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178 rows where experiment.library_layout = "PAIRED", technology = "celseq" and tissue_curation_coarse = "All anatomical structures"

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devstage_curation 6

devstage_curation_coarse 3

tissue_curation 2

tissue_curation_coarse 1

  • All anatomical structures · 178 ✖

technology 1

  • celseq · 178 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

  • PAIRED · 178 ✖
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
38099 38099 SRR1531457 SRX665245 SRS670059 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from dorsal to ventral end replicate GSM1448802   tissue:whole embryo|Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from dorsal to ventral end replicate Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo GSM1448802 GSM1448802: shield stage secti1d from dorsal to ventral end replicate; Danio rerio; RNA Seq GSM1448802   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448802 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_shield_DV2_R2.fastq.gz dr_shield_DV2_R1.fastq.gz fastq fastq 2735350014.0 26817157.0 GSM1448802 r1 0:51 1:51 A:650077339;C:412458828;G:411687121;T:1237686190;N:23440536 51 51     650077339 412458828 411687121 1237686190 23440536 SRX665245 SRS670059 SRA177126 GEO Hubrecht Institute 2 0.02556 0.75175 0.01912 0.10697 0.99076 0.79819 0.54093 0.55229 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38100 38100 SRR1531455 SRX665244 SRS670058 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from dorsal to ventral end GSM1448801   tissue:whole embryo|Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from dorsal to ventral end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo GSM1448801 GSM1448801: shield stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq GSM1448801   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448801 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_shield_DV_R1.fastq.gz dr_shield_DV_R2.fastq.gz fastq fastq 1605318738.0 15738419.0 GSM1448801 r1 0:51 1:51 A:361176217;C:248822696;G:253372108;T:726629351;N:15318366 51 51     361176217 248822696 253372108 726629351 15318366 SRX665244 SRS670058 SRA177126 GEO Hubrecht Institute 2 0.02633 0.68496 0.02344 0.10104 0.99638 0.80006 0.46031 0.57655 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38101 38101 SRR1531456 SRX665244 SRS670058 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from dorsal to ventral end GSM1448801   tissue:whole embryo|Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from dorsal to ventral end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo GSM1448801 GSM1448801: shield stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq GSM1448801   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448801 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_shield_DV_R1.fastq.gz miseq_dr_shield_DV_R2.fastq.gz fastq fastq 114907294.0 229320.0 GSM1448801 r2 0:251 1:250.08 A:37813553;C:24168661;G:19441624;T:33483456;N:0 251 250     37813553 24168661 19441624 33483456 0 SRX665244 SRS670058 SRA177126 GEO Hubrecht Institute 2 0.26022 0.46204 0.03083 0.05933 0.94627 0.89301 0.56728 0.55478 251 250 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38102 38102 SRR1531453 SRX665243 SRS670056 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from ventral to dorsal end GSM1448800   tissue:whole embryo|Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from ventral to dorsal end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo GSM1448800 GSM1448800: shield stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq GSM1448800   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448800 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_shield_VD_R1.fastq.gz dr_shield_VD_R2.fastq.gz fastq fastq 1840839492.0 18047446.0 GSM1448800 r1 0:51 1:51 A:421253850;C:292045914;G:295175858;T:814744774;N:17619096 51 51     421253850 292045914 295175858 814744774 17619096 SRX665243 SRS670056 SRA177126 GEO Hubrecht Institute 2 0.01815 0.6287 0.01468 0.09567 0.99452 0.80975 0.5259 0.58926 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38103 38103 SRR1531454 SRX665243 SRS670056 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from ventral to dorsal end GSM1448800   tissue:whole embryo|Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from ventral to dorsal end Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo GSM1448800 GSM1448800: shield stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq GSM1448800   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448800 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_shield_VD_R2.fastq.gz miseq_dr_shield_VD_R1.fastq.gz fastq fastq 158531701.0 316379.0 GSM1448800 r2                       SRX665243 SRS670056 SRA177126 GEO Hubrecht Institute 2 0.06803 0.1733 0.00916 0.026 0.94085 0.88899 0.58254 0.5723 251 251 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38104 38104 SRR1531451 SRX665242 SRS670055 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from right to left GSM1448799   tissue:whole embryo|Stage:shield stage|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from right to left Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo GSM1448799 GSM1448799: shield stage secti1d from right to left; Danio rerio; RNA Seq GSM1448799   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448799 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_shield_RL_R1.fastq.gz dr_shield_RL_R2.fastq.gz fastq fastq 2003076918.0 19638009.0 GSM1448799 r1 0:51 1:51 A:457537608;C:308292947;G:312973612;T:905317961;N:18954790 51 51     457537608 308292947 312973612 905317961 18954790 SRX665242 SRS670055 SRA177126 GEO Hubrecht Institute 2 0.02111 0.7573 0.01656 0.11316 0.99364 0.8005 0.4501 0.59142 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38105 38105 SRR1531452 SRX665242 SRS670055 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from right to left GSM1448799   tissue:whole embryo|Stage:shield stage|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from right to left Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo GSM1448799 GSM1448799: shield stage secti1d from right to left; Danio rerio; RNA Seq GSM1448799   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448799 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_shield_RL_R1.fastq.gz miseq_dr_shield_RL_R2.fastq.gz fastq fastq 154180181.0 307695.0 GSM1448799 r2 0:251 1:250.08 A:50801230;C:32293099;G:25917988;T:45167860;N:4 251 250     50801230 32293099 25917988 45167860 4 SRX665242 SRS670055 SRA177126 GEO Hubrecht Institute 2 0.31553 0.64085 0.03613 0.06829 0.94101 0.8938 0.60272 0.58117 251 251 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38106 38106 SRR1531449 SRX665241 SRS670053 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from left to right GSM1448798   tissue:whole embryo|Stage:shield stage|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from left to right Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo GSM1448798 GSM1448798: shield stage secti1d from left to right; Danio rerio; RNA Seq GSM1448798   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448798 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_shield_LR_R1.fastq.gz dr_shield_LR_R2.fastq.gz fastq fastq 1755442542.0 17210221.0 GSM1448798 r1 0:51 1:51 A:401133098;C:265688355;G:264899378;T:807011867;N:16709844 51 51     401133098 265688355 264899378 807011867 16709844 SRX665241 SRS670053 SRA177126 GEO Hubrecht Institute 2 0.02829 0.71918 0.02455 0.14486 0.99484 0.79866 0.50383 0.57925 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38107 38107 SRR1531450 SRX665241 SRS670053 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from left to right GSM1448798   tissue:whole embryo|Stage:shield stage|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from left to right Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo GSM1448798 GSM1448798: shield stage secti1d from left to right; Danio rerio; RNA Seq GSM1448798   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448798 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_shield_LR_R1.fastq.gz miseq_dr_shield_LR_R2.fastq.gz fastq fastq 139755993.0 278913.0 GSM1448798 r2 0:251 1:250.07 A:46536591;C:28346077;G:23036783;T:41836538;N:4 251 250     46536591 28346077 23036783 41836538 4 SRX665241 SRS670053 SRA177126 GEO Hubrecht Institute 2 0.27443 0.57858 0.06346 0.09954 0.94194 0.89522 0.55896 0.56169 251 251 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38108 38108 SRR1531448 SRX665240 SRS670054 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from vegetal to animal pole replicate GSM1448797   tissue:whole embryo|Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from vegetal to animal pole replicate Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo GSM1448797 GSM1448797: shield stage secti1d from vegetal to animal pole replicate; Danio rerio; RNA Seq GSM1448797   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448797 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_shield_VA2_R1.fastq.gz dr_shield_VA2_R2.fastq.gz fastq fastq 1962884532.0 19243966.0 GSM1448797 r1 0:51 1:51 A:449529690;C:292065368;G:287973067;T:916330652;N:16985755 51 51     449529690 292065368 287973067 916330652 16985755 SRX665240 SRS670054 SRA177126 GEO Hubrecht Institute 2 0.04512 0.77455 0.03997 0.11233 0.99293 0.78488 0.50931 0.5171 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38109 38109 SRR1531446 SRX665239 SRS670057 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from vegetal to animal pole GSM1448796   tissue:whole embryo|Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from vegetal to animal pole Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo GSM1448796 GSM1448796: shield stage secti1d from vegetal to animal pole; Danio rerio; RNA Seq GSM1448796   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448796 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_shield_VA_R2.fastq.gz dr_shield_VA_R1.fastq.gz fastq fastq 2367839934.0 23214117.0 GSM1448796 r1 0:51 1:51 A:544061124;C:369321045;G:383489434;T:1047897582;N:23070749 51 51     544061124 369321045 383489434 1047897582 23070749 SRX665239 SRS670057 SRA177126 GEO Hubrecht Institute 2 0.02284 0.57831 0.0199 0.08251 0.99579 0.81653 0.4451 0.5792 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38110 38110 SRR1531447 SRX665239 SRS670057 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from vegetal to animal pole GSM1448796   tissue:whole embryo|Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from vegetal to animal pole Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo GSM1448796 GSM1448796: shield stage secti1d from vegetal to animal pole; Danio rerio; RNA Seq GSM1448796   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448796 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_shield_VA_R1.fastq.gz miseq_dr_shield_VA_R2.fastq.gz fastq fastq 139677889.0 278764.0 GSM1448796 r2 0:251 1:250.06 A:45877333;C:29821713;G:24032460;T:39946380;N:3 251 250     45877333 29821713 24032460 39946380 3 SRX665239 SRS670057 SRA177126 GEO Hubrecht Institute 2 0.21444 0.33364 0.02489 0.04529 0.95156 0.901 0.56549 0.55749 251 251 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38111 38111 SRR1531444 SRX665238 SRS670052 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from animal to vegetal pole GSM1448795   tissue:whole embryo|Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from animal to vegetal pole Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 µm|embedding strategy:intact embryo GSM1448795 GSM1448795: shield stage secti1d from animal to vegetal pole; Danio rerio; RNA Seq GSM1448795   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448795 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064     dr_shield_AV_R1.fastq.gz dr_shield_AV_R2.fastq.gz fastq fastq 2059615110.0 20192305.0 GSM1448795 r1 0:51 1:51 A:487942041;C:328047311;G:336282927;T:886836259;N:20506572 51 51     487942041 328047311 336282927 886836259 20506572 SRX665238 SRS670052 SRA177126 GEO Hubrecht Institute 2 0.01633 0.50842 0.0136 0.07269 0.99541 0.82183 0.51242 0.59281 51 51 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
38112 38112 SRR1531445 SRX665238 SRS670052 SRP045064 PRJNA256975 Genome wide RNA tomography in the zebrafish embryo GSE59873 Other Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.   pubmed:25417113   shield stage secti1d from animal to vegetal pole GSM1448795   tissue:whole embryo|Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 µm|embedding strategy:intact embryo shield stage secti1d from animal to vegetal pole Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections whole embryo Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice. RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012   Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 µm|embedding strategy:intact embryo GSM1448795 GSM1448795: shield stage secti1d from animal to vegetal pole; Danio rerio; RNA Seq GSM1448795   1 RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 GEO Accession:GSM1448795 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP045064   instrument model:Illumina MiSeq miseq_dr_shield_AV_R1.fastq.gz miseq_dr_shield_AV_R2.fastq.gz fastq fastq 176530873.0 352271.0 GSM1448795 r2 0:251 1:250.12 A:57029265;C:38838035;G:30065677;T:50597891;N:5 251 250     57029265 38838035 30065677 50597891 5 SRX665238 SRS670052 SRA177126 GEO Hubrecht Institute 2 0.20318 0.26844 0.02342 0.03751 0.95499 0.9069 0.4325 0.57102 251 251 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown sc single_cell_plate celseq   Netherlands 2014-07-29 Gastrula Embryo Whole Organism All anatomical structures
39741 39741 SRR2089842 SRX1085056 SRS981139 SRP060505 PRJNA289199 Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors GSE70623 Transcriptome Analysis We integrate zebrafish embryology with photoactivatable caged morpholinos cMO the photoactivatable lineage tracer caged fluorescein dextran cFD fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf. Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm. Embryos were permitted to develop until 9 hpf dechorionated and dissociated into single cells. Fluorescein positive cells were then isolated by FACS. Five experimental replicates were performed. Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony T et al. Cell Reports. 2012. In short total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.   pubmed:27376691   cFD + spt cMO replicate 5 GSM1812032   tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO cFD + spt cMO replicate 5 Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode filtering/truncation of read 2 quality score >20; 35 bp alignment of read 2 35 bp reads to Zv8 reference and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis embryo 1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf. Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously. Embryos were then allowed to develop until 9 hpf and then dissociated into single cells. Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed. Lysed cells in lysis buffer were then stored in 80 °C until all samples for 5 biological replicates were obtained. post collection of 5 biological replicates total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1 9.9 Libraries were constructed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012. Barcode information on read 1 of paired end reads: cntrl 1 CATCACGC; cntrl 2 GTCGTTCC; cntrl 3 GTCGTGAA; cntrl 4 TCACACGC; cntrl 5 TCACAGAG; cMO 1 TGATGCGC; cMO 2 ACGACTCC; cMO 3 ACGACGAA; cMO 4 ATGTGCGC; cMO 5 CGTGTGAG. Zebrafish embryos were obtained from natural spawning strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO GSM1812032 GSM1812032: cFD + spt cMO replicate 5; Danio rerio; RNA Seq GSM1812032   1 post collection of 5 biological replicates total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1 9.9 Libraries were constructed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012. Barcode information on read 1 of paired end reads: cntrl 1 CATCACGC; cntrl 2 GTCGTTCC; cntrl 3 GTCGTGAA; cntrl 4 TCACACGC; cntrl 5 TCACAGAG; cMO 1 TGATGCGC; cMO 2 ACGACTCC; cMO 3 ACGACGAA; cMO 4 ATGTGCGC; cMO 5 CGTGTGAG. GEO Accession:GSM1812032 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP060505     cMO_5_1.bz2 cMO_5_2.bz2 fastq fastq 2590806954.0 12825777.0 GSM1812032 r1 0:101 1:101 A:729527639;C:388090931;G:473627524;T:996733909;N:2826951 101 101     729527639 388090931 473627524 996733909 2826951 SRX1085056 SRS981139 SRA276152 GEO James Chen, Chemical and Systems Biology, Stanford University 2 0.34765 0.81821 0.09574 0.11092 0.96846 0.84273 0.56486 0.60514 101 101 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   United States 2015-07-08 Gastrula Embryo Embryo Imprecise All anatomical structures
