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26 rows where devstage_curation = "Segmentation" and technology = "celseq"

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tissue_curation 2

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technology 1

  • celseq · 26 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

devstage_curation_coarse 1

devstage_curation 1

  • Segmentation · 26 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
38073 38073 SRR1531483 SRX665263 SRS670077 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   18 somites stage straightened secti1d tail to head GSM1448820   tissue:deyolked embryo head removed|Stage:18 somites|sectioning direction:tail to head|section thickness:24 µm|embedding strategy:deyolked and straightened embryo 18 somites stage straightened secti1d tail to head Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections deyolked embryo head removed Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:18 somites|sectioning direction:tail to head|section thickness:24 µm|embedding strategy:deyolked and straightened embryo GSM1448820 GSM1448820: 18 somites stage straightened secti1d tail to head; Danio rerio; RNA Seq GSM1448820   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448820 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_18ss_TH_R2.fastq.gz dr_18ss_TH_R1.fastq.gz fastq fastq 15779230884.0 154698342.0 GSM1448820 r1 0:51 1:51 A:3451000604;C:2392800593;G:2522666152;T:7412137093;N:626442 51 51     3451000604 2392800593 2522666152 7412137093 626442 SRX665263 SRS670077 SRA177126 GEO Hubrecht Institute 2 0.11555 0.70031 0.08647 0.12212 0.98238 0.78946 0.48905 0.5514 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Embryo Imprecise All anatomical structures
38074 38074 SRR1531482 SRX665262 SRS670076 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somites stage straightened secti1d tail to head replicate GSM1448819   tissue:deyolked embryo|Stage:15 somites|sectioning direction:tail to head|section thickness:18 µm|embedding strategy:deyolked and straightened embryo 15 somites stage straightened secti1d tail to head replicate Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections deyolked embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:tail to head|section thickness:18 µm|embedding strategy:deyolked and straightened embryo GSM1448819 GSM1448819: 15 somites stage straightened secti1d tail to head replicate; Danio rerio; RNA Seq GSM1448819   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448819 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_15ss_TH2_R2.fastq.gz dr_15ss_TH2_R1.fastq.gz fastq fastq 4502603442.0 44143171.0 GSM1448819 r1 0:51 1:51 A:1010801791;C:688133305;G:712006267;T:2047960758;N:43701321 51 51     1010801791 688133305 712006267 2047960758 43701321 SRX665262 SRS670076 SRA177126 GEO Hubrecht Institute 2 0.0903 0.78618 0.08054 0.12953 0.98703 0.78046 0.53574 0.52775 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Embryo Imprecise All anatomical structures
38075 38075 SRR1531481 SRX665261 SRS670075 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   sections 97 108 for samples dr 15ss TH and dr 15ss HT GSM1448818   tissue:deyolked embryo|Stage:15 somites|sectioning direction:head to tail and tail to head|section thickness:18 µm|embedding strategy:deyolked and straightened embryo sections 97 108 for samples dr 15ss TH and dr 15ss HT Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections deyolked embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:head to tail and tail to head|section thickness:18 µm|embedding strategy:deyolked and straightened embryo GSM1448818 GSM1448818: sections 97 108 for samples dr 15ss TH and dr 15ss HT; Danio rerio; RNA Seq GSM1448818   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448818 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_15ss_TH97-108_HT97-108_R2.fastq.gz dr_15ss_TH97-108_HT97-108_R1.fastq.gz fastq fastq 472071606.0 4628153.0 GSM1448818 r1 0:51 1:51 A:108013079;C:76852222;G:73612321;T:208300498;N:5293486 51 51     108013079 76852222 73612321 208300498 5293486 SRX665261 SRS670075 SRA177126 GEO Hubrecht Institute 2 0.06997 0.71056 0.06103 0.12966 0.9865 0.79446 0.53118 0.53673 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Embryo Imprecise All anatomical structures
