_25hpf.fastq,fastq,1053160038.0,16716826.0,GSM4648227 r1,0:63,A:309310336;C:174248829;G:236443053;T:332944871;N:212949,63,,,,309310336,174248829,236443053,332944871,212949,SRX8646698,SRS6930240,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84084,,0.0644,,0.77297,,0.55261,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60069,SRR12125378,SRX8646697,SRS6930242,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb5 3.25hpf,GSM4648226,,source name:Whole embryo|strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb5 3.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648226,GSM4648226: AB emb5 3.25hpf; Danio rerio; RNA Seq,GSM4648226,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648226,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb5_3_25hpf.fastq,fastq,767622366.0,12184482.0,GSM4648226 r1,0:63,A:230696545;C:135055273;G:178818369;T:222896193;N:155986,63,,,,230696545,135055273,178818369,222896193,155986,SRX8646697,SRS6930242,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.87843,,0.04331,,0.79555,,0.72222,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60070,SRR12125377,SRX8646696,SRS6930239,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb4 3.25hpf,GSM4648225,,source name:Whole embryo|strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb4 3.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648225,GSM4648225: AB emb4 3.25hpf; Danio rerio; RNA Seq,GSM4648225,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648225,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb4_3_25hpf.fastq,fastq,579009312.0,9190624.0,GSM4648225 r1,0:63,A:175049727;C:97082374;G:133102260;T:173656136;N:118815,63,,,,175049727,97082374,133102260,173656136,118815,SRX8646696,SRS6930239,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.86011,,0.05008,,0.78492,,0.67432,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60071,SRR12125376,SRX8646695,SRS6930238,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb3 3.25hpf,GSM4648224,,source name:Whole embryo|strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb3 3.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648224,GSM4648224: TL emb3 3.25hpf; Danio rerio; RNA Seq,GSM4648224,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648224,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb3_3_25hpf.fastq,fastq,718330718.0,10721354.0,GSM4648224 r1,0:67,A:219495085;C:119739206;G:164136215;T:214827087;N:133125,67,,,,219495085,119739206,164136215,214827087,133125,SRX8646695,SRS6930238,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.82675,,0.05622,,0.7864,,0.61084,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60072,SRR12125423,SRX8646694,SRS6930237,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb2 3.25hpf,GSM4648223,,source name:Whole embryo|strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb2 3.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648223,GSM4648223: TL emb2 3.25hpf; Danio rerio; RNA Seq,GSM4648223,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648223,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb2_3_25hpf.fastq,fastq,846806836.0,12638908.0,GSM4648223 r1,0:67,A:258192271;C:142127876;G:194759995;T:251567003;N:159691,67,,,,258192271,142127876,194759995,251567003,159691,SRX8646694,SRS6930237,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.82715,,0.05329,,0.7891,,0.63308,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60073,SRR12125422,SRX8646693,SRS6930236,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb1 3.25hpf,GSM4648222,,source name:Whole embryo|strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb1 3.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648222,GSM4648222: TL emb1 3.25hpf; Danio rerio; RNA Seq,GSM4648222,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648222,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb1_3_25hpf.fastq,fastq,967198332.0,14435796.0,GSM4648222 r1,0:67,A:295354111;C:161347921;G:222828106;T:287484566;N:183628,67,,,,295354111,161347921,222828106,287484566,183628,SRX8646693,SRS6930236,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.82551,,0.05319,,0.78474,,0.63465,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60074,SRR12125421,SRX8646692,SRS6930235,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb3 3.25hpf,GSM4648221,,source name:Whole embryo|strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb3 3.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648221,GSM4648221: AB emb3 3.25hpf; Danio rerio; RNA Seq,GSM4648221,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648221,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb3_3_25hpf.fastq,fastq,1097446667.0,16379801.0,GSM4648221 r1,0:67,A:335650326;C:184923523;G:253014446;T:323651876;N:206496,67,,,,335650326,184923523,253014446,323651876,206496,SRX8646692,SRS6930235,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83064,,0.05743,,0.78236,,0.62817,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60075,SRR12125420,SRX8646691,SRS6930234,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb2 3.25hpf,GSM4648220,,source name:Whole embryo|strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb2 3.