39742 39742 SRR2089841 SRX1085055 SRS981140 SRP060505 PRJNA289199 Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors GSE70623 Transcriptome Analysis We integrate zebrafish embryology with photoactivatable caged morpholinos cMO the photoactivatable lineage tracer caged fluorescein dextran cFD fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf. Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm. Embryos were permitted to develop until 9 hpf dechorionated and dissociated into single cells. Fluorescein positive cells were then isolated by FACS. Five experimental replicates were performed. Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony T et al. Cell Reports. 2012. In short total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.   pubmed:27376691   cFD + spt cMO replicate 4 GSM1812031   tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO cFD + spt cMO replicate 4 Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode filtering/truncation of read 2 quality score >20; 35 bp alignment of read 2 35 bp reads to Zv8 reference and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis embryo 1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf. Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously. Embryos were then allowed to develop until 9 hpf and then dissociated into single cells. Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed. Lysed cells in lysis buffer were then stored in 80 °C until all samples for 5 biological replicates were obtained. post collection of 5 biological replicates total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1 9.9 Libraries were constructed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012. Barcode information on read 1 of paired end reads: cntrl 1 CATCACGC; cntrl 2 GTCGTTCC; cntrl 3 GTCGTGAA; cntrl 4 TCACACGC; cntrl 5 TCACAGAG; cMO 1 TGATGCGC; cMO 2 ACGACTCC; cMO 3 ACGACGAA; cMO 4 ATGTGCGC; cMO 5 CGTGTGAG. Zebrafish embryos were obtained from natural spawning strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO GSM1812031 GSM1812031: cFD + spt cMO replicate 4; Danio rerio; RNA Seq GSM1812031   1 post collection of 5 biological replicates total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1 9.9 Libraries were constructed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012. Barcode information on read 1 of paired end reads: cntrl 1 CATCACGC; cntrl 2 GTCGTTCC; cntrl 3 GTCGTGAA; cntrl 4 TCACACGC; cntrl 5 TCACAGAG; cMO 1 TGATGCGC; cMO 2 ACGACTCC; cMO 3 ACGACGAA; cMO 4 ATGTGCGC; cMO 5 CGTGTGAG. GEO Accession:GSM1812031 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP060505     cMO_4_2.bz2 cMO_4_1.bz2 fastq fastq 4576986902.0 22658351.0 GSM1812031 r1 0:101 1:101 A:1236262881;C:739179623;G:837030962;T:1759535468;N:4977968 101 101     1236262881 739179623 837030962 1759535468 4977968 SRX1085055 SRS981140 SRA276152 GEO James Chen, Chemical and Systems Biology, Stanford University 2 0.4938 0.83831 0.1798 0.13149 0.96593 0.84766 0.57231 0.63621 101 101 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   United States 2015-07-08 Gastrula Embryo Embryo Imprecise All anatomical structures
39743 39743 SRR2089840 SRX1085054 SRS981143 SRP060505 PRJNA289199 Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors GSE70623 Transcriptome Analysis We integrate zebrafish embryology with photoactivatable caged morpholinos cMO the photoactivatable lineage tracer caged fluorescein dextran cFD fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf. Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm. Embryos were permitted to develop until 9 hpf dechorionated and dissociated into single cells. Fluorescein positive cells were then isolated by FACS. Five experimental replicates were performed. Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony T et al. Cell Reports. 2012. In short total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.   pubmed:27376691   cFD + spt cMO replicate 3 GSM1812030   tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO cFD + spt cMO replicate 3 Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode filtering/truncation of read 2 quality score >20; 35 bp alignment of read 2 35 bp reads to Zv8 reference and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis embryo 1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf. Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously. Embryos were then allowed to develop until 9 hpf and then dissociated into single cells. Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed. Lysed cells in lysis buffer were then stored in 80 °C until all samples for 5 biological replicates were obtained. post collection of 5 biological replicates total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1 9.9 Libraries were constructed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012. Barcode information on read 1 of paired end reads: cntrl 1 CATCACGC; cntrl 2 GTCGTTCC; cntrl 3 GTCGTGAA; cntrl 4 TCACACGC; cntrl 5 TCACAGAG; cMO 1 TGATGCGC; cMO 2 ACGACTCC; cMO 3 ACGACGAA; cMO 4 ATGTGCGC; cMO 5 CGTGTGAG. Zebrafish embryos were obtained from natural spawning strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO GSM1812030 GSM1812030: cFD + spt cMO replicate 3; Danio rerio; RNA Seq GSM1812030   1 post collection of 5 biological replicates total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1 9.9 Libraries were constructed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012. Barcode information on read 1 of paired end reads: cntrl 1 CATCACGC; cntrl 2 GTCGTTCC; cntrl 3 GTCGTGAA; cntrl 4 TCACACGC; cntrl 5 TCACAGAG; cMO 1 TGATGCGC; cMO 2 ACGACTCC; cMO 3 ACGACGAA; cMO 4 ATGTGCGC; cMO 5 CGTGTGAG. GEO Accession:GSM1812030 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP060505     cMO_3_1.bz2 cMO_3_2.bz2 fastq fastq 2769659976.0 13711188.0 GSM1812030 r1 0:101 1:101 A:801844710;C:425581810;G:477170945;T:1062200254;N:2862257 101 101     801844710 425581810 477170945 1062200254 2862257 SRX1085054 SRS981143 SRA276152 GEO James Chen, Chemical and Systems Biology, Stanford University 2 0.36913 0.82247 0.20581 0.12151 0.97656 0.84589 0.57375 0.61151 101 101 T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   United States 2015-07-08 Gastrula Embryo Embryo Imprecise All anatomical structures
39744 39744 SRR2089839 SRX1085053 SRS981142 SRP060505 PRJNA289199 Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors GSE70623 Transcriptome Analysis We integrate zebrafish embryology with photoactivatable caged morpholinos cMO the photoactivatable lineage tracer caged fluorescein dextran cFD fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf. Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm. Embryos were permitted to develop until 9 hpf dechorionated and dissociated into single cells. Fluorescein positive cells were then isolated by FACS. Five experimental replicates were performed. Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony T et al. Cell Reports. 2012. In short total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.   pubmed:27376691   cFD + spt cMO replicate 2 GSM1812029   tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO cFD + spt cMO replicate 2 Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode filtering/truncation of read 2 quality score >20; 35 bp alignment of read 2 35 bp reads to Zv8 reference and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis embryo 1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf. Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously. Embryos were then allowed to develop until 9 hpf and then dissociated into single cells. Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed. Lysed cells in lysis buffer were then stored in 80 °C until all samples for 5 biological replicates were obtained. post collection of 5 biological replicates total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1 9.9 Libraries were constructed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012. Barcode information on read 1 of paired end reads: cntrl 1 CATCACGC; cntrl 2 GTCGTTCC; cntrl 3 GTCGTGAA; cntrl 4 TCACACGC; cntrl 5 TCACAGAG; cMO 1 TGATGCGC; cMO 2 ACGACTCC; cMO 3 ACGACGAA; cMO 4 ATGTGCGC; cMO 5 CGTGTGAG. Zebrafish embryos were obtained from natural spawning strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO GSM1812029 GSM1812029: cFD + spt cMO replicate 2; Danio rerio; RNA Seq GSM1812029   1 post collection of 5 biological replicates total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1 9.9 Libraries were constructed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012. Barcode information on read 1 of paired end reads: cntrl 1 CATCACGC; cntrl 2 GTCGTTCC; cntrl 3 GTCGTGAA; cntrl 4 TCACACGC; cntrl 5 TCACAGAG; cMO 1 TGATGCGC; cMO 2 ACGACTCC; cMO 3 ACGACGAA; cMO 4 ATGTGCGC; cMO 5 CGTGTGAG. GEO Accession:GSM1812029 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP060505     cMO_2_1.bz2 cMO_2_2.bz2 fastq fastq 2482029348.0 12287274.0 GSM1812029 r1 0:101 1:101 A:675627490;C:417393063;G:437628865;T:948867297;N:2512633 101 101     675627490 417393063 437628865 948867297 2512633 SRX1085053 SRS981142 SRA276152 GEO James Chen, Chemical and Systems Biology, Stanford University 2 0.49124 0.82814 0.19593 0.12778 0.96694 0.84814 0.61289 0.65915 101 101 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   United States 2015-07-08 Gastrula Embryo Embryo Imprecise All anatomical structures
39745 39745 SRR2089838 SRX1085052 SRS981141 SRP060505 PRJNA289199 Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors GSE70623 Transcriptome Analysis We integrate zebrafish embryology with photoactivatable caged morpholinos cMO the photoactivatable lineage tracer caged fluorescein dextran cFD fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf. Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm. Embryos were permitted to develop until 9 hpf dechorionated and dissociated into single cells. Fluorescein positive cells were then isolated by FACS. Five experimental replicates were performed. Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony T et al. Cell Reports. 2012. In short total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.   pubmed:27376691   cFD + spt cMO replicate 1 GSM1812028   tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO cFD + spt cMO replicate 1 Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode filtering/truncation of read 2 quality score >20; 35 bp alignment of read 2 35 bp reads to Zv8 reference and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis embryo 1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf. Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously. Embryos were then allowed to develop until 9 hpf and then dissociated into single cells. Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed. Lysed cells in lysis buffer were then stored in 80 °C until all samples for 5 biological replicates were obtained. post collection of 5 biological replicates total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1 9.9 Libraries were constructed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012. Barcode information on read 1 of paired end reads: cntrl 1 CATCACGC; cntrl 2 GTCGTTCC; cntrl 3 GTCGTGAA; cntrl 4 TCACACGC; cntrl 5 TCACAGAG; cMO 1 TGATGCGC; cMO 2 ACGACTCC; cMO 3 ACGACGAA; cMO 4 ATGTGCGC; cMO 5 CGTGTGAG. Zebrafish embryos were obtained from natural spawning strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO GSM1812028 GSM1812028: cFD + spt cMO replicate 1; Danio rerio; RNA Seq GSM1812028   1 post collection of 5 biological replicates total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1 9.9 Libraries were constructed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012. Barcode information on read 1 of paired end reads: cntrl 1 CATCACGC; cntrl 2 GTCGTTCC; cntrl 3 GTCGTGAA; cntrl 4 TCACACGC; cntrl 5 TCACAGAG; cMO 1 TGATGCGC; cMO 2 ACGACTCC; cMO 3 ACGACGAA; cMO 4 ATGTGCGC; cMO 5 CGTGTGAG. GEO Accession:GSM1812028 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP060505     cMO_1_1.bz2 cMO_1_2.bz2 fastq fastq 7585699334.0 37552967.0 GSM1812028 r1 0:101 1:101 A:1977695961;C:1274396713;G:1452711269;T:2871964961;N:8930430 101 101     1977695961 1274396713 1452711269 2871964961 8930430 SRX1085052 SRS981141 SRA276152 GEO James Chen, Chemical and Systems Biology, Stanford University 2 0.48942 0.85323 0.16329 0.18148 0.97236 0.8565 0.59311 0.63618 101 101 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   United States 2015-07-08 Gastrula Embryo Embryo Imprecise All anatomical structures
39746 39746 SRR2089837 SRX1085051 SRS981144 SRP060505 PRJNA289199 Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors GSE70623 Transcriptome Analysis We integrate zebrafish embryology with photoactivatable caged morpholinos cMO the photoactivatable lineage tracer caged fluorescein dextran cFD fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf. Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm. Embryos were permitted to develop until 9 hpf dechorionated and dissociated into single cells. Fluorescein positive cells were then isolated by FACS. Five experimental replicates were performed. Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony T et al. Cell Reports. 2012. In short total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.   pubmed:27376691   cFD only replicate 5 GSM1812027   tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1 cFD only replicate 5 Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode filtering/truncation of read 2 quality score >20; 35 bp alignment of read 2 35 bp reads to Zv8 reference and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis embryo 1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf. Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously. Embryos were then allowed to develop until 9 hpf and then dissociated into single cells. Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed. Lysed cells in lysis buffer were then stored in 80 °C until all samples for 5 biological replicates were obtained. post collection of 5 biological replicates total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1 9.9 Libraries were constructed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012. Barcode information on read 1 of paired end reads: cntrl 1 CATCACGC; cntrl 2 GTCGTTCC; cntrl 3 GTCGTGAA; cntrl 4 TCACACGC; cntrl 5 TCACAGAG; cMO 1 TGATGCGC; cMO 2 ACGACTCC; cMO 3 ACGACGAA; cMO 4 ATGTGCGC; cMO 5 CGTGTGAG. Zebrafish embryos were obtained from natural spawning strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1 GSM1812027 GSM1812027: cFD only replicate 5; Danio rerio; RNA Seq GSM1812027   1 post collection of 5 biological replicates total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1 9.9 Libraries were constructed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012. Barcode information on read 1 of paired end reads: cntrl 1 CATCACGC; cntrl 2 GTCGTTCC; cntrl 3 GTCGTGAA; cntrl 4 TCACACGC; cntrl 5 TCACAGAG; cMO 1 TGATGCGC; cMO 2 ACGACTCC; cMO 3 ACGACGAA; cMO 4 ATGTGCGC; cMO 5 CGTGTGAG. GEO Accession:GSM1812027 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP060505     cntrl_5_1.bz2 cntrl_5_2.bz2 fastq fastq 4762488754.0 23576677.0 GSM1812027 r1 0:101 1:101 A:1380401515;C:716191196;G:808857049;T:1851642812;N:5396182 101 101     1380401515 716191196 808857049 1851642812 5396182 SRX1085051 SRS981144 SRA276152 GEO James Chen, Chemical and Systems Biology, Stanford University 2 0.4168 0.81605 0.16291 0.11435 0.97185 0.84354 0.6892 0.61855 101 101 T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   United States 2015-07-08 Gastrula Embryo Embryo Imprecise All anatomical structures