38076 38076 SRR1531480 SRX665260 SRS670074 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somites stage straightened secti1d tail to head GSM1448817   tissue:deyolked embryo|Stage:15 somites|sectioning direction:tail to head|section thickness:18 µm|embedding strategy:deyolked and straightened embryo 15 somites stage straightened secti1d tail to head Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections deyolked embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:tail to head|section thickness:18 µm|embedding strategy:deyolked and straightened embryo GSM1448817 GSM1448817: 15 somites stage straightened secti1d tail to head; Danio rerio; RNA Seq GSM1448817   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448817 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_15ss_TH_R1.fastq.gz dr_15ss_TH_R2.fastq.gz fastq fastq 3381229314.0 33149307.0 GSM1448817 r1 0:51 1:51 A:806003850;C:517726785;G:527487361;T:1491678004;N:38333314 51 51     806003850 517726785 527487361 1491678004 38333314 SRX665260 SRS670074 SRA177126 GEO Hubrecht Institute 2 0.06812 0.69273 0.05849 0.1511 0.98502 0.7834 0.47808 0.53868 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Embryo Imprecise All anatomical structures
38077 38077 SRR1531479 SRX665259 SRS670073 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somites stage straightened secti1d head to tail GSM1448816   tissue:deyolked embryo|Stage:15 somites|sectioning direction:head to tail|section thickness:18 µm|embedding strategy:deyolked and straightened embryo 15 somites stage straightened secti1d head to tail Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections deyolked embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:head to tail|section thickness:18 µm|embedding strategy:deyolked and straightened embryo GSM1448816 GSM1448816: 15 somites stage straightened secti1d head to tail; Danio rerio; RNA Seq GSM1448816   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448816 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_15ss_HT_R1.fastq.gz dr_15ss_HT_R2.fastq.gz fastq fastq 3476174076.0 34080138.0 GSM1448816 r1 0:51 1:51 A:800519794;C:540890287;G:554165272;T:1542680760;N:37917963 51 51     800519794 540890287 554165272 1542680760 37917963 SRX665259 SRS670073 SRA177126 GEO Hubrecht Institute 2 0.06769 0.70036 0.05945 0.13184 0.98849 0.79026 0.50058 0.57003 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Embryo Imprecise All anatomical structures
38078 38078 SRR1531477 SRX665258 SRS670072 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somite stage secti1d from right to left GSM1448815   tissue:whole embryo|Stage:15 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo 15 somite stage secti1d from right to left Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo GSM1448815 GSM1448815: 15 somite stage secti1d from right to left; Danio rerio; RNA Seq GSM1448815   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448815 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_15ss_RL_R1.fastq.gz dr_15ss_RL_R2.fastq.gz fastq fastq 3840123336.0 37648268.0 GSM1448815 r1 0:51 1:51 A:915153174;C:577478134;G:648196113;T:1695635476;N:3660439 51 51     915153174 577478134 648196113 1695635476 3660439 SRX665258 SRS670072 SRA177126 GEO Hubrecht Institute 2 0.05313 0.71589 0.0419 0.15174 0.97717 0.77484 0.5218 0.45828 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38079 38079 SRR1531478 SRX665258 SRS670072 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somite stage secti1d from right to left GSM1448815   tissue:whole embryo|Stage:15 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo 15 somite stage secti1d from right to left Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo GSM1448815 GSM1448815: 15 somite stage secti1d from right to left; Danio rerio; RNA Seq GSM1448815   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448815 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_15ss_RL_R1.fastq.gz miseq_dr_15ss_RL_R2.fastq.gz fastq fastq 619303490.0 1235999.0 GSM1448815 r2 0:251 1:250.06 A:196814024;C:126079066;G:111585151;T:184825248;N:1 251 250     196814024 126079066 111585151 184825248 1 SRX665258 SRS670072 SRA177126 GEO Hubrecht Institute 2 0.37674 0.6743 0.06734 0.08523 0.92516 0.86196 0.56151 0.54745 251 251 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38080 38080 SRR1531475 SRX665257 SRS670070 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somite stage secti1d from left to right GSM1448814   tissue:whole embryo|Stage:15 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo 15 somite stage secti1d from left to right Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo GSM1448814 GSM1448814: 15 somite stage secti1d from left to right; Danio