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648220,GSM4648220: AB emb2 3.25hpf; Danio rerio; RNA Seq,GSM4648220,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648220,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb2_3_25hpf.fastq,fastq,1052234397.0,15704991.0,GSM4648220 r1,0:67,A:323684738;C:185585498;G:254328718;T:288441126;N:194317,67,,,,323684738,185585498,254328718,288441126,194317,SRX8646691,SRS6930234,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.87949,,0.03749,,0.80779,,0.79902,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60076,SRR12125419,SRX8646690,SRS6930233,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb1 3.25hpf,GSM4648219,,source name:Whole embryo|strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb1 3.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648219,GSM4648219: AB emb1 3.25hpf; Danio rerio; RNA Seq,GSM4648219,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648219,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb1_3_25hpf.fastq,fastq,1673968267.0,24984601.0,GSM4648219 r1,0:67,A:518959586;C:292464694;G:402352389;T:459881035;N:310563,67,,,,518959586,292464694,402352389,459881035,310563,SRX8646690,SRS6930233,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.86486,,0.03996,,0.80647,,0.78106,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60077,SRR12125418,SRX8646689,SRS6930232,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb6 2.25hpf,GSM4648218,,source name:Whole embryo|strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb6 2.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648218,GSM4648218: TL emb6 2.25hpf; Danio rerio; RNA Seq,GSM4648218,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648218,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb6_2_25hpf.fastq,fastq,653742054.0,10376858.0,GSM4648218 r1,0:63,A:191909466;C:110924763;G:150375764;T:200399289;N:132772,63,,,,191909466,110924763,150375764,200399289,132772,SRX8646689,SRS6930232,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83788,,0.05116,,0.78354,,0.60585,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60078,SRR12125417,SRX8646688,SRS6930230,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb5 2.25hpf,GSM4648217,,source name:Whole embryo|strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb5 2.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648217,GSM4648217: TL emb5 2.25hpf; Danio rerio; RNA Seq,GSM4648217,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648217,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb5_2_25hpf.fastq,fastq,781357626.0,12402502.0,GSM4648217 r1,0:63,A:228115778;C:132378621;G:181704836;T:238999917;N:158474,63,,,,228115778,132378621,181704836,238999917,158474,SRX8646688,SRS6930230,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84083,,0.05244,,0.78226,,0.60881,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60079,SRR12125416,SRX8646687,SRS6930229,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb4 2.25hpf,GSM4648216,,source name:Whole embryo|strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb4 2.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648216,GSM4648216: TL emb4 2.25hpf; Danio rerio; RNA Seq,GSM4648216,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648216,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb4_2_25hpf.fastq,fastq,421965369.0,6697863.0,GSM4648216 r1,0:63,A:124392499;C:67934245;G:96491307;T:133060705;N:86613,63,,,,124392499,67934245,96491307,133060705,86613,SRX8646687,SRS6930229,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83068,,0.05472,,0.78311,,0.5438,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60080,SRR12125415,SRX8646686,SRS6930228,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb6 2.25hpf,GSM4648215,,source name:Whole embryo|strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb6 2.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648215,GSM4648215: AB emb6 2.25hpf; Danio rerio; RNA Seq,GSM4648215,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648215,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb6_2_25hpf.fastq,fastq,628644744.0,9978488.0,GSM4648215 r1,0:63,A:184633079;C:102913810;G:143484876;T:197486280;N:126699,63,,,,184633079,102913810,143484876,197486280,126699,SRX8646686,SRS6930228,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83277,,0.06148,,0.77617,,0.55775,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60081,SRR12125414,SRX8646685,SRS6930231,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb5 2.25hpf,GSM4648214,,source name:Whole embryo|strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb5 2.