39747 39747 SRR2089836 SRX1085050 SRS981145 SRP060505 PRJNA289199 Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors GSE70623 Transcriptome Analysis We integrate zebrafish embryology with photoactivatable caged morpholinos cMO the photoactivatable lineage tracer caged fluorescein dextran cFD fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf. Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm. Embryos were permitted to develop until 9 hpf dechorionated and dissociated into single cells. Fluorescein positive cells were then isolated by FACS. Five experimental replicates were performed. Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony T et al. Cell Reports. 2012. In short total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.   pubmed:27376691   cFD only replicate 4 GSM1812026   tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1 cFD only replicate 4 Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode filtering/truncation of read 2 quality score >20; 35 bp alignment of read 2 35 bp reads to Zv8 reference and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis embryo 1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf. Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously. Embryos were then allowed to develop until 9 hpf and then dissociated into single cells. Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed. Lysed cells in lysis buffer were then stored in 80 °C until all samples for 5 biological replicates were obtained. post collection of 5 biological replicates total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1 9.9 Libraries were constructed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012. Barcode information on read 1 of paired end reads: cntrl 1 CATCACGC; cntrl 2 GTCGTTCC; cntrl 3 GTCGTGAA; cntrl 4 TCACACGC; cntrl 5 TCACAGAG; cMO 1 TGATGCGC; cMO 2 ACGACTCC; cMO 3 ACGACGAA; cMO 4 ATGTGCGC; cMO 5 CGTGTGAG. Zebrafish embryos were obtained from natural spawning strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1 GSM1812026 GSM1812026: cFD only replicate 4; Danio rerio; RNA Seq GSM1812026   1 post collection of 5 biological replicates total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1 9.9 Libraries were constructed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012. Barcode information on read 1 of paired end reads: cntrl 1 CATCACGC; cntrl 2 GTCGTTCC; cntrl 3 GTCGTGAA; cntrl 4 TCACACGC; cntrl 5 TCACAGAG; cMO 1 TGATGCGC; cMO 2 ACGACTCC; cMO 3 ACGACGAA; cMO 4 ATGTGCGC; cMO 5 CGTGTGAG. GEO Accession:GSM1812026 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP060505     cntrl_4_1.bz2 cntrl_4_2.bz2 fastq fastq 3719006042.0 18410921.0 GSM1812026 r1 0:101 1:101 A:1038933535;C:615185731;G:647242496;T:1413253009;N:4391271 101 101     1038933535 615185731 647242496 1413253009 4391271 SRX1085050 SRS981145 SRA276152 GEO James Chen, Chemical and Systems Biology, Stanford University 2 0.46956 0.82686 0.12167 0.11363 0.97025 0.85074 0.58699 0.63586 101 101 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   United States 2015-07-08 Gastrula Embryo Embryo Imprecise All anatomical structures
39748 39748 SRR2089835 SRX1085049 SRS981146 SRP060505 PRJNA289199 Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors GSE70623 Transcriptome Analysis We integrate zebrafish embryology with photoactivatable caged morpholinos cMO the photoactivatable lineage tracer caged fluorescein dextran cFD fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf. Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm. Embryos were permitted to develop until 9 hpf dechorionated and dissociated into single cells. Fluorescein positive cells were then isolated by FACS. Five experimental replicates were performed. Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony T et al. Cell Reports. 2012. In short total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.   pubmed:27376691   cFD only replicate 3 GSM1812025   tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1 cFD only replicate 3 Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode filtering/truncation of read 2 quality score >20; 35 bp alignment of read 2 35 bp reads to Zv8 reference and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis embryo 1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf. Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously. Embryos were then allowed to develop until 9 hpf and then dissociated into single cells. Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed. Lysed cells in lysis buffer were then stored in 80 °C until all samples for 5 biological replicates were obtained. post collection of 5 biological replicates total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1 9.9 Libraries were constructed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012. Barcode information on read 1 of paired end reads: cntrl 1 CATCACGC; cntrl 2 GTCGTTCC; cntrl 3 GTCGTGAA; cntrl 4 TCACACGC; cntrl 5 TCACAGAG; cMO 1 TGATGCGC; cMO 2 ACGACTCC; cMO 3 ACGACGAA; cMO 4 ATGTGCGC; cMO 5 CGTGTGAG. Zebrafish embryos were obtained from natural spawning strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1 GSM1812025 GSM1812025: cFD only replicate 3; Danio rerio; RNA Seq GSM1812025   1 post collection of 5 biological replicates total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1 9.9 Libraries were constructed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012. Barcode information on read 1 of paired end reads: cntrl 1 CATCACGC; cntrl 2 GTCGTTCC; cntrl 3 GTCGTGAA; cntrl 4 TCACACGC; cntrl 5 TCACAGAG; cMO 1 TGATGCGC; cMO 2 ACGACTCC; cMO 3 ACGACGAA; cMO 4 ATGTGCGC; cMO 5 CGTGTGAG. GEO Accession:GSM1812025 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP060505     cntrl_3_2.bz2 cntrl_3_1.bz2 fastq fastq 2513713250.0 12444125.0 GSM1812025 r1 0:101 1:101 A:709549704;C:390305955;G:451783096;T:959236114;N:2838381 101 101     709549704 390305955 451783096 959236114 2838381 SRX1085049 SRS981146 SRA276152 GEO James Chen, Chemical and Systems Biology, Stanford University 2 0.41236 0.81226 0.11339 0.11567 0.97051 0.85305 0.60801 0.4295 101 101 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   United States 2015-07-08 Gastrula Embryo Embryo Imprecise All anatomical structures
39749 39749 SRR2089834 SRX1085048 SRS981148 SRP060505 PRJNA289199 Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors GSE70623 Transcriptome Analysis We integrate zebrafish embryology with photoactivatable caged morpholinos cMO the photoactivatable lineage tracer caged fluorescein dextran cFD fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf. Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm. Embryos were permitted to develop until 9 hpf dechorionated and dissociated into single cells. Fluorescein positive cells were then isolated by FACS. Five experimental replicates were performed. Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony T et al. Cell Reports. 2012. In short total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.   pubmed:27376691   cFD only replicate 2 GSM1812024   tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1 cFD only replicate 2 Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode filtering/truncation of read 2 quality score >20; 35 bp alignment of read 2 35 bp reads to Zv8 reference and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis embryo 1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf. Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously. Embryos were then allowed to develop until 9 hpf and then dissociated into single cells. Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed. Lysed cells in lysis buffer were then stored in 80 °C until all samples for 5 biological replicates were obtained. post collection of 5 biological replicates total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1 9.9 Libraries were constructed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012. Barcode information on read 1 of paired end reads: cntrl 1 CATCACGC; cntrl 2 GTCGTTCC; cntrl 3 GTCGTGAA; cntrl 4 TCACACGC; cntrl 5 TCACAGAG; cMO 1 TGATGCGC; cMO 2 ACGACTCC; cMO 3 ACGACGAA; cMO 4 ATGTGCGC; cMO 5 CGTGTGAG. Zebrafish embryos were obtained from natural spawning strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1 GSM1812024 GSM1812024: cFD only replicate 2; Danio rerio; RNA Seq GSM1812024   1 post collection of 5 biological replicates total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1 9.9 Libraries were constructed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012. Barcode information on read 1 of paired end reads: cntrl 1 CATCACGC; cntrl 2 GTCGTTCC; cntrl 3 GTCGTGAA; cntrl 4 TCACACGC; cntrl 5 TCACAGAG; cMO 1 TGATGCGC; cMO 2 ACGACTCC; cMO 3 ACGACGAA; cMO 4 ATGTGCGC; cMO 5 CGTGTGAG. GEO Accession:GSM1812024 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP060505     cntrl_2_1.bz2 cntrl_2_2.bz2 fastq fastq 6157457728.0 30482464.0 GSM1812024 r1 0:101 1:101 A:1679764131;C:1000368713;G:1086099790;T:2384200862;N:7024232 101 101     1679764131 1000368713 1086099790 2384200862 7024232 SRX1085048 SRS981148 SRA276152 GEO James Chen, Chemical and Systems Biology, Stanford University 2 0.47785 0.82086 0.20529 0.14023 0.97226 0.85232 0.65332 0.66262 101 101 T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   United States 2015-07-08 Gastrula Embryo Embryo Imprecise All anatomical structures
39750 39750 SRR2089833 SRX1085047 SRS981147 SRP060505 PRJNA289199 Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors GSE70623 Transcriptome Analysis We integrate zebrafish embryology with photoactivatable caged morpholinos cMO the photoactivatable lineage tracer caged fluorescein dextran cFD fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf. Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm. Embryos were permitted to develop until 9 hpf dechorionated and dissociated into single cells. Fluorescein positive cells were then isolated by FACS. Five experimental replicates were performed. Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony T et al. Cell Reports. 2012. In short total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.   pubmed:27376691   cFD only replicate 1 GSM1812023   tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1 cFD only replicate 1 Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode filtering/truncation of read 2 quality score >20; 35 bp alignment of read 2 35 bp reads to Zv8 reference and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis embryo 1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf. Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously. Embryos were then allowed to develop until 9 hpf and then dissociated into single cells. Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed. Lysed cells in lysis buffer were then stored in 80 °C until all samples for 5 biological replicates were obtained. post collection of 5 biological replicates total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1 9.9 Libraries were constructed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012. Barcode information on read 1 of paired end reads: cntrl 1 CATCACGC; cntrl 2 GTCGTTCC; cntrl 3 GTCGTGAA; cntrl 4 TCACACGC; cntrl 5 TCACAGAG; cMO 1 TGATGCGC; cMO 2 ACGACTCC; cMO 3 ACGACGAA; cMO 4 ATGTGCGC; cMO 5 CGTGTGAG. Zebrafish embryos were obtained from natural spawning strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1 GSM1812023 GSM1812023: cFD only replicate 1; Danio rerio; RNA Seq GSM1812023   1 post collection of 5 biological replicates total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1 9.9 Libraries were constructed according to the CEL seq protocol Hashimshony T et al. Cell Reports. 2012. Barcode information on read 1 of paired end reads: cntrl 1 CATCACGC; cntrl 2 GTCGTTCC; cntrl 3 GTCGTGAA; cntrl 4 TCACACGC; cntrl 5 TCACAGAG; cMO 1 TGATGCGC; cMO 2 ACGACTCC; cMO 3 ACGACGAA; cMO 4 ATGTGCGC; cMO 5 CGTGTGAG. GEO Accession:GSM1812023 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP060505     cntrl_1_1.bz2 cntrl_1_2.bz2 fastq fastq 4291177304.0 21243452.0 GSM1812023 r1 0:101 1:101 A:1182202535;C:708780301;G:753724632;T:1641921837;N:4547999 101 101     1182202535 708780301 753724632 1641921837 4547999 SRX1085047 SRS981147 SRA276152 GEO James Chen, Chemical and Systems Biology, Stanford University 2 0.45088 0.8425 0.11253 0.11641 0.97835 0.84778 0.46728 0.64503 101 101 B B mate1-mate2 similar by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   United States 2015-07-08 Gastrula Embryo Embryo Imprecise All anatomical structures
40998 40998 SRR3996126 SRX1997151 SRS1598494 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       CtrlRNAR GSM2258261   tissue:Single embryos|developmental stage:24h CtrlRNAR Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Single embryos Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2258261 GSM2258261: CtrlRNAR; Danio rerio; RNA Seq GSM2258261   1 TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2258261 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     CtrlRNAR_HVL3NBGXX_S8_L001_R2_001.fastq.gz CtrlRNAR_HVL3NBGXX_S8_L001_R1_001.fastq.gz fastq fastq 122148536.0 803714.0 GSM2258261 r1 0:75.99 1:75.99 A:22296766;C:36021766;G:45626801;T:18125967;N:77236 75 75     22296766 36021766 45626801 18125967 77236 SRX1997151 SRS1598494 SRA426643 GEO Max Delbrück Center 2 1e-05 0.0 0.0 0.0 1.0 1.0     76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-08-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
40999 40999 SRR3996127 SRX1997151 SRS1598494 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       CtrlRNAR GSM2258261   tissue:Single embryos|developmental stage:24h CtrlRNAR Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Single embryos Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2258261 GSM2258261: CtrlRNAR; Danio rerio; RNA Seq GSM2258261   1 TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2258261 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     CtrlRNAR_HVL3NBGXX_S8_L002_R1_001.fastq.gz CtrlRNAR_HVL3NBGXX_S8_L002_R2_001.fastq.gz fastq fastq 113008241.0 743600.0 GSM2258261 r2 0:75.99 1:75.99 A:20637948;C:33145860;G:42408819;T:16743893;N:71721 75 75     20637948 33145860 42408819 16743893 71721 SRX1997151 SRS1598494 SRA426643 GEO Max Delbrück Center 2 0.00017 0.00998 4e-05 0.00226 0.99967 0.99973 0.72727 0.52941 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-08-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