rerio; RNA Seq GSM1448814   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448814 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_15ss_LR_R2.fastq.gz dr_15ss_LR_R1.fastq.gz fastq fastq 2077803342.0 20370621.0 GSM1448814 r1 0:51 1:51 A:487276259;C:320933398;G:342175116;T:925418636;N:1999933 51 51     487276259 320933398 342175116 925418636 1999933 SRX665257 SRS670070 SRA177126 GEO Hubrecht Institute 2 0.04544 0.77533 0.03741 0.15439 0.98435 0.77662 0.56397 0.57005 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38081 38081 SRR1531476 SRX665257 SRS670070 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somite stage secti1d from left to right GSM1448814   tissue:whole embryo|Stage:15 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo 15 somite stage secti1d from left to right Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo GSM1448814 GSM1448814: 15 somite stage secti1d from left to right; Danio rerio; RNA Seq GSM1448814   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448814 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_15ss_LR_R1.fastq.gz miseq_dr_15ss_LR_R2.fastq.gz fastq fastq 648479770.0 1294232.0 GSM1448814 r2 0:251 1:250.05 A:208271519;C:133135452;G:114142609;T:192930139;N:51 251 250     208271519 133135452 114142609 192930139 51 SRX665257 SRS670070 SRA177126 GEO Hubrecht Institute 2 0.34992 0.64011 0.08713 0.16967 0.92103 0.83853 0.54292 0.52547 251 250 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38082 38082 SRR1531473 SRX665256 SRS670071 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somite stage secti1d from dorsal to ventral end GSM1448813   tissue:whole embryo|Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo 15 somite stage secti1d from dorsal to ventral end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo GSM1448813 GSM1448813: 15 somite stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq GSM1448813   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448813 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_15ss_DV_R1.fastq.gz dr_15ss_DV_R2.fastq.gz fastq fastq 2516804610.0 24674555.0 GSM1448813 r1 0:51 1:51 A:579818006;C:406550753;G:379205422;T:1129932140;N:21298289 51 51     579818006 406550753 379205422 1129932140 21298289 SRX665256 SRS670071 SRA177126 GEO Hubrecht Institute 2 0.04189 0.74891 0.03368 0.12625 0.98695 0.78423 0.46823 0.53429 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38083 38083 SRR1531474 SRX665256 SRS670071 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somite stage secti1d from dorsal to ventral end GSM1448813   tissue:whole embryo|Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo 15 somite stage secti1d from dorsal to ventral end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo GSM1448813 GSM1448813: 15 somite stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq GSM1448813   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448813 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_15ss_DV_R1.fastq.gz miseq_dr_15ss_DV_R2.fastq.gz fastq fastq 1831352383.0 3654695.0 GSM1448813 r2 0:251 1:250.10 A:593055798;C:392880040;G:312965357;T:532451118;N:70 251 250     593055798 392880040 312965357 532451118 70 SRX665256 SRS670071 SRA177126 GEO Hubrecht Institute 2 0.27976 0.58087 0.05423 0.08127 0.93943 0.88868 0.51246 0.50653 251 251 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38084 38084 SRR1531471 SRX665255 SRS670069 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somite stage secti1d from ventral to dorsal end GSM1448812   tissue:whole embryo|Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo 15 somite stage secti1d from ventral to dorsal end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo GSM1448812 GSM1448812: 15 somite stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq GSM1448812   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448812 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_15ss_VD_R1.fastq.gz dr_15ss_VD_R2.fastq.gz fastq fastq 1673808678.0 16409889.0 GSM1448812 r1 0:51 1:51 A:397744759;C:269067687;G:250815180;T:740808813;N:15372239 51 51     397744759 269067687 250815180 740808813 15372239 SRX665255 SRS670069 SRA177126 GEO Hubrecht Institute 2 0.05917 0.69313 0.0499 0.19364 0.98364 0.78232 0.54626 0.5434 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38085 38085 SRR1531472 SRX665255 SRS670069 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somite stage secti1d from ventral to dorsal end GSM1448812   tissue:whole embryo|Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo 