{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Segmentation\" and technology = \"celseq\"", "rows": [[38073, "SRR1531483", "SRX665263", "SRS670077", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "18 somites stage  straightened  secti1d tail to head", "GSM1448820", null, "tissue:deyolked embryo  head removed|Stage:18 somites|sectioning direction:tail to head|section thickness:24 \u00b5m|embedding strategy:deyolked and straightened embryo", "18 somites stage  straightened  secti1d tail to head", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "deyolked embryo  head removed", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:18 somites|sectioning direction:tail to head|section thickness:24 \u00b5m|embedding strategy:deyolked and straightened embryo", "GSM1448820", "GSM1448820: 18 somites stage  straightened  secti1d tail to head; Danio rerio; RNA Seq", "GSM1448820", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  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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.", null, "pubmed:25417113", null, "15 somites stage  straightened  secti1d tail to head  replicate", "GSM1448819", null, "tissue:deyolked embryo|Stage:15 somites|sectioning direction:tail to head|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "15 somites stage  straightened  secti1d tail to head  replicate", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "deyolked embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  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Cell Reports  2012", "GEO Accession:GSM1448819", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_TH2_R2.fastq.gz dr_15ss_TH2_R1.fastq.gz", "fastq fastq", 4502603442.0, 44143171.0, "GSM1448819 r1", "0:51 1:51", "A:1010801791;C:688133305;G:712006267;T:2047960758;N:43701321", 51, 51, null, null, 1010801791, 688133305, 712006267, 2047960758, 43701321, "SRX665262", "SRS670076", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.0903, 0.78618, 0.08054, 0.12953, 0.98703, 0.78046, 0.53574, 0.52775, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38075, "SRR1531481", "SRX665261", "SRS670075", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "sections 97 108 for samples dr 15ss TH and dr 15ss HT", "GSM1448818", null, "tissue:deyolked embryo|Stage:15 somites|sectioning direction:head to tail and tail to head|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "sections 97 108 for samples dr 15ss TH and dr 15ss HT", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "deyolked embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:head to tail and tail to head|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "GSM1448818", "GSM1448818: sections 97 108 for samples dr 15ss TH and dr 15ss HT; Danio rerio; RNA Seq", "GSM1448818", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448818", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_TH97-108_HT97-108_R2.fastq.gz dr_15ss_TH97-108_HT97-108_R1.fastq.gz", "fastq fastq", 472071606.0, 4628153.0, "GSM1448818 r1", "0:51 1:51", "A:108013079;C:76852222;G:73612321;T:208300498;N:5293486", 51, 51, null, null, 108013079, 76852222, 73612321, 208300498, 5293486, "SRX665261", "SRS670075", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.06997, 0.71056, 0.06103, 0.12966, 0.9865, 0.79446, 0.53118, 0.53673, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38076, "SRR1531480", "SRX665260", "SRS670074", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somites stage  straightened  secti1d tail to head", "GSM1448817", null, "tissue:deyolked embryo|Stage:15 somites|sectioning direction:tail to head|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "15 somites stage  straightened  secti1d tail to head", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "deyolked embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:tail to head|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "GSM1448817", "GSM1448817: 15 somites stage  straightened  secti1d tail to head; Danio rerio; RNA Seq", "GSM1448817", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448817", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_TH_R1.fastq.gz dr_15ss_TH_R2.fastq.gz", "fastq fastq", 3381229314.0, 33149307.0, "GSM1448817 r1", "0:51 1:51", "A:806003850;C:517726785;G:527487361;T:1491678004;N:38333314", 51, 51, null, null, 806003850, 517726785, 527487361, 1491678004, 38333314, "SRX665260", "SRS670074", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.06812, 0.69273, 0.05849, 0.1511, 0.98502, 0.7834, 0.47808, 0.53868, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38077, "SRR1531479", "SRX665259", "SRS670073", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somites stage  straightened  secti1d head to tail", "GSM1448816", null, "tissue:deyolked embryo|Stage:15 somites|sectioning direction:head to tail|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "15 somites stage  straightened  secti1d head to tail", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "deyolked embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:head to tail|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "GSM1448816", "GSM1448816: 15 somites stage  straightened  secti1d head to tail; Danio rerio; RNA Seq", "GSM1448816", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  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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.", null, "pubmed:25417113", null, "15 somite stage  secti1d from right to left", "GSM1448815", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:right left|section thickness:18 \u00b5m|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", null, "Stage:15 somites|sectioning direction:right left|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448815", "GSM1448815: 15 somite stage  secti1d from right to left; Danio rerio; RNA Seq", "GSM1448815", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  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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.", null, "pubmed:25417113", null, "15 somite stage  secti1d from right to left", "GSM1448815", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:right left|section thickness:18 \u00b5m|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", null, "Stage:15 somites|sectioning direction:right left|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448815", "GSM1448815: 15 somite stage  secti1d from right to left; Danio rerio; RNA Seq", "GSM1448815", null, "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", null, "SRP045064", null, "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, null, null, 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", null, "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.", null, "pubmed:25417113", null, "15 somite stage  secti1d from left to right", "GSM1448814", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:left right|section thickness:18 \u00b5m|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", null, "Stage:15 somites|sectioning direction:left right|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448814", "GSM1448814: 15 somite stage  secti1d from left to right; Danio rerio; RNA Seq", "GSM1448814", null, "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", null, "SRP045064", null, null, "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, null, null, 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", null, "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.", null, "pubmed:25417113", null, "15 somite stage  secti1d from left to right", "GSM1448814", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:left right|section thickness:18 \u00b5m|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", null, "Stage:15 somites|sectioning direction:left right|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448814", "GSM1448814: 15 somite stage  secti1d from left to right; Danio rerio; RNA Seq", "GSM1448814", null, "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", null, "SRP045064", null, "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, null, null, 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", null, "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.", null, "pubmed:25417113", null, "15 somite stage  secti1d from dorsal to ventral