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648214,GSM4648214: AB emb5 2.25hpf; Danio rerio; RNA Seq,GSM4648214,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648214,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb5_2_25hpf.fastq,fastq,814541301.0,12929227.0,GSM4648214 r1,0:63,A:242788318;C:140374211;G:193168440;T:238045602;N:164730,63,,,,242788318,140374211,193168440,238045602,164730,SRX8646685,SRS6930231,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.86463,,0.04609,,0.78914,,0.69402,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60082,SRR12125413,SRX8646684,SRS6930227,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb4 2.25hpf,GSM4648213,,source name:Whole embryo|strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb4 2.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648213,GSM4648213: AB emb4 2.25hpf; Danio rerio; RNA Seq,GSM4648213,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648213,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb4_2_25hpf.fastq,fastq,616851396.0,9791292.0,GSM4648213 r1,0:63,A:184681235;C:102359437;G:145006560;T:184679393;N:124771,63,,,,184681235,102359437,145006560,184679393,124771,SRX8646684,SRS6930227,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.85058,,0.04957,,0.79017,,0.66075,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60083,SRR12125412,SRX8646683,SRS6930226,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb3 2.25hpf,GSM4648212,,source name:Whole embryo|strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb3 2.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648212,GSM4648212: TL emb3 2.25hpf; Danio rerio; RNA Seq,GSM4648212,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648212,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb3_2_25hpf.fastq,fastq,1186700114.0,17711942.0,GSM4648212 r1,0:67,A:370074693;C:200098953;G:261433673;T:354868674;N:224121,67,,,,370074693,200098953,261433673,354868674,224121,SRX8646683,SRS6930226,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.82908,,0.0523,,0.7837,,0.61246,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60084,SRR12125411,SRX8646682,SRS6930225,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb2 2.25hpf,GSM4648211,,source name:Whole embryo|strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb2 2.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648211,GSM4648211: TL emb2 2.25hpf; Danio rerio; RNA Seq,GSM4648211,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648211,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb2_2_25hpf.fastq,fastq,952230197.0,14212391.0,GSM4648211 r1,0:67,A:293613397;C:158998327;G:211896479;T:287542246;N:179748,67,,,,293613397,158998327,211896479,287542246,179748,SRX8646682,SRS6930225,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.82682,,0.05463,,0.78581,,0.60992,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60085,SRR12125410,SRX8646681,SRS6930224,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb1 2.25hpf,GSM4648210,,source name:Whole embryo|strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb1 2.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648210,GSM4648210: TL emb1 2.25hpf; Danio rerio; RNA Seq,GSM4648210,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648210,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb1_2_25hpf.fastq,fastq,889434246.0,13275138.0,GSM4648210 r1,0:67,A:284892995;C:151063100;G:198507402;T:254807861;N:162888,67,,,,284892995,151063100,198507402,254807861,162888,SRX8646681,SRS6930224,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.81409,,0.04129,,0.79819,,0.67976,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60086,SRR12125409,SRX8646680,SRS6930223,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb3 2.25hpf,GSM4648209,,source name:Whole embryo|strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb3 2.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648209,GSM4648209: AB emb3 2.25hpf; Danio rerio; RNA Seq,GSM4648209,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648209,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb3_2_25hpf.fastq,fastq,1018630279.0,15203437.0,GSM4648209 r1,0:67,A:317428176;C:175810114;G:228314923;T:296891187;N:185879,67,,,,317428176,175810114,228314923,296891187,185879,SRX8646680,SRS6930223,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83444,,0.04892,,0.78577,,0.65007,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60087,SRR12125408,SRX8646679,SRS6930222,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb2 2.25hpf,GSM4648208,,source name:Whole embryo|strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb2 2.