15 somite stage secti1d from ventral to dorsal end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo GSM1448812 GSM1448812: 15 somite stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq GSM1448812   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448812 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_15ss_VD_R2.fastq.gz miseq_dr_15ss_VD_R1.fastq.gz fastq fastq 587520609.0 1172567.0 GSM1448812 r2 0:251 1:250.06 A:194391951;C:123162952;G:98682047;T:171283648;N:11 251 250     194391951 123162952 98682047 171283648 11 SRX665255 SRS670069 SRA177126 GEO Hubrecht Institute 2 0.25906 0.51091 0.10052 0.13544 0.94274 0.90015 0.54255 0.53365 251 251 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38086 38086 SRR1531470 SRX665254 SRS670068 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somite stage secti1d from posterior to anterior end GSM1448811   tissue:whole embryo|Stage:15 somites|sectioning direction:posterior anterior|section thickness:18 µm|embedding strategy:intact embryo 15 somite stage secti1d from posterior to anterior end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:posterior anterior|section thickness:18 µm|embedding strategy:intact embryo GSM1448811 GSM1448811: 15 somite stage secti1d from posterior to anterior end; Danio rerio; RNA Seq GSM1448811   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448811 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_15ss_PA_R2.fastq.gz dr_15ss_PA_R1.fastq.gz fastq fastq 2483143794.0 24344547.0 GSM1448811 r1 0:51 1:51 A:563038776;C:400378151;G:372280878;T:1126633332;N:20812657 51 51     563038776 400378151 372280878 1126633332 20812657 SRX665254 SRS670068 SRA177126 GEO Hubrecht Institute 2 0.04278 0.78001 0.03367 0.11539 0.98727 0.77865 0.49734 0.53041 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38087 38087 SRR1531469 SRX665253 SRS670067 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   15 somite stage secti1d from anterior to posterior end GSM1448810   tissue:whole embryo|Stage:15 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo 15 somite stage secti1d from anterior to posterior end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:15 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo GSM1448810 GSM1448810: 15 somite stage secti1d from anterior to posterior end; Danio rerio; RNA Seq GSM1448810   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448810 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_15ss_AP_R2.fastq.gz dr_15ss_AP_R1.fastq.gz fastq fastq 3436281570.0 33689035.0 GSM1448810 r1 0:51 1:51 A:794842891;C:552474558;G:514289189;T:1545720661;N:28954271 51 51     794842891 552474558 514289189 1545720661 28954271 SRX665253 SRS670067 SRA177126 GEO Hubrecht Institute 2 0.04616 0.72787 0.03714 0.11902 0.98636 0.78372 0.50428 0.54252 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38088 38088 SRR1531468 SRX665252 SRS670066 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   10 somite stage secti1d from right to left GSM1448809   tissue:whole embryo|Stage:10 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo 10 somite stage secti1d from right to left Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:10 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo GSM1448809 GSM1448809: 10 somite stage secti1d from right to left; Danio rerio; RNA Seq GSM1448809   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448809 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_10ss_RL_R2.fastq.gz dr_10ss_RL_R1.fastq.gz fastq fastq 2058025848.0 20176724.0 GSM1448809 r1 0:51 1:51 A:466388690;C:327195544;G:324646168;T:921984274;N:17811172 51 51     466388690 327195544 324646168 921984274 17811172 SRX665252 SRS670066 SRA177126 GEO Hubrecht Institute 2 0.03352 0.82842 0.02775 0.10176 0.99019 0.7878 0.56827 0.53664 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38089 38089 SRR1531467 SRX665251 SRS670065 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   10 somite stage secti1d from left to right GSM1448808   tissue:whole embryo|Stage:10 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo 10 somite stage secti1d from left to right Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:10 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo GSM1448808 GSM1448808: 10 somite stage secti1d from left to right; Danio rerio; RNA Seq GSM1448808   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448808 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_10ss_LR_R1.fastq.gz dr_10ss_LR_R2.fastq.gz fastq fastq 