41000 41000 SRR3996128 SRX1997151 SRS1598494 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       CtrlRNAR GSM2258261   tissue:Single embryos|developmental stage:24h CtrlRNAR Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Single embryos Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2258261 GSM2258261: CtrlRNAR; Danio rerio; RNA Seq GSM2258261   1 TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2258261 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     CtrlRNAR_HVL3NBGXX_S8_L003_R1_001.fastq.gz CtrlRNAR_HVL3NBGXX_S8_L003_R2_001.fastq.gz fastq fastq 108228662.0 712150.0 GSM2258261 r3 0:75.99 1:75.99 A:19849294;C:31892676;G:40324932;T:16132730;N:29030 75 75     19849294 31892676 40324932 16132730 29030 SRX1997151 SRS1598494 SRA426643 GEO Max Delbrück Center 2 2e-05 0.0012 0.0 0.0 0.99995 0.99997 1.0 1.0 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-08-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
41001 41001 SRR3996129 SRX1997151 SRS1598494 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       CtrlRNAR GSM2258261   tissue:Single embryos|developmental stage:24h CtrlRNAR Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Single embryos Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2258261 GSM2258261: CtrlRNAR; Danio rerio; RNA Seq GSM2258261   1 TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2258261 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     CtrlRNAR_HVL3NBGXX_S8_L004_R1_001.fastq.gz CtrlRNAR_HVL3NBGXX_S8_L004_R2_001.fastq.gz fastq fastq 111312836.0 732495.0 GSM2258261 r4 0:75.98 1:75.98 A:20513000;C:32586302;G:41550816;T:16635032;N:27686 75 75     20513000 32586302 41550816 16635032 27686 SRX1997151 SRS1598494 SRA426643 GEO Max Delbrück Center 2 0.00035 0.01956 0.00011 0.00409 0.99953 0.99955 0.69767 0.67647 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-08-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
41002 41002 SRR3996122 SRX1997150 SRS1598493 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       CtrlRNAP GSM2258260   tissue:Single embryos|developmental stage:24h CtrlRNAP Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Single embryos Embryos were injected at the 1 cell stage with 1 nl Cas9 protein final concentration 1590 ng/ul TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2258260 GSM2258260: CtrlRNAP; Danio rerio; RNA Seq GSM2258260   1 TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2258260 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     CtrlRNAP_HVL3NBGXX_S7_L001_R1_001.fastq.gz CtrlRNAP_HVL3NBGXX_S7_L001_R2_001.fastq.gz fastq fastq 108531563.0 714105.0 GSM2258260 r1 0:75.99 1:75.99 A:19184954;C:32230923;G:40631595;T:16417885;N:66206 75 75     19184954 32230923 40631595 16417885 66206 SRX1997150 SRS1598493 SRA426643 GEO Max Delbrück Center 2 3e-05 0.00362 0.0 0.00288 0.99997 0.99997 0.0 1.0 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-08-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
41003 41003 SRR3996123 SRX1997150 SRS1598493 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       CtrlRNAP GSM2258260   tissue:Single embryos|developmental stage:24h CtrlRNAP Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Single embryos Embryos were injected at the 1 cell stage with 1 nl Cas9 protein final concentration 1590 ng/ul TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2258260 GSM2258260: CtrlRNAP; Danio rerio; RNA Seq GSM2258260   1 TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2258260 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     CtrlRNAP_HVL3NBGXX_S7_L002_R1_001.fastq.gz CtrlRNAP_HVL3NBGXX_S7_L002_R2_001.fastq.gz fastq fastq 101227523.0 666088.0 GSM2258260 r2 0:75.98 1:75.99 A:17949430;C:29881418;G:37998433;T:15333962;N:64280 75 75     17949430 29881418 37998433 15333962 64280 SRX1997150 SRS1598493 SRA426643 GEO Max Delbrück Center 2 0.00025 0.01395 5e-05 0.00403 0.99955 0.99959 0.68571 0.74074 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-08-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
41004 41004 SRR3996124 SRX1997150 SRS1598493 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       CtrlRNAP GSM2258260   tissue:Single embryos|developmental stage:24h CtrlRNAP Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Single embryos Embryos were injected at the 1 cell stage with 1 nl Cas9 protein final concentration 1590 ng/ul TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2258260 GSM2258260: CtrlRNAP; Danio rerio; RNA Seq GSM2258260   1 TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2258260 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     CtrlRNAP_HVL3NBGXX_S7_L003_R1_001.fastq.gz CtrlRNAP_HVL3NBGXX_S7_L003_R2_001.fastq.gz fastq fastq 96887228.0 637499.0 GSM2258260 r3 0:75.99 1:75.99 A:17147788;C:28784101;G:36238086;T:14692025;N:25228 75 75     17147788 28784101 36238086 14692025 25228 SRX1997150 SRS1598493 SRA426643 GEO Max Delbrück Center 2 2e-05 0.00088 1e-05 0.0 1.0 0.99997   1.0 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-08-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
41005 41005 SRR3996125 SRX1997150 SRS1598493 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       CtrlRNAP GSM2258260   tissue:Single embryos|developmental stage:24h CtrlRNAP Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Single embryos Embryos were injected at the 1 cell stage with 1 nl Cas9 protein final concentration 1590 ng/ul TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2258260 GSM2258260: CtrlRNAP; Danio rerio; RNA Seq GSM2258260   1 TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2258260 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     CtrlRNAP_HVL3NBGXX_S7_L004_R1_001.fastq.gz CtrlRNAP_HVL3NBGXX_S7_L004_R2_001.fastq.gz fastq fastq 100376357.0 660556.0 GSM2258260 r4 0:75.98 1:75.98 A:17996732;C:29527900;G:37433615;T:15391508;N:26602 75 75     17996732 29527900 37433615 15391508 26602 SRX1997150 SRS1598493 SRA426643 GEO Max Delbrück Center 2 0.00061 0.027 0.0001 0.00825 0.99928 0.99945 0.74444 0.64406 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-08-03 Pharyngula Embryo Embryo Imprecise All anatomical structures
41006 41006 SRR3996110 SRX1997147 SRS1598490 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       dynamics RNA GSM2258257   tissue:Single embryos|developmental stage:48h dynamics RNA Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Single embryos Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:48h GSM2258257 GSM2258257: dynamics RNA; Danio rerio; RNA Seq GSM2258257   1 TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2258257 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     Philipp-dynamics-RNA_HKLJYBGXX_S8_L001_R1_001.fastq.gz Philipp-dynamics-RNA_HKLJYBGXX_S8_L001_R2_001.fastq.gz fastq fastq 80515624.0 530034.0 GSM2258257 r1 0:75.99 1:75.92 A:14695730;C:23934258;G:29464421;T:12392506;N:28709 75 75     14695730 23934258 29464421 12392506 28709 SRX1997147 SRS1598490 SRA426643 GEO Max Delbrück Center 2 0.0 1e-05 0.0 0.0 1.0 0.99997   0.0 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-08-03 Hatching Embryo Embryo Imprecise All anatomical structures
41007 41007 SRR3996111 SRX1997147 SRS1598490 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       dynamics RNA GSM2258257   tissue:Single embryos|developmental stage:48h dynamics RNA Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Single embryos Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:48h GSM2258257 GSM2258257: dynamics RNA; Danio rerio; RNA Seq GSM2258257   1 TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2258257 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     Philipp-dynamics-RNA_HKLJYBGXX_S8_L002_R1_001.fastq.gz Philipp-dynamics-RNA_HKLJYBGXX_S8_L002_R2_001.fastq.gz fastq fastq 80995216.0 533194.0 GSM2258257 r2 0:75.99 1:75.92 A:14785958;C:24008314;G:29766059;T:12409358;N:25527 75 75     14785958 24008314 29766059 12409358 25527 SRX1997147 SRS1598490 SRA426643 GEO Max Delbrück Center 2 1e-05 1e-05 0.0 0.0 0.99997 1.0 0.0   76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-08-03 Hatching Embryo Embryo Imprecise All anatomical structures
41008 41008 SRR3996112 SRX1997147 SRS1598490 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       dynamics RNA GSM2258257   tissue:Single embryos|developmental stage:48h dynamics RNA Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Single embryos Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:48h GSM2258257 GSM2258257: dynamics RNA; Danio rerio; RNA Seq GSM2258257   1 TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2258257 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     Philipp-dynamics-RNA_HKLJYBGXX_S8_L003_R1_001.fastq.gz Philipp-dynamics-RNA_HKLJYBGXX_S8_L003_R2_001.fastq.gz fastq fastq 73436227.0 483449.0 GSM2258257 r3 0:75.98 1:75.92 A:13427325;C:21824372;G:26876634;T:11306254;N:1642 75 75     13427325 21824372 26876634 11306254 1642 SRX1997147 SRS1598490 SRA426643 GEO Max Delbrück Center 2 2e-05 1e-05 0.0 0.0 0.99997 1.0 0.0   76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-08-03 Hatching Embryo Embryo Imprecise All anatomical structures
41009 41009 SRR3996113 SRX1997147 SRS1598490 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       dynamics RNA GSM2258257   tissue:Single embryos|developmental stage:48h dynamics RNA Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Single embryos Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:48h GSM2258257 GSM2258257: dynamics RNA; Danio rerio; RNA Seq GSM2258257   1 TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2258257 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     Philipp-dynamics-RNA_HKLJYBGXX_S8_L004_R1_001.fastq.gz Philipp-dynamics-RNA_HKLJYBGXX_S8_L004_R2_001.fastq.gz fastq fastq 78694337.0 518048.0 GSM2258257 r4 0:75.98 1:75.92 A:14385406;C:23351418;G:28887789;T:12068521;N:1203 75 75     14385406 23351418 28887789 12068521 1203 SRX1997147 SRS1598490 SRA426643 GEO Max Delbrück Center 2 0.0 0.0 0.0 0.0 1.0 1.0     76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-08-03 Hatching Embryo Embryo Imprecise All anatomical structures
41010 41010 SRR3536535 SRX1770315 SRS1442798 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       Protein injections GSM2155530   tissue:Single embryos|developmental stage:24h Protein injections For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Single embryos Embryos were injected at the 1 cell stage with 1 nl Cas9 protein final concentration 1590 ng/ul in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155530 GSM2155530: Protein injections; Danio rerio; RNA Seq GSM2155530   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155530 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     zfGFP4protein_AHG7CMBGXX_S11_L001_R2_001.fastq.gz fastq 113791000.0 749237.0 GSM2155530 r1 0:75.98 1:75.90 A:20602049;C:33698647;G:40809975;T:18435912;N:244417 75 75     20602049 33698647 40809975 18435912 244417 SRX1770315 SRS1442798 SRA426643 GEO Max Delbrück Center 2 0.0 0.0 0.0 0.0 1.0 1.0     76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
41011 41011 SRR3536536 SRX1770315 SRS1442798 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       Protein injections GSM2155530   tissue:Single embryos|developmental stage:24h Protein injections For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Single embryos Embryos were injected at the 1 cell stage with 1 nl Cas9 protein final concentration 1590 ng/ul in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155530 GSM2155530: Protein injections; Danio rerio; RNA Seq GSM2155530   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155530 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     zfGFP4protein_AHG7CMBGXX_S11_L002_R1_001.fastq.gz zfGFP4protein_AHG7CMBGXX_S11_L002_R2_001.fastq.gz fastq fastq 114510782.0 753967.0 GSM2155530 r2 0:75.98 1:75.90 A:20684140;C:33805645;G:41313135;T:18471924;N:235938 75 75     20684140 33805645 41313135 18471924 235938 SRX1770315 SRS1442798 SRA426643 GEO Max Delbrück Center 2 0.0 0.0 0.0 0.0 1.0 1.0     76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
41012 41012 SRR3536537 SRX1770315 SRS1442798 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       Protein injections GSM2155530   tissue:Single embryos|developmental stage:24h Protein injections For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Single embryos Embryos were injected at the 1 cell stage with 1 nl Cas9 protein final concentration 1590 ng/ul in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155530 GSM2155530: Protein injections; Danio rerio; RNA Seq GSM2155530   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155530 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286         109968569.0 724055.0 GSM2155530 r3 0:75.98 1:75.90 A:19878654;C:32566435;G:39496562;T:17888872;N:138046 75 75     19878654 32566435 39496562 17888872 138046 SRX1770315 SRS1442798 SRA426643 GEO Max Delbrück Center 2 0.0 0.0 0.0 0.0 1.0 1.0     76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
41013 41013 SRR3536538 SRX1770315 SRS1442798 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       Protein injections GSM2155530   tissue:Single embryos|developmental stage:24h Protein injections For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Single embryos Embryos were injected at the 1 cell stage with 1 nl Cas9 protein final concentration 1590 ng/ul in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155530 GSM2155530: Protein injections; Danio rerio; RNA Seq GSM2155530   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155530 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286         110729697.0 729061.0 GSM2155530 r4 0:75.98 1:75.90 A:19967167;C:32715452;G:39992653;T:17912669;N:141756 75 75     19967167 32715452 39992653 17912669 141756 SRX1770315 SRS1442798 SRA426643 GEO Max Delbrück Center 2 1e-05 1e-05 0.0 0.0 0.99997 0.99997 0.0 1.0 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
41014 41014 SRR3536479 SRX1770301 SRS1442785 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       TOMO 3 GSM2155516   tissue:Secti1d embryo|developmental stage:24h TOMO 3 For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Sectioned embryo Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155516 GSM2155516: TOMO 3; Danio rerio; RNA Seq GSM2155516   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155516 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     zfGFP4tomo3_AHF5FNBGXX_S9_L001_R1_001.fastq.gz zfGFP4tomo3_AHF5FNBGXX_S9_L001_R2_001.fastq.gz fastq fastq 616561738.0 4058387.0 GSM2155516 r1 0:75.99 1:75.94 A:113223336;C:179378849;G:225550023;T:98403521;N:6009 75 75     113223336 179378849 225550023 98403521 6009 SRX1770301 SRS1442785 SRA426643 GEO Max Delbrück Center 2 0.0031 0.00224 0.00298 0.00037 0.99997 0.99815 0.0 0.54485 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
41015 41015 SRR3536480 SRX1770301 SRS1442785 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       TOMO 3 GSM2155516   tissue:Secti1d embryo|developmental stage:24h TOMO 3 For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Sectioned embryo Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155516 GSM2155516: TOMO 3; Danio rerio; RNA Seq GSM2155516   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155516 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     zfGFP4tomo3_AHF5FNBGXX_S9_L002_R1_001.fastq.gz zfGFP4tomo3_AHF5FNBGXX_S9_L002_R2_001.fastq.gz fastq fastq 612631229.0 4032528.0 GSM2155516 r2 0:75.99 1:75.94 A:112250860;C:177589654;G:225470620;T:97316352;N:3743 75 75     112250860 177589654 225470620 97316352 3743 SRX1770301 SRS1442785 SRA426643 GEO Max Delbrück Center 2 0.00328 0.00181 0.00318 0.00027 0.99993 0.99833 0.0 0.5232 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