end", "GSM1448813", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|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", null, "Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448813", "GSM1448813: 15 somite stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq", "GSM1448813", null, "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", null, "SRP045064", null, null, "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, null, null, 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", null, "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.", null, "pubmed:25417113", null, "15 somite stage  secti1d from dorsal to ventral end", "GSM1448813", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|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", null, "Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448813", "GSM1448813: 15 somite stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq", "GSM1448813", null, "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", null, "SRP045064", null, "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, null, null, 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", null, "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.", null, "pubmed:25417113", null, "15 somite stage  secti1d from ventral to dorsal end", "GSM1448812", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|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", null, "Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448812", "GSM1448812: 15 somite stage  secti1d from ventral to dorsal end; Danio rerio; RNA Seq", "GSM1448812", null, "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", null, "SRP045064", null, null, "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, null, null, 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", null, "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.", null, "pubmed:25417113", null, "15 somite stage  secti1d from ventral to dorsal end", "GSM1448812", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|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", null, "Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448812", "GSM1448812: 15 somite stage  secti1d from ventral to dorsal end; Danio rerio; RNA Seq", "GSM1448812", null, "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", null, "SRP045064", null, "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, null, null, 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", null, "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.", null, "pubmed:25417113", null, "15 somite stage  secti1d from posterior to anterior end", "GSM1448811", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:posterior anterior|section thickness:18 \u00b5m|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", null, "Stage:15 somites|sectioning direction:posterior anterior|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448811", "GSM1448811: 15 somite stage  secti1d from posterior to anterior end; Danio rerio; RNA Seq", "GSM1448811", null, "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", null, "SRP045064", null, null, "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, null, null, 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", null, "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.", null, "pubmed:25417113", null, "15 somite stage  secti1d from anterior to posterior end", "GSM1448810", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|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", null, "Stage:15 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448810", "GSM1448810: 15 somite stage  secti1d from anterior to posterior end; Danio rerio; RNA Seq", "GSM1448810", null, "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", null, "SRP045064", null, null, "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, null, null, 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", null, "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.", null, "pubmed:25417113", null, "10 somite stage  secti1d from right to left", "GSM1448809", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:right left|section thickness:18 \u00b5m|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", null, "Stage:10 somites|sectioning direction:right left|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448809", "GSM1448809: 10 somite stage  secti1d from right to left; Danio rerio; RNA Seq", "GSM1448809", null, "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", null, "SRP045064", null, null, "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, null, null, 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", null, "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.", null, "pubmed:25417113", null, "10 somite stage  secti1d from left to right", "GSM1448808", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:left right|section thickness:18 \u00b5m|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", null, "Stage:10 somites|sectioning direction:left right|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448808", "GSM1448808: 10 somite stage  secti1d from left to right; Danio rerio; RNA Seq", "GSM1448808", null, "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", null, "SRP045064", null, null, "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, null, null, 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", null, "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.", null, "pubmed:25417113", null, "10 somite stage  secti1d from dorsal to ventral end", "GSM1448807", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|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", null, "Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448807", "GSM1448807: 10 somite stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq", "GSM1448807", null, "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", null, "SRP045064", null, null, "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, null, null, 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", null, "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.", null, "pubmed:25417113", null, "10 somite stage  secti1d from dorsal to ventral end", "GSM1448807", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|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", null, "Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448807", "GSM1448807: 10 somite stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq", "GSM1448807", null, "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", null, "SRP045064", null, "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, null, null, 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", null, "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.", null, "pubmed:25417113", null, "10 somite stage  secti1d from ventral to dorsal end", "GSM1448806", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|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", null, "Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448806", "GSM1448806: 10 somite stage  secti1d from ventral to dorsal end; Danio rerio; RNA Seq", "GSM1448806", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  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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.", null, "pubmed:25417113", null, "10 somite stage  secti1d from ventral to dorsal end", "GSM1448806", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|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.  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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. 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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. 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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. 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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.  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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. 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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.  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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. 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