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648208,GSM4648208: AB emb2 2.25hpf; Danio rerio; RNA Seq,GSM4648208,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648208,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb2_2_25hpf.fastq,fastq,1455828193.0,21728779.0,GSM4648208 r1,0:67,A:456676551;C:251609741;G:334731434;T:412538456;N:272011,67,,,,456676551,251609741,334731434,412538456,272011,SRX8646679,SRS6930222,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.85982,,0.04242,,0.79399,,0.72904,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 60088,SRR12125407,SRX8646678,SRS6930221,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here we quantified embryo to embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm the dorsal forerunner cells which later forms the left right organizer is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells and we observed that these fluctuations are largely stochastic. Hence a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25 3.25 4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb1 2.25hpf,GSM4648207,,source name:Whole embryo|strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb1 2.25hpf,R1 contains only barcode information not used for mapping not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1 the following options were used: mask short adapter reads = 12 and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648207,GSM4648207: AB emb1 2.25hpf; Danio rerio; RNA Seq,GSM4648207,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony et al. Genome Biology 2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648207,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb1_2_25hpf.fastq,fastq,1156150325.0,17255975.0,GSM4648207 r1,0:67,A:367116449;C:201866700;G:266919704;T:320031593;N:215879,67,,,,367116449,201866700,266919704,320031593,215879,SRX8646678,SRS6930221,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.85881,,0.03651,,0.80346,,0.76662,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures 64110,SRR14270307,SRX10631968,SRS8728218,SRP315277,PRJNA722846,Shp1 protein tyrosine phosphatase function in the early development of the hematopoietic system of zebrafish,GSE172292,Transcriptome Analysis,We developed a ptpn6 knock out zebrafish and found a disruption in the early development of the hematopoietic system. Marcrophage subpopulation size en numbers of macrophage progenitors differ between mutants and siblings. Overall design: 5dpf zebrafish embryos were dissociated and FACS sorted. Macrophages mpeg were sorted in 384 well plates.,,,,PB 04,GSM5252012,,tissue:Whole embryo|developmental stage:5 dpf|sort day:2|genotype:Ptpn6 siblings,PB 04,"Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. ""Validation of noise models for single cell transcriptomics."" Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. Supplementary files format and content: cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio",Whole embryo,,Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols,,developmental stage:5 dpf|sort day:2|genotype:Ptpn6 siblings,GSM5252012,GSM5252012: PB 04; Danio rerio; RNA Seq,GSM5252012,,1,Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5252012,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP315277,,,HUB-PB-004_HK7YNBGXB_S2_L001_R1_001.fastq.gz HUB-PB-004_HK7YNBGXB_S2_L001_R2_001.fastq.gz,fastq fastq,986010210.0,11465235.0,GSM5252012 r1,0:26 1:60,A:254263542;C:174689279;G:187203726;T:369678029;N:175634,26,60,,,254263542,174689279,187203726,369678029,175634,SRX10631968,SRS8728218,SRA1220139,GEO,Hubrecht Institute,2,0.12751,0.84787,0.11742,0.27807,0.99261,0.83319,0.57778,0.58131,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2021-04-19,Larval,Larval,Whole Organism,All anatomical structures 64111,SRR14270308,SRX10631968,SRS8728218,SRP315277,PRJNA722846,Shp1 protein tyrosine phosphatase function in the early development of the hematopoietic system of zebrafish,GSE172292,Transcriptome Analysis,We developed a ptpn6 knock out zebrafish and found a disruption in the early development of the hematopoietic system. Marcrophage subpopulation size en numbers of macrophage progenitors differ between mutants and siblings. Overall design: 5dpf zebrafish embryos were dissociated and FACS sorted. Macrophages mpeg were sorted in 384 well plates.,,,,PB 04,GSM5252012,,tissue:Whole embryo|developmental stage:5 dpf|sort day:2|genotype:Ptpn6 siblings,PB 04,"Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. ""Validation of noise models for single cell transcriptomics."" Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. Supplementary files format and content: cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio",Whole embryo,,Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols,,developmental stage:5 dpf|sort day:2|genotype:Ptpn6 siblings,GSM5252012,GSM5252012: PB 04; Danio rerio; RNA Seq,GSM5252012,,1,Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5252012,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP315277,,,HUB-PB-004_HK7YNBGXB_S2_L002_R1_001.fastq.gz HUB-PB-004_HK7YNBGXB_S2_L002_R2_001.fastq.gz,fastq fastq,975991726.0,11348741.0,GSM5252012 r2,0:26 1:60,A:249739805;C:171614646;G:190634015;T:363955671;N:47589,26,60,,,249739805,171614646,190634015,363955671,47589,SRX10631968,SRS8728218,SRA1220139,GEO,Hubrecht Institute,2,0.12666,0.84406,0.11676,0.27662,0.99226,0.834,0.57962,0.58473,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2021-04-19,Larval,Larval,Whole Organism,All anatomical structures