41016 41016 SRR3536481 SRX1770301 SRS1442785 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       TOMO 3 GSM2155516   tissue:Secti1d embryo|developmental stage:24h TOMO 3 For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Sectioned embryo Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155516 GSM2155516: TOMO 3; Danio rerio; RNA Seq GSM2155516   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155516 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     zfGFP4tomo3_AHF5FNBGXX_S9_L003_R1_001.fastq.gz zfGFP4tomo3_AHF5FNBGXX_S9_L003_R2_001.fastq.gz fastq fastq 616370738.0 4057190.0 GSM2155516 r3 0:75.99 1:75.93 A:113279678;C:179263048;G:225399046;T:98410557;N:18409 75 75     113279678 179263048 225399046 98410557 18409 SRX1770301 SRS1442785 SRA426643 GEO Max Delbrück Center 2 0.00317 0.00192 0.00306 0.00033 0.99997 0.99827 0.0 0.55294 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
41017 41017 SRR3536482 SRX1770301 SRS1442785 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       TOMO 3 GSM2155516   tissue:Secti1d embryo|developmental stage:24h TOMO 3 For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Sectioned embryo Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155516 GSM2155516: TOMO 3; Danio rerio; RNA Seq GSM2155516   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155516 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     zfGFP4tomo3_AHF5FNBGXX_S9_L004_R1_001.fastq.gz zfGFP4tomo3_AHF5FNBGXX_S9_L004_R2_001.fastq.gz fastq fastq 624786188.0 4112554.0 GSM2155516 r4 0:75.99 1:75.94 A:114515054;C:181154041;G:229755683;T:99341492;N:19918 75 75     114515054 181154041 229755683 99341492 19918 SRX1770301 SRS1442785 SRA426643 GEO Max Delbrück Center 2 0.00297 0.00211 0.00286 0.00033 0.99997 0.99821 0.0 0.53287 76 75 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
41018 41018 SRR3536475 SRX1770300 SRS1442784 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       TOMO 2 GSM2155515   tissue:Secti1d embryo|developmental stage:24h TOMO 2 For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Sectioned embryo Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155515 GSM2155515: TOMO 2; Danio rerio; RNA Seq GSM2155515   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155515 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286         648114567.0 4265856.0 GSM2155515 r1 0:75.99 1:75.94 A:117475168;C:188313577;G:240281561;T:102038272;N:5989 75 75     117475168 188313577 240281561 102038272 5989 SRX1770300 SRS1442784 SRA426643 GEO Max Delbrück Center 2 2e-05 2e-05 0.0 0.0 0.99995 0.99997 0.0 0.0 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
41019 41019 SRR3536476 SRX1770300 SRS1442784 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       TOMO 2 GSM2155515   tissue:Secti1d embryo|developmental stage:24h TOMO 2 For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Sectioned embryo Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155515 GSM2155515: TOMO 2; Danio rerio; RNA Seq GSM2155515   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155515 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     zfGFP4tomo2_AHF5FNBGXX_S8_L002_R1_001.fastq.gz zfGFP4tomo2_AHF5FNBGXX_S8_L002_R2_001.fastq.gz fastq fastq 645912335.0 4251368.0 GSM2155515 r2 0:75.99 1:75.94 A:116787859;C:186995532;G:240912198;T:101212725;N:4021 75 75     116787859 186995532 240912198 101212725 4021 SRX1770300 SRS1442784 SRA426643 GEO Max Delbrück Center 2 3e-05 2e-05 1e-05 1e-05 0.99997 1.0 0.0   76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
41020 41020 SRR3536477 SRX1770300 SRS1442784 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       TOMO 2 GSM2155515   tissue:Secti1d embryo|developmental stage:24h TOMO 2 For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Sectioned embryo Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155515 GSM2155515: TOMO 2; Danio rerio; RNA Seq GSM2155515   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155515 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     zfGFP4tomo2_AHF5FNBGXX_S8_L003_R1_001.fastq.gz fastq 650554243.0 4281969.0 GSM2155515 r3 0:75.99 1:75.94 A:118039991;C:188970659;G:241065842;T:102458188;N:19563 75 75     118039991 188970659 241065842 102458188 19563 SRX1770300 SRS1442784 SRA426643 GEO Max Delbrück Center 2 2e-05 1e-05 0.0 0.0 0.99997 1.0 0.0   76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
41021 41021 SRR3536478 SRX1770300 SRS1442784 SRP075286 PRJNA321866 Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars GSE81533 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.       TOMO 2 GSM2155515   tissue:Secti1d embryo|developmental stage:24h TOMO 2 For samples 1 32 Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin Sectioned embryo Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.   developmental stage:24h GSM2155515 GSM2155515: TOMO 2; Danio rerio; RNA Seq GSM2155515   1 RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit. GEO Accession:GSM2155515 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP075286     zfGFP4tomo2_AHF5FNBGXX_S8_L004_R1_001.fastq.gz fastq 657902363.0 4330308.0 GSM2155515 r4 0:75.99 1:75.94 A:119079652;C:190479252;G:245168127;T:103153508;N:21824 75 75     119079652 190479252 245168127 103153508 21824 SRX1770300 SRS1442784 SRA426643 GEO Max Delbrück Center 2 0.0 4e-05 0.0 2e-05 1.0 0.99995   0.5 76 76 T T mates < 9% mapping rate illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Germany 2016-05-17 Pharyngula Embryo Embryo Imprecise All anatomical structures
48248 48248 SRR7119805 SRX4041448 SRS3258926 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq 3dpf mut8 GSM3131196   tissue:whole embryo|strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / Danio rerio RNAseq 3dpf mut8 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format whole embryo   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / GSM3131196 GSM3131196: Danio rerio RNAseq 3dpf mut8; Danio rerio; RNA Seq GSM3131196   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131196 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP144601     NDC-ring1b-3dpf-repl8-13282_R1.fastq.gz NDC-ring1b-3dpf-repl8-13282_R2.fastq.gz fastq fastq 2586301116.0 30789299.0 GSM3131196 r1 0:42 1:42 A:689082798;C:590336938;G:600860389;T:705094245;N:926746 42 42     689082798 590336938 600860389 705094245 926746 SRX4041448 SRS3258926 SRA699717 GEO Molecular Biology, Radboud University 2 0.87813 0.89136 0.27656 0.27012 0.67351 0.6745 0.44828 0.44382 42 42 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Larval Larval Whole Organism All anatomical structures
48249 48249 SRR7119804 SRX4041447 SRS3258925 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq 3dpf mut7 GSM3131195   tissue:whole embryo|strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / Danio rerio RNAseq 3dpf mut7 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format whole embryo   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / GSM3131195 GSM3131195: Danio rerio RNAseq 3dpf mut7; Danio rerio; RNA Seq GSM3131195   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131195 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP144601     NDC-ring1b-3dpf-repl7-13281_R2.fastq.gz NDC-ring1b-3dpf-repl7-13281_R1.fastq.gz fastq fastq 1514220876.0 18026439.0 GSM3131195 r1 0:42 1:42 A:409686548;C:340910820;G:347249065;T:415826325;N:548118 42 42     409686548 340910820 347249065 415826325 548118 SRX4041447 SRS3258925 SRA699717 GEO Molecular Biology, Radboud University 2 0.88991 0.90191 0.30704 0.30119 0.66695 0.66922 0.45618 0.46008 42 42 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Larval Larval Whole Organism All anatomical structures
48250 48250 SRR7119802 SRX4041446 SRS3258924 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq 3dpf mut6 GSM3131194   tissue:whole embryo|strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / Danio rerio RNAseq 3dpf mut6 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format whole embryo   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / GSM3131194 GSM3131194: Danio rerio RNAseq 3dpf mut6; Danio rerio; RNA Seq GSM3131194   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131194 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP144601     NDC-ring1b-3dpf-repl6-13280_R1.fastq.gz NDC-ring1b-3dpf-repl6-13280_R2.fastq.gz fastq fastq 2265837168.0 26974252.0 GSM3131194 r1 0:42 1:42 A:528919905;C:579225021;G:616897328;T:539985252;N:809662 42 42     528919905 579225021 616897328 539985252 809662 SRX4041446 SRS3258924 SRA699717 GEO Molecular Biology, Radboud University 2 0.73468 0.76482 0.24568 0.25398 0.70516 0.70414 0.44042 0.43826 42 42 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Larval Larval Whole Organism All anatomical structures
48251 48251 SRR7119801 SRX4041445 SRS3258923 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq 3dpf mut5 GSM3131193   tissue:whole embryo|strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / Danio rerio RNAseq 3dpf mut5 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format whole embryo   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / GSM3131193 GSM3131193: Danio rerio RNAseq 3dpf mut5; Danio rerio; RNA Seq GSM3131193   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131193 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP144601     NDC-ring1b-3dpf-repl5-13279_R1.fastq.gz NDC-ring1b-3dpf-repl5-13279_R2.fastq.gz fastq fastq 2434539072.0 28982608.0 GSM3131193 r1 0:42 1:42 A:657750716;C:546331298;G:559727917;T:669858999;N:870142 42 42     657750716 546331298 559727917 669858999 870142 SRX4041445 SRS3258923 SRA699717 GEO Molecular Biology, Radboud University 2 0.88994 0.9052 0.31921 0.31753 0.67105 0.67245 0.43524 0.44685 42 42 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Larval Larval Whole Organism All anatomical structures
48252 48252 SRR7119800 SRX4041444 SRS3258922 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq 3dpf mut3 GSM3131192   tissue:whole embryo|strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / Danio rerio RNAseq 3dpf mut3 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format whole embryo   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / GSM3131192 GSM3131192: Danio rerio RNAseq 3dpf mut3; Danio rerio; RNA Seq GSM3131192   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131192 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP144601     Ring1b-3dpf-replicate3-12247_R1.fastq.gz Ring1b-3dpf-replicate3-12247_R2.fastq.gz fastq fastq 932865948.0 11105547.0 GSM3131192 r1 0:42 1:42 A:254207252;C:191875016;G:235114678;T:251619175;N:49827 42 42     254207252 191875016 235114678 251619175 49827 SRX4041444 SRS3258922 SRA699717 GEO Molecular Biology, Radboud University 2 0.83623 0.84228 0.56402 0.55503 0.69193 0.69045 0.46635 0.47045 42 42 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Larval Larval Whole Organism All anatomical structures
48253 48253 SRR7119799 SRX4041443 SRS3258933 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq 3dpf mut2 GSM3131191   tissue:whole embryo|strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / Danio rerio RNAseq 3dpf mut2 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format whole embryo   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / GSM3131191 GSM3131191: Danio rerio RNAseq 3dpf mut2; Danio rerio; RNA Seq GSM3131191   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131191 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP144601     Ring1b-3dpf-replicate2-12246_R1.fastq.gz Ring1b-3dpf-replicate2-12246_R2.fastq.gz fastq fastq 1428569856.0 17006784.0 GSM3131191 r1 0:42 1:42 A:375553518;C:323985274;G:352887011;T:376064416;N:79637 42 42     375553518 323985274 352887011 376064416 79637 SRX4041443 SRS3258933 SRA699717 GEO Molecular Biology, Radboud University 2 0.80267 0.81635 0.42059 0.41851 0.67598 0.67564 0.46878 0.47374 42 42 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Larval Larval Whole Organism All anatomical structures
48254 48254 SRR7119798 SRX4041442 SRS3258921 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq 3dpf mut1 GSM3131190   tissue:whole embryo|strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / Danio rerio RNAseq 3dpf mut1 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format whole embryo   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TU/TLF mixed background|cell type:whole embryo|age:3 dpf|genotype:rnf2 / GSM3131190 GSM3131190: Danio rerio RNAseq 3dpf mut1; Danio rerio; RNA Seq GSM3131190   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131190 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP144601     Ring1b-3dpf-replicate1-12245_R1.fastq.gz Ring1b-3dpf-replicate1-12245_R2.fastq.gz fastq fastq 1619814000.0 19283500.0 GSM3131190 r1 0:42 1:42 A:434648048;C:363147668;G:388048793;T:433881736;N:87755 42 42     434648048 363147668 388048793 433881736 87755 SRX4041442 SRS3258921 SRA699717 GEO Molecular Biology, Radboud University 2 0.79912 0.81304 0.45971 0.46081 0.67556 0.6759 0.46577 0.46988 42 42 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Larval Larval Whole Organism All anatomical structures
48255 48255 SRR7119797 SRX4041441 SRS3258932 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq 3dpf wt13 GSM3131189   tissue:whole embryo|strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type Danio rerio RNAseq 3dpf wt13 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format whole embryo   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type GSM3131189 GSM3131189: Danio rerio RNAseq 3dpf wt13; Danio rerio; RNA Seq GSM3131189   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131189 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP144601     NDC-TLF-3dpf-repl13-13287_R1.fastq.gz NDC-TLF-3dpf-repl13-13287_R2.fastq.gz fastq fastq 1535721936.0 18282404.0 GSM3131189 r1 0:42 1:42 A:403114263;C:355464889;G:362868285;T:413725995;N:548504 42 42     403114263 355464889 362868285 413725995 548504 SRX4041441 SRS3258932 SRA699717 GEO Molecular Biology, Radboud University 2 0.89271 0.90739 0.24124 0.23374 0.67292 0.67349 0.45333 0.45657 42 42 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Larval Larval Whole Organism All anatomical structures
48256 48256 SRR7119796 SRX4041440 SRS3258920 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq 3dpf wt12 GSM3131188   tissue:whole embryo|strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type Danio rerio RNAseq 3dpf wt12 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format whole embryo   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type GSM3131188 GSM3131188: Danio rerio RNAseq 3dpf wt12; Danio rerio; RNA Seq GSM3131188   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131188 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP144601     NDC-TLF-3dpf-repl12-13286_R1.fastq.gz NDC-TLF-3dpf-repl12-13286_R2.fastq.gz fastq fastq 1296768900.0 15437725.0 GSM3131188 r1 0:42 1:42 A:342053865;C:298842079;G:305530839;T:349875429;N:466688 42 42     342053865 298842079 305530839 349875429 466688 SRX4041440 SRS3258920 SRA699717 GEO Molecular Biology, Radboud University 2 0.88405 0.90076 0.25686 0.24808 0.67365 0.67156 0.44757 0.45604 42 42 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Larval Larval Whole Organism All anatomical structures