2372600886.0 23260793.0 GSM1448808 r1 0:51 1:51 A:539978604;C:369014393;G:373430985;T:1069557826;N:20619078 51 51     539978604 369014393 373430985 1069557826 20619078 SRX665251 SRS670065 SRA177126 GEO Hubrecht Institute 2 0.04947 0.82594 0.04114 0.11817 0.98703 0.77727 0.5181 0.46105 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38090 38090 SRR1531465 SRX665250 SRS670064 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   10 somite stage secti1d from dorsal to ventral end GSM1448807   tissue:whole embryo|Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo 10 somite stage secti1d from dorsal to ventral end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo GSM1448807 GSM1448807: 10 somite stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq GSM1448807   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448807 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_10ss_DV_R1.fastq.gz dr_10ss_DV_R2.fastq.gz fastq fastq 4808137200.0 47138600.0 GSM1448807 r1 0:51 1:51 A:1069537756;C:773357615;G:788490520;T:2131916220;N:44835089 51 51     1069537756 773357615 788490520 2131916220 44835089 SRX665250 SRS670064 SRA177126 GEO Hubrecht Institute 2 0.05336 0.7348 0.04376 0.11098 0.98311 0.78829 0.55869 0.5169 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38091 38091 SRR1531466 SRX665250 SRS670064 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   10 somite stage secti1d from dorsal to ventral end GSM1448807   tissue:whole embryo|Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo 10 somite stage secti1d from dorsal to ventral end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo GSM1448807 GSM1448807: 10 somite stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq GSM1448807   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448807 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_10ss_DV_R1.fastq.gz miseq_dr_10ss_DV_R2.fastq.gz fastq fastq 981031778.0 1957880.0 GSM1448807 r2 0:251 1:250.07 A:318017696;C:204637111;G:170546834;T:287830124;N:13 251 250     318017696 204637111 170546834 287830124 13 SRX665250 SRS670064 SRA177126 GEO Hubrecht Institute 2 0.28421 0.5957 0.04748 0.07361 0.93917 0.88298 0.53618 0.53493 251 251 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38092 38092 SRR1531463 SRX665249 SRS670063 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   10 somite stage secti1d from ventral to dorsal end GSM1448806   tissue:whole embryo|Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo 10 somite stage secti1d from ventral to dorsal end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo GSM1448806 GSM1448806: 10 somite stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq GSM1448806   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448806 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_10ss_VD_R1.fastq.gz dr_10ss_VD_R2.fastq.gz fastq fastq 4042242048.0 39629824.0 GSM1448806 r1 0:51 1:51 A:880941046;C:636899286;G:642176352;T:1845085169;N:37140195 51 51     880941046 636899286 642176352 1845085169 37140195 SRX665249 SRS670063 SRA177126 GEO Hubrecht Institute 2 0.04898 0.80518 0.04234 0.10309 0.99044 0.78437 0.4974 0.53264 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38093 38093 SRR1531464 SRX665249 SRS670063 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   10 somite stage secti1d from ventral to dorsal end GSM1448806   tissue:whole embryo|Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo 10 somite stage secti1d from ventral to dorsal end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo GSM1448806 GSM1448806: 10 somite stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq GSM1448806   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448806 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_10ss_VD_R1.fastq.gz miseq_dr_10ss_VD_R2.fastq.gz fastq fastq 738071470.0 1473056.0 GSM1448806 r2 0:251 1:250.05 A:241662059;C:148514183;G:127467910;T:220427298;N:20 251 250     241662059 148514183 127467910 220427298 20 SRX665249 SRS670063 SRA177126 GEO Hubrecht Institute 2 0.33554 0.65168 0.04798 0.07375 0.93334 0.87121 0.53425 0.51721 251 251 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38094 38094 SRR1531461 SRX665248 SRS670062 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   10 somite stage secti1d from posterior to anterior end GSM1448805   tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo 10 somite stage secti1d from posterior to anterior end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo GSM1448805 GSM1448805: 10 somite stage secti1d