48257 48257 SRR7119795 SRX4041439 SRS3258919 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq 3dpf wt11 GSM3131187   tissue:whole embryo|strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type Danio rerio RNAseq 3dpf wt11 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format whole embryo   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type GSM3131187 GSM3131187: Danio rerio RNAseq 3dpf wt11; Danio rerio; RNA Seq GSM3131187   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131187 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP144601     NDC-TLF-3dpf-repl11-13285_R1.fastq.gz NDC-TLF-3dpf-repl11-13285_R2.fastq.gz fastq fastq 2485819560.0 29593090.0 GSM3131187 r1 0:42 1:42 A:637012348;C:587468873;G:621718352;T:638709810;N:910177 42 42     637012348 587468873 621718352 638709810 910177 SRX4041439 SRS3258919 SRA699717 GEO Molecular Biology, Radboud University 2 0.81173 0.83081 0.26441 0.27241 0.69572 0.69863 0.46814 0.46844 42 42 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Larval Larval Whole Organism All anatomical structures
48258 48258 SRR7119794 SRX4041438 SRS3258918 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq 3dpf wt5 GSM3131186   tissue:whole embryo|strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type Danio rerio RNAseq 3dpf wt5 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format whole embryo   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type GSM3131186 GSM3131186: Danio rerio RNAseq 3dpf wt5; Danio rerio; RNA Seq GSM3131186   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131186 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP144601     NDC-TLF-3dpf-repl5-13284_R1.fastq.gz NDC-TLF-3dpf-repl5-13284_R2.fastq.gz fastq fastq 854422548.0 10171697.0 GSM3131186 r1 0:42 1:42 A:227799696;C:189132544;G:207116976;T:230065989;N:307343 42 42     227799696 189132544 207116976 230065989 307343 SRX4041438 SRS3258918 SRA699717 GEO Molecular Biology, Radboud University 2 0.8869 0.89921 0.29991 0.30201 0.67259 0.67466 0.43395 0.45782 42 42 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Larval Larval Whole Organism All anatomical structures
48259 48259 SRR7119793 SRX4041437 SRS3258917 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq 3dpf wt4 GSM3131185   tissue:whole embryo|strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type Danio rerio RNAseq 3dpf wt4 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format whole embryo   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type GSM3131185 GSM3131185: Danio rerio RNAseq 3dpf wt4; Danio rerio; RNA Seq GSM3131185   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131185 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP144601     NDC-TLF-3dpf-repl4-13283_R1.fastq.gz NDC-TLF-3dpf-repl4-13283_R2.fastq.gz fastq fastq 1884789312.0 22437968.0 GSM3131185 r1 0:42 1:42 A:516338681;C:420191388;G:421311695;T:526266145;N:681403 42 42     516338681 420191388 421311695 526266145 681403 SRX4041437 SRS3258917 SRA699717 GEO Molecular Biology, Radboud University 2 0.89533 0.90768 0.30891 0.30384 0.66492 0.66636 0.44687 0.45358 42 42 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Larval Larval Whole Organism All anatomical structures
48260 48260 SRR7119792 SRX4041436 SRS3258916 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq 3dpf wt3 GSM3131184   tissue:whole embryo|strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type Danio rerio RNAseq 3dpf wt3 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format whole embryo   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type GSM3131184 GSM3131184: Danio rerio RNAseq 3dpf wt3; Danio rerio; RNA Seq GSM3131184   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131184 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP144601     TLF-3dpf-replicate3-12250_R1.fastq.gz TLF-3dpf-replicate3-12250_R2.fastq.gz fastq fastq 1781685444.0 21210541.0 GSM3131184 r1 0:42 1:42 A:454462414;C:421206578;G:449348079;T:456572027;N:96346 42 42     454462414 421206578 449348079 456572027 96346 SRX4041436 SRS3258916 SRA699717 GEO Molecular Biology, Radboud University 2 0.77224 0.79091 0.333 0.33343 0.67229 0.67265 0.46461 0.47357 42 42 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Larval Larval Whole Organism All anatomical structures
48261 48261 SRR7119790 SRX4041435 SRS3258915 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq 3dpf wt2 GSM3131183   tissue:whole embryo|strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type Danio rerio RNAseq 3dpf wt2 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format whole embryo   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type GSM3131183 GSM3131183: Danio rerio RNAseq 3dpf wt2; Danio rerio; RNA Seq GSM3131183   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131183 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP144601     TLF-3dpf-replicate2-12249_R1.fastq.gz TLF-3dpf-replicate2-12249_R2.fastq.gz fastq fastq 1548027852.0 18428903.0 GSM3131183 r1 0:42 1:42 A:396847823;C:364731299;G:388571797;T:397788001;N:88932 42 42     396847823 364731299 388571797 397788001 88932 SRX4041435 SRS3258915 SRA699717 GEO Molecular Biology, Radboud University 2 0.79516 0.81734 0.30973 0.3124 0.67095 0.67381 0.45609 0.4615 42 42 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Larval Larval Whole Organism All anatomical structures
48262 48262 SRR7119789 SRX4041434 SRS3258914 SRP144601 PRJNA459724 The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis GSE114038 Other Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively   pubmed:30867528   Danio rerio RNAseq 3dpf wt1 GSM3131182   tissue:whole embryo|strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type Danio rerio RNAseq 3dpf wt1 RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format whole embryo   RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995. strain:TLF|cell type:whole embryo|age:3 dpf|genotype:wild type GSM3131182 GSM3131182: Danio rerio RNAseq 3dpf wt1; Danio rerio; RNA Seq GSM3131182   1 RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation GEO Accession:GSM3131182 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP144601     TLF-3dpf-replicate1-12248_R1.fastq.gz TLF-3dpf-replicate1-12248_R2.fastq.gz fastq fastq 1443284556.0 17181959.0 GSM3131182 r1 0:42 1:42 A:371226822;C:343019970;G:358627075;T:370330892;N:79797 42 42     371226822 343019970 358627075 370330892 79797 SRX4041434 SRS3258914 SRA699717 GEO Molecular Biology, Radboud University 2 0.82734 0.83906 0.35561 0.35376 0.68816 0.69112 0.53167 0.53342 42 42 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero sc single_cell_plate celseq   Netherlands 2018-05-04 Larval Larval Whole Organism All anatomical structures
51311 51311 SRR8732849 SRX5525702 SRS4492378 SRP188515 PRJNA527216 Multi species tomo sequencing identifies new major hematopoietic stem cell regulators in the microenvironment of the embryonic aorta GSE128350 Other The behavior of stem cells is regulated by their local microenvironment through biochemical and biophysical interactions. To advance our understanding of the molecular characteristics and key components of the microenvironment we applied a genome wide RNA tomography sequencing approach in zebrafish chicken mouse and human embryos. The resulting anterior posterior and/or dorsal ventral transcriptional maps provide a powerful resource for identifying and comparing expression patterns in a given tissue or microenvironment along the embryonic axes of multiple species. We used these maps to explore the regulatory function of the aortic microenvironment where the first hematopoietic stem cells are generated during embryonic development. By performing inter species comparative analyses we identified and functionally validated new conserved regulators of hematopoietic stem cell generation. Further analysis of spatial transcriptomics will elucidate the regulatory functions of the local microenvironment in vivo paving the way for improved stem cell production in vitro and clinical cell therapy. Overall design: Spatial transcriptomics by RNA tomography Tomo seq on whole or sub dissected embryos processed along the anterior to posterior axis and on transversal thick slices processed along the dorsal to ventral axis.   pubmed:32457985   Extracted RNA 28 hpf whole zebrafish embryo #3 from posterior to anterior axis GSM3672158   source name:whole embryo|strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:whole embryo|developmental stage:28 hpf Extracted RNA 28 hpf whole zebrafish embryo #3 from posterior to anterior axis CEL seq were mapped with bwa using custom scripts as previously described Grün et al. Nature Methods 2014 Genome build: mouse: mm10; chicken: galGal4 with improved 3’UTR annotations see Junker et al. Cell 2014; zebrafish: Zv9 with improved 3’UTR annotations see Junker et al. Cell 2014; human: hg19 Supplementary files format and content: *.coutc.csv: Tab separated data file for each sequencing library. The first column lists the official gene symbol followed by the chromosome name separated by a double underscore. Column names indicate the number of sections/primers separated by an underscore. For 'ggcells2.coutc.csv' Tab which belongs to the chicken IAHC sorted cells the two last columns indicate the number of reads obtained for experiment#1 and experiment#2 primer#95 and primer#96 respectively. The order of the columns/primers follows the description of the sample from the title. For instance: "Extracted RNA 3 dpf chicken embryo from posterior to anterior axis": the column 1 = most posterior section while the column 96 = most anterior. This is the case for all the samples listed. whole embryo   Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer’s manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. Zebrafish were maintained and propagated according to standard laboratory conditions. Kdrl:mcherry/cd41:eGFP reporter fish line was used for tomo seq at both 28hpf and 40hpf. Fertilized chicken eggs Bovans Brown were incubated at 37±1°C in a humidified atmosphere until they reached the appropriate developmental stage. E3 and E4 chicken embryos were used for tomo seq. C57BL/6 mouse strain was housed according to institutional guidelines and procedures were performed in compliance with Standards for Care and Use of Laboratory Animals with approval from the Hubrecht Institute ethical review board. E10.5 and E11.5 mouse embryos were used for tomo seq. Human embryos were obtained from Dr. Chuva de Sousa Lopes laboratory LUMC Leiden Netherlands. The Medical Ethical Committee of the Leiden University Medical Center P08.087 approved all procedures regarding the collection and use of human embryonic material. strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:whole embryo|developmental stage:28 hpf GSM3672158 GSM3672158: Extracted RNA 28 hpf whole zebrafish embryo #3 from posterior to anterior axis; Danio rerio; RNA Seq GSM3672158   1 Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer's manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. GEO Accession:GSM3672158 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP188515     Sample17_R1_zcat.fastq.gz Sample17_R2_zcat.fastq.gz fastq fastq 8156614941.0 54091984.0 GSM3672158 r1 0:75.34 1:75.45 A:2414004672;C:1132746308;G:1388606792;T:3220760873;N:496296 75 75     2414004672 1132746308 1388606792 3220760873 496296 SRX5525702 SRS4492378 SRA860716 GEO Hubrecht Institute 2 0.0447 0.79211 0.03174 0.19541 0.99622 0.84413 0.42608 0.54026 75 76 T B mate1 technical by mapping diff illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Netherlands 2019-03-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
51312 51312 SRR8732848 SRX5525701 SRS4492377 SRP188515 PRJNA527216 Multi species tomo sequencing identifies new major hematopoietic stem cell regulators in the microenvironment of the embryonic aorta GSE128350 Other The behavior of stem cells is regulated by their local microenvironment through biochemical and biophysical interactions. To advance our understanding of the molecular characteristics and key components of the microenvironment we applied a genome wide RNA tomography sequencing approach in zebrafish chicken mouse and human embryos. The resulting anterior posterior and/or dorsal ventral transcriptional maps provide a powerful resource for identifying and comparing expression patterns in a given tissue or microenvironment along the embryonic axes of multiple species. We used these maps to explore the regulatory function of the aortic microenvironment where the first hematopoietic stem cells are generated during embryonic development. By performing inter species comparative analyses we identified and functionally validated new conserved regulators of hematopoietic stem cell generation. Further analysis of spatial transcriptomics will elucidate the regulatory functions of the local microenvironment in vivo paving the way for improved stem cell production in vitro and clinical cell therapy. Overall design: Spatial transcriptomics by RNA tomography Tomo seq on whole or sub dissected embryos processed along the anterior to posterior axis and on transversal thick slices processed along the dorsal to ventral axis.   pubmed:32457985   Extracted RNA 40 hpf whole zebrafish embryo #2 from anterior to posterior axis GSM3672157   source name:whole embryo|strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:whole embryo|developmental stage:40 hpf Extracted RNA 40 hpf whole zebrafish embryo #2 from anterior to posterior axis CEL seq were mapped with bwa using custom scripts as previously described Grün et al. Nature Methods 2014 Genome build: mouse: mm10; chicken: galGal4 with improved 3’UTR annotations see Junker et al. Cell 2014; zebrafish: Zv9 with improved 3’UTR annotations see Junker et al. Cell 2014; human: hg19 Supplementary files format and content: *.coutc.csv: Tab separated data file for each sequencing library. The first column lists the official gene symbol followed by the chromosome name separated by a double underscore. Column names indicate the number of sections/primers separated by an underscore. For 'ggcells2.coutc.csv' Tab which belongs to the chicken IAHC sorted cells the two last columns indicate the number of reads obtained for experiment#1 and experiment#2 primer#95 and primer#96 respectively. The order of the columns/primers follows the description of the sample from the title. For instance: "Extracted RNA 3 dpf chicken embryo from posterior to anterior axis": the column 1 = most posterior section while the column 96 = most anterior. This is the case for all the samples listed. whole embryo   Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer’s manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. Zebrafish were maintained and propagated according to standard laboratory conditions. Kdrl:mcherry/cd41:eGFP reporter fish line was used for tomo seq at both 28hpf and 40hpf. Fertilized chicken eggs Bovans Brown were incubated at 37±1°C in a humidified atmosphere until they reached the appropriate developmental stage. E3 and E4 chicken embryos were used for tomo seq. C57BL/6 mouse strain was housed according to institutional guidelines and procedures were performed in compliance with Standards for Care and Use of Laboratory Animals with approval from the Hubrecht Institute ethical review board. E10.5 and E11.5 mouse embryos were used for tomo seq. Human embryos were obtained from Dr. Chuva de Sousa Lopes laboratory LUMC Leiden Netherlands. The Medical Ethical Committee of the Leiden University Medical Center P08.087 approved all procedures regarding the collection and use of human embryonic material. strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:whole embryo|developmental stage:40 hpf GSM3672157 GSM3672157: Extracted RNA 40 hpf whole zebrafish embryo #2 from anterior to posterior axis; Danio rerio; RNA Seq GSM3672157   1 Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer's manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. GEO Accession:GSM3672157 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP188515     Sample15_R1_zcat.fastq.gz Sample15_R2_zcat.fastq.gz fastq fastq 6313331656.0 41861859.0 GSM3672157 r1 0:75.35 1:75.46 A:1835394541;C:855041539;G:1018382135;T:2604142980;N:370461 75 75     1835394541 855041539 1018382135 2604142980 370461 SRX5525701 SRS4492377 SRA860716 GEO Hubrecht Institute 2 0.05321 0.82346 0.04331 0.23083 0.99786 0.83345 0.40714 0.54319 75 76 T B mate1 technical by mapping diff illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Netherlands 2019-03-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
51313 51313 SRR8732840 SRX5525693 SRS4492370 SRP188515 PRJNA527216 Multi species tomo sequencing identifies new major hematopoietic stem cell regulators in the microenvironment of the embryonic aorta GSE128350 Other The behavior of stem cells is regulated by their local microenvironment through biochemical and biophysical interactions. To advance our understanding of the molecular characteristics and key components of the microenvironment we applied a genome wide RNA tomography sequencing approach in zebrafish chicken mouse and human embryos. The resulting anterior posterior and/or dorsal ventral transcriptional maps provide a powerful resource for identifying and comparing expression patterns in a given tissue or microenvironment along the embryonic axes of multiple species. We used these maps to explore the regulatory function of the aortic microenvironment where the first hematopoietic stem cells are generated during embryonic development. By performing inter species comparative analyses we identified and functionally validated new conserved regulators of hematopoietic stem cell generation. Further analysis of spatial transcriptomics will elucidate the regulatory functions of the local microenvironment in vivo paving the way for improved stem cell production in vitro and clinical cell therapy. Overall design: Spatial transcriptomics by RNA tomography Tomo seq on whole or sub dissected embryos processed along the anterior to posterior axis and on transversal thick slices processed along the dorsal to ventral axis.   pubmed:32457985   Extracted RNA 40 hpf zebrafish trunk #1 and #2 from dorsal to ventral axis GSM3672149   source name:Dissected trunk|strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:Dissected trunk|developmental stage:40 hpf Extracted RNA 40 hpf zebrafish trunk #1 and #2 from dorsal to ventral axis CEL seq were mapped with bwa using custom scripts as previously described Grün et al. Nature Methods 2014 Genome build: mouse: mm10; chicken: galGal4 with improved 3’UTR annotations see Junker et al. Cell 2014; zebrafish: Zv9 with improved 3’UTR annotations see Junker et al. Cell 2014; human: hg19 Supplementary files format and content: *.coutc.csv: Tab separated data file for each sequencing library. The first column lists the official gene symbol followed by the chromosome name separated by a double underscore. Column names indicate the number of sections/primers separated by an underscore. For 'ggcells2.coutc.csv' Tab which belongs to the chicken IAHC sorted cells the two last columns indicate the number of reads obtained for experiment#1 and experiment#2 primer#95 and primer#96 respectively. The order of the columns/primers follows the description of the sample from the title. For instance: "Extracted RNA 3 dpf chicken embryo from posterior to anterior axis": the column 1 = most posterior section while the column 96 = most anterior. This is the case for all the samples listed. Dissected trunk   Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer’s manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. Zebrafish were maintained and propagated according to standard laboratory conditions. Kdrl:mcherry/cd41:eGFP reporter fish line was used for tomo seq at both 28hpf and 40hpf. Fertilized chicken eggs Bovans Brown were incubated at 37±1°C in a humidified atmosphere until they reached the appropriate developmental stage. E3 and E4 chicken embryos were used for tomo seq. C57BL/6 mouse strain was housed according to institutional guidelines and procedures were performed in compliance with Standards for Care and Use of Laboratory Animals with approval from the Hubrecht Institute ethical review board. E10.5 and E11.5 mouse embryos were used for tomo seq. Human embryos were obtained from Dr. Chuva de Sousa Lopes laboratory LUMC Leiden Netherlands. The Medical Ethical Committee of the Leiden University Medical Center P08.087 approved all procedures regarding the collection and use of human embryonic material. strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:Dissected trunk|developmental stage:40 hpf GSM3672149 GSM3672149: Extracted RNA 40 hpf zebrafish trunk #1 and #2 from dorsal to ventral axis; Danio rerio; RNA Seq GSM3672149   1 Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer's manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. GEO Accession:GSM3672149 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP188515     Sample6_R1_zcat.fastq.gz Sample6_R2_zcat.fastq.gz fastq fastq 5587592853.0 37062063.0 GSM3672149 r1 0:75.36 1:75.41 A:1734543706;C:744561818;G:859917019;T:2246189990;N:2380320 75 75     1734543706 744561818 859917019 2246189990 2380320 SRX5525693 SRS4492370 SRA860716 GEO Hubrecht Institute 2 0.0668 0.83117 0.05405 0.29997 0.99669 0.90299 0.45595 0.48918 75 75 T B mate1 technical by mapping diff illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Netherlands 2019-03-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
51314 51314 SRR8732839 SRX5525692 SRS4492369 SRP188515 PRJNA527216 Multi species tomo sequencing identifies new major hematopoietic stem cell regulators in the microenvironment of the embryonic aorta GSE128350 Other The behavior of stem cells is regulated by their local microenvironment through biochemical and biophysical interactions. To advance our understanding of the molecular characteristics and key components of the microenvironment we applied a genome wide RNA tomography sequencing approach in zebrafish chicken mouse and human embryos. The resulting anterior posterior and/or dorsal ventral transcriptional maps provide a powerful resource for identifying and comparing expression patterns in a given tissue or microenvironment along the embryonic axes of multiple species. We used these maps to explore the regulatory function of the aortic microenvironment where the first hematopoietic stem cells are generated during embryonic development. By performing inter species comparative analyses we identified and functionally validated new conserved regulators of hematopoietic stem cell generation. Further analysis of spatial transcriptomics will elucidate the regulatory functions of the local microenvironment in vivo paving the way for improved stem cell production in vitro and clinical cell therapy. Overall design: Spatial transcriptomics by RNA tomography Tomo seq on whole or sub dissected embryos processed along the anterior to posterior axis and on transversal thick slices processed along the dorsal to ventral axis.   pubmed:32457985   Extracted RNA 28 hpf zebrafish trunk #1 and #2 from dorsal to ventral axis GSM3672148   source name:Dissected trunk|strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:Dissected trunk|developmental stage:28 hpf Extracted RNA 28 hpf zebrafish trunk #1 and #2 from dorsal to ventral axis CEL seq were mapped with bwa using custom scripts as previously described Grün et al. Nature Methods 2014 Genome build: mouse: mm10; chicken: galGal4 with improved 3’UTR annotations see Junker et al. Cell 2014; zebrafish: Zv9 with improved 3’UTR annotations see Junker et al. Cell 2014; human: hg19 Supplementary files format and content: *.coutc.csv: Tab separated data file for each sequencing library. The first column lists the official gene symbol followed by the chromosome name separated by a double underscore. Column names indicate the number of sections/primers separated by an underscore. For 'ggcells2.coutc.csv' Tab which belongs to the chicken IAHC sorted cells the two last columns indicate the number of reads obtained for experiment#1 and experiment#2 primer#95 and primer#96 respectively. The order of the columns/primers follows the description of the sample from the title. For instance: "Extracted RNA 3 dpf chicken embryo from posterior to anterior axis": the column 1 = most posterior section while the column 96 = most anterior. This is the case for all the samples listed. Dissected trunk   Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer’s manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. Zebrafish were maintained and propagated according to standard laboratory conditions. Kdrl:mcherry/cd41:eGFP reporter fish line was used for tomo seq at both 28hpf and 40hpf. Fertilized chicken eggs Bovans Brown were incubated at 37±1°C in a humidified atmosphere until they reached the appropriate developmental stage. E3 and E4 chicken embryos were used for tomo seq. C57BL/6 mouse strain was housed according to institutional guidelines and procedures were performed in compliance with Standards for Care and Use of Laboratory Animals with approval from the Hubrecht Institute ethical review board. E10.5 and E11.5 mouse embryos were used for tomo seq. Human embryos were obtained from Dr. Chuva de Sousa Lopes laboratory LUMC Leiden Netherlands. The Medical Ethical Committee of the Leiden University Medical Center P08.087 approved all procedures regarding the collection and use of human embryonic material. strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:Dissected trunk|developmental stage:28 hpf GSM3672148 GSM3672148: Extracted RNA 28 hpf zebrafish trunk #1 and #2 from dorsal to ventral axis; Danio rerio; RNA Seq GSM3672148   1 Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer's manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. GEO Accession:GSM3672148 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP188515     Sample5_R1_zcat.fastq.gz Sample5_R2_zcat.fastq.gz fastq fastq 5347713824.0 35489697.0 GSM3672148 r1 0:75.32 1:75.36 A:1730992334;C:750666631;G:941260179;T:1922636857;N:2157823 75 75     1730992334 750666631 941260179 1922636857 2157823 SRX5525692 SRS4492369 SRA860716 GEO Hubrecht Institute 2 0.02738 0.73853 0.02205 0.35749 0.99774 0.93188 0.50877 0.56198 75 76 T B mate1 technical by mapping diff illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Netherlands 2019-03-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
51315 51315 SRR8732838 SRX5525691 SRS4492367 SRP188515 PRJNA527216 Multi species tomo sequencing identifies new major hematopoietic stem cell regulators in the microenvironment of the embryonic aorta GSE128350 Other The behavior of stem cells is regulated by their local microenvironment through biochemical and biophysical interactions. To advance our understanding of the molecular characteristics and key components of the microenvironment we applied a genome wide RNA tomography sequencing approach in zebrafish chicken mouse and human embryos. The resulting anterior posterior and/or dorsal ventral transcriptional maps provide a powerful resource for identifying and comparing expression patterns in a given tissue or microenvironment along the embryonic axes of multiple species. We used these maps to explore the regulatory function of the aortic microenvironment where the first hematopoietic stem cells are generated during embryonic development. By performing inter species comparative analyses we identified and functionally validated new conserved regulators of hematopoietic stem cell generation. Further analysis of spatial transcriptomics will elucidate the regulatory functions of the local microenvironment in vivo paving the way for improved stem cell production in vitro and clinical cell therapy. Overall design: Spatial transcriptomics by RNA tomography Tomo seq on whole or sub dissected embryos processed along the anterior to posterior axis and on transversal thick slices processed along the dorsal to ventral axis.   pubmed:32457985   Extracted RNA 28 hpf whole zebrafish embryo #2 from anterior to posterior axis GSM3672147   source name:whole embryo|strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:whole embryo|developmental stage:28 hpf Extracted RNA 28 hpf whole zebrafish embryo #2 from anterior to posterior axis CEL seq were mapped with bwa using custom scripts as previously described Grün et al. Nature Methods 2014 Genome build: mouse: mm10; chicken: galGal4 with improved 3’UTR annotations see Junker et al. Cell 2014; zebrafish: Zv9 with improved 3’UTR annotations see Junker et al. Cell 2014; human: hg19 Supplementary files format and content: *.coutc.csv: Tab separated data file for each sequencing library. The first column lists the official gene symbol followed by the chromosome name separated by a double underscore. Column names indicate the number of sections/primers separated by an underscore. For 'ggcells2.coutc.csv' Tab which belongs to the chicken IAHC sorted cells the two last columns indicate the number of reads obtained for experiment#1 and experiment#2 primer#95 and primer#96 respectively. The order of the columns/primers follows the description of the sample from the title. For instance: "Extracted RNA 3 dpf chicken embryo from posterior to anterior axis": the column 1 = most posterior section while the column 96 = most anterior. This is the case for all the samples listed. whole embryo   Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer’s manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. Zebrafish were maintained and propagated according to standard laboratory conditions. Kdrl:mcherry/cd41:eGFP reporter fish line was used for tomo seq at both 28hpf and 40hpf. Fertilized chicken eggs Bovans Brown were incubated at 37±1°C in a humidified atmosphere until they reached the appropriate developmental stage. E3 and E4 chicken embryos were used for tomo seq. C57BL/6 mouse strain was housed according to institutional guidelines and procedures were performed in compliance with Standards for Care and Use of Laboratory Animals with approval from the Hubrecht Institute ethical review board. E10.5 and E11.5 mouse embryos were used for tomo seq. Human embryos were obtained from Dr. Chuva de Sousa Lopes laboratory LUMC Leiden Netherlands. The Medical Ethical Committee of the Leiden University Medical Center P08.087 approved all procedures regarding the collection and use of human embryonic material. strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:whole embryo|developmental stage:28 hpf GSM3672147 GSM3672147: Extracted RNA 28 hpf whole zebrafish embryo #2 from anterior to posterior axis; Danio rerio; RNA Seq GSM3672147   1 Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer's manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. GEO Accession:GSM3672147 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP188515     Sample4_R2_zcat.fastq.gz Sample4_R1_zcat.fastq.gz fastq fastq 5574969530.0 36993436.0 GSM3672147 r1 0:75.32 1:75.38 A:1776560856;C:755982699;G:888659557;T:2151535116;N:2231302 75 75     1776560856 755982699 888659557 2151535116 2231302 SRX5525691 SRS4492367 SRA860716 GEO Hubrecht Institute 2 0.02327 0.77704 0.01701 0.20977 0.99791 0.89873 0.40944 0.50295 75 76 T B mate1 technical by mapping diff illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Netherlands 2019-03-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