from posterior to anterior end; Danio rerio; RNA Seq GSM1448805   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448805 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_10ss_PA_R1.fastq.gz dr_10ss_PA_R2.fastq.gz fastq fastq 4759203720.0 46658860.0 GSM1448805 r1 0:51 1:51 A:1044025561;C:745846492;G:761494052;T:2164007108;N:43830507 51 51     1044025561 745846492 761494052 2164007108 43830507 SRX665248 SRS670062 SRA177126 GEO Hubrecht Institute 2 0.04594 0.81204 0.0388 0.10992 0.98938 0.78244 0.51272 0.52639 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38095 38095 SRR1531462 SRX665248 SRS670062 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   10 somite stage secti1d from posterior to anterior end GSM1448805   tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo 10 somite stage secti1d from posterior to anterior end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo GSM1448805 GSM1448805: 10 somite stage secti1d from posterior to anterior end; Danio rerio; RNA Seq GSM1448805   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448805 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_10ss_PA_R2.fastq.gz miseq_dr_10ss_PA_R1.fastq.gz fastq fastq 923948352.0 1843960.0 GSM1448805 r2 0:251 1:250.07 A:301981474;C:189568545;G:157916393;T:274481921;N:19 251 250     301981474 189568545 157916393 274481921 19 SRX665248 SRS670062 SRA177126 GEO Hubrecht Institute 2 0.33803 0.65569 0.05131 0.07917 0.93419 0.87355 0.4399 0.52526 251 251 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38096 38096 SRR1531460 SRX665247 SRS670061 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   10 somite stage secti1d from anterior to posterior end replicate GSM1448804   tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo 10 somite stage secti1d from anterior to posterior end replicate Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo GSM1448804 GSM1448804: 10 somite stage secti1d from anterior to posterior end replicate; Danio rerio; RNA Seq GSM1448804   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448804 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_10ss_AP2_R1.fastq.gz dr_10ss_AP2_R2.fastq.gz fastq fastq 2096761878.0 20556489.0 GSM1448804 r1 0:51 1:51 A:486131317;C:330426143;G:323887100;T:938024368;N:18292950 51 51     486131317 330426143 323887100 938024368 18292950 SRX665247 SRS670061 SRA177126 GEO Hubrecht Institute 2 0.0484 0.78914 0.0396 0.12303 0.9866 0.78234 0.53395 0.53422 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38097 38097 SRR1531458 SRX665246 SRS670060 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   10 somite stage secti1d from anterior to posterior end GSM1448803   tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo 10 somite stage secti1d from anterior to posterior end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo GSM1448803 GSM1448803: 10 somite stage secti1d from anterior to posterior end; Danio rerio; RNA Seq GSM1448803   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448803 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_10ss_AP_R2.fastq.gz dr_10ss_AP_R1.fastq.gz fastq fastq 3873169500.0 37972250.0 GSM1448803 r1 0:51 1:51 A:844434990;C:614503150;G:615061181;T:1763736099;N:35434080 51 51     844434990 614503150 615061181 1763736099 35434080 SRX665246 SRS670060 SRA177126 GEO Hubrecht Institute 2 0.0354 0.81065 0.02893 0.12263 0.98944 0.77386 0.52631 0.52007 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures
38098 38098 SRR1531459 SRX665246 SRS670060 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   10 somite stage secti1d from anterior to posterior end GSM1448803   tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo 10 somite stage secti1d from anterior to posterior end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo GSM1448803 GSM1448803: 10 somite stage secti1d from anterior to posterior end; Danio rerio; RNA Seq GSM1448803   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448803 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_10ss_AP_R1.fastq.gz miseq_dr_10ss_AP_R2.fastq.gz fastq fastq 496084013.0 990096.0 GSM1448803 r2 0:251 1:250.05 A:161790706;C:99237964;G:85634725;T:149420610;N:8 251 250     161790706 99237964 85634725 149420610 8 SRX665246 SRS670060 SRA177126 GEO Hubrecht Institute 2 0.35483 0.66804 0.06659 0.09269 0.92699 0.86113 0.53381 0.51797 251 251 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Segmentation Embryo Whole Organism All anatomical structures

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