51316 51316 SRR8732837 SRX5525690 SRS4492365 SRP188515 PRJNA527216 Multi species tomo sequencing identifies new major hematopoietic stem cell regulators in the microenvironment of the embryonic aorta GSE128350 Other The behavior of stem cells is regulated by their local microenvironment through biochemical and biophysical interactions. To advance our understanding of the molecular characteristics and key components of the microenvironment we applied a genome wide RNA tomography sequencing approach in zebrafish chicken mouse and human embryos. The resulting anterior posterior and/or dorsal ventral transcriptional maps provide a powerful resource for identifying and comparing expression patterns in a given tissue or microenvironment along the embryonic axes of multiple species. We used these maps to explore the regulatory function of the aortic microenvironment where the first hematopoietic stem cells are generated during embryonic development. By performing inter species comparative analyses we identified and functionally validated new conserved regulators of hematopoietic stem cell generation. Further analysis of spatial transcriptomics will elucidate the regulatory functions of the local microenvironment in vivo paving the way for improved stem cell production in vitro and clinical cell therapy. Overall design: Spatial transcriptomics by RNA tomography Tomo seq on whole or sub dissected embryos processed along the anterior to posterior axis and on transversal thick slices processed along the dorsal to ventral axis.   pubmed:32457985   Extracted RNA 28 hpf whole zebrafish embryo #1 from anterior to posterior axis GSM3672146   source name:whole embryo|strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:whole embryo|developmental stage:28 hpf Extracted RNA 28 hpf whole zebrafish embryo #1 from anterior to posterior axis CEL seq were mapped with bwa using custom scripts as previously described Grün et al. Nature Methods 2014 Genome build: mouse: mm10; chicken: galGal4 with improved 3’UTR annotations see Junker et al. Cell 2014; zebrafish: Zv9 with improved 3’UTR annotations see Junker et al. Cell 2014; human: hg19 Supplementary files format and content: *.coutc.csv: Tab separated data file for each sequencing library. The first column lists the official gene symbol followed by the chromosome name separated by a double underscore. Column names indicate the number of sections/primers separated by an underscore. For 'ggcells2.coutc.csv' Tab which belongs to the chicken IAHC sorted cells the two last columns indicate the number of reads obtained for experiment#1 and experiment#2 primer#95 and primer#96 respectively. The order of the columns/primers follows the description of the sample from the title. For instance: "Extracted RNA 3 dpf chicken embryo from posterior to anterior axis": the column 1 = most posterior section while the column 96 = most anterior. This is the case for all the samples listed. whole embryo   Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer’s manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. Zebrafish were maintained and propagated according to standard laboratory conditions. Kdrl:mcherry/cd41:eGFP reporter fish line was used for tomo seq at both 28hpf and 40hpf. Fertilized chicken eggs Bovans Brown were incubated at 37±1°C in a humidified atmosphere until they reached the appropriate developmental stage. E3 and E4 chicken embryos were used for tomo seq. C57BL/6 mouse strain was housed according to institutional guidelines and procedures were performed in compliance with Standards for Care and Use of Laboratory Animals with approval from the Hubrecht Institute ethical review board. E10.5 and E11.5 mouse embryos were used for tomo seq. Human embryos were obtained from Dr. Chuva de Sousa Lopes laboratory LUMC Leiden Netherlands. The Medical Ethical Committee of the Leiden University Medical Center P08.087 approved all procedures regarding the collection and use of human embryonic material. strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:whole embryo|developmental stage:28 hpf GSM3672146 GSM3672146: Extracted RNA 28 hpf whole zebrafish embryo #1 from anterior to posterior axis; Danio rerio; RNA Seq GSM3672146   1 Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer's manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. GEO Accession:GSM3672146 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP188515     Sample2_R2_zcat.fastq.gz Sample2_R1_zcat.fastq.gz fastq fastq 7138373773.0 47379140.0 GSM3672146 r1 0:75.32 1:75.34 A:2341329013;C:975718419;G:1157227064;T:2661209213;N:2890064 75 75     2341329013 975718419 1157227064 2661209213 2890064 SRX5525690 SRS4492365 SRA860716 GEO Hubrecht Institute 2 0.01395 0.71038 0.00951 0.19462 0.99835 0.91056 0.44 0.55129 75 76 T B mate1 technical by mapping diff illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Netherlands 2019-03-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
51317 51317 SRR8732836 SRX5525689 SRS4492366 SRP188515 PRJNA527216 Multi species tomo sequencing identifies new major hematopoietic stem cell regulators in the microenvironment of the embryonic aorta GSE128350 Other The behavior of stem cells is regulated by their local microenvironment through biochemical and biophysical interactions. To advance our understanding of the molecular characteristics and key components of the microenvironment we applied a genome wide RNA tomography sequencing approach in zebrafish chicken mouse and human embryos. The resulting anterior posterior and/or dorsal ventral transcriptional maps provide a powerful resource for identifying and comparing expression patterns in a given tissue or microenvironment along the embryonic axes of multiple species. We used these maps to explore the regulatory function of the aortic microenvironment where the first hematopoietic stem cells are generated during embryonic development. By performing inter species comparative analyses we identified and functionally validated new conserved regulators of hematopoietic stem cell generation. Further analysis of spatial transcriptomics will elucidate the regulatory functions of the local microenvironment in vivo paving the way for improved stem cell production in vitro and clinical cell therapy. Overall design: Spatial transcriptomics by RNA tomography Tomo seq on whole or sub dissected embryos processed along the anterior to posterior axis and on transversal thick slices processed along the dorsal to ventral axis.   pubmed:32457985   Extracted RNA 40 hpf whole zebrafish embryo #1 from anterior to posterior axis GSM3672145   source name:whole embryo|strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:whole embryo|developmental stage:40 hpf Extracted RNA 40 hpf whole zebrafish embryo #1 from anterior to posterior axis CEL seq were mapped with bwa using custom scripts as previously described Grün et al. Nature Methods 2014 Genome build: mouse: mm10; chicken: galGal4 with improved 3’UTR annotations see Junker et al. Cell 2014; zebrafish: Zv9 with improved 3’UTR annotations see Junker et al. Cell 2014; human: hg19 Supplementary files format and content: *.coutc.csv: Tab separated data file for each sequencing library. The first column lists the official gene symbol followed by the chromosome name separated by a double underscore. Column names indicate the number of sections/primers separated by an underscore. For 'ggcells2.coutc.csv' Tab which belongs to the chicken IAHC sorted cells the two last columns indicate the number of reads obtained for experiment#1 and experiment#2 primer#95 and primer#96 respectively. The order of the columns/primers follows the description of the sample from the title. For instance: "Extracted RNA 3 dpf chicken embryo from posterior to anterior axis": the column 1 = most posterior section while the column 96 = most anterior. This is the case for all the samples listed. whole embryo   Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer’s manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. Zebrafish were maintained and propagated according to standard laboratory conditions. Kdrl:mcherry/cd41:eGFP reporter fish line was used for tomo seq at both 28hpf and 40hpf. Fertilized chicken eggs Bovans Brown were incubated at 37±1°C in a humidified atmosphere until they reached the appropriate developmental stage. E3 and E4 chicken embryos were used for tomo seq. C57BL/6 mouse strain was housed according to institutional guidelines and procedures were performed in compliance with Standards for Care and Use of Laboratory Animals with approval from the Hubrecht Institute ethical review board. E10.5 and E11.5 mouse embryos were used for tomo seq. Human embryos were obtained from Dr. Chuva de Sousa Lopes laboratory LUMC Leiden Netherlands. The Medical Ethical Committee of the Leiden University Medical Center P08.087 approved all procedures regarding the collection and use of human embryonic material. strain:Kdrl:mcherry/cd41:eGFP|tissue:embryo|tissue preparation:whole embryo|developmental stage:40 hpf GSM3672145 GSM3672145: Extracted RNA 40 hpf whole zebrafish embryo #1 from anterior to posterior axis; Danio rerio; RNA Seq GSM3672145   1 Total RNA was isolated from individual cryosection using TRIzol reagent Ambion according to the manufacturer's manual. RNA extraction amplification and sequencing libraries were performed as described in {Junker et al. 2014}. Briefly RNA samples were treated according to the CEL seq protocol {Hashimshony 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit Illumina. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing. GEO Accession:GSM3672145 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP188515     Sample1_R1_zcat.fastq.gz Sample1_R2_zcat.fastq.gz fastq fastq 5326304022.0 35338371.0 GSM3672145 r1 0:75.34 1:75.39 A:1700388888;C:661186330;G:779653520;T:2182932216;N:2143068 75 75     1700388888 661186330 779653520 2182932216 2143068 SRX5525689 SRS4492366 SRA860716 GEO Hubrecht Institute 2 0.03106 0.82256 0.02777 0.13469 0.99943 0.8957 0.61538 0.5437 75 75 T B mate1 technical by mapping diff illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   Netherlands 2019-03-15 Pharyngula Embryo Embryo Imprecise All anatomical structures
55357 55357 SRR10321296 SRX7032110 SRS5552216 SRP226527 PRJNA578764 Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart. GSE139218 Transcriptome Analysis While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.   pubmed:31868166   LG B GSM4134189   source name:Tgmyl7:GFP 2dpf embryo|Stage:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo LG B Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to single cells. Tgmyl7:GFP 2dpf embryo Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016   Stage:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo GSM4134189 GSM4134189: LG B; Danio rerio; RNA Seq GSM4134189   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016 GEO Accession:GSM4134189 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP226527     LG-B_HF2K3BGXC_S8_L001_R1_001.fastq.gz LG-B_HF2K3BGXC_S8_L001_R2_001.fastq.gz fastq fastq 1267797208.0 14741828.0 GSM4134189 r1 0:26 1:60 A:311335670;C:234211034;G:233670769;T:488236082;N:343653 26 60     311335670 234211034 233670769 488236082 343653 SRX7032110 SRS5552216 SRA982819 GEO Bakkers, Hubrecht Institute 2 0.11947 0.86802 0.10602 0.33834 0.97402 0.77475 0.53341 0.48502 26 60 T B sc-like readlen illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2019-10-21 Hatching Embryo Embryo Imprecise All anatomical structures
55358 55358 SRR10321297 SRX7032110 SRS5552216 SRP226527 PRJNA578764 Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart. GSE139218 Transcriptome Analysis While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.   pubmed:31868166   LG B GSM4134189   source name:Tgmyl7:GFP 2dpf embryo|Stage:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo LG B Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to single cells. Tgmyl7:GFP 2dpf embryo Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016   Stage:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo GSM4134189 GSM4134189: LG B; Danio rerio; RNA Seq GSM4134189   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016 GEO Accession:GSM4134189 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP226527     LG-B_HF2K3BGXC_S8_L002_R1_001.fastq.gz LG-B_HF2K3BGXC_S8_L002_R2_001.fastq.gz fastq fastq 1243626134.0 14460769.0 GSM4134189 r2 0:26 1:60 A:303377313;C:228128597;G:235179890;T:476626682;N:313652 26 60     303377313 228128597 235179890 476626682 313652 SRX7032110 SRS5552216 SRA982819 GEO Bakkers, Hubrecht Institute 2 0.11708 0.86416 0.10403 0.33647 0.9751 0.77494 0.53712 0.49135 26 60 T B sc-like readlen illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2019-10-21 Hatching Embryo Embryo Imprecise All anatomical structures
55359 55359 SRR10321298 SRX7032110 SRS5552216 SRP226527 PRJNA578764 Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart. GSE139218 Transcriptome Analysis While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.   pubmed:31868166   LG B GSM4134189   source name:Tgmyl7:GFP 2dpf embryo|Stage:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo LG B Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to single cells. Tgmyl7:GFP 2dpf embryo Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016   Stage:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo GSM4134189 GSM4134189: LG B; Danio rerio; RNA Seq GSM4134189   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016 GEO Accession:GSM4134189 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP226527     LG-B_HF2K3BGXC_S8_L003_R1_001.fastq.gz LG-B_HF2K3BGXC_S8_L003_R2_001.fastq.gz fastq fastq 1279414002.0 14876907.0 GSM4134189 r3 0:26 1:60 A:313771869;C:236451307;G:236190971;T:492760785;N:239070 26 60     313771869 236451307 236190971 492760785 239070 SRX7032110 SRS5552216 SRA982819 GEO Bakkers, Hubrecht Institute 2 0.11797 0.86817 0.10442 0.33882 0.97394 0.7713 0.54719 0.48818 26 60 T B sc-like readlen illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2019-10-21 Hatching Embryo Embryo Imprecise All anatomical structures
55360 55360 SRR10321299 SRX7032110 SRS5552216 SRP226527 PRJNA578764 Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart. GSE139218 Transcriptome Analysis While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.   pubmed:31868166   LG B GSM4134189   source name:Tgmyl7:GFP 2dpf embryo|Stage:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo LG B Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to single cells. Tgmyl7:GFP 2dpf embryo Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016   Stage:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo GSM4134189 GSM4134189: LG B; Danio rerio; RNA Seq GSM4134189   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016 GEO Accession:GSM4134189 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP226527     LG-B_HF2K3BGXC_S8_L004_R1_001.fastq.gz LG-B_HF2K3BGXC_S8_L004_R2_001.fastq.gz fastq fastq 1253047262.0 14570317.0 GSM4134189 r4 0:26 1:60 A:305572355;C:230224915;G:236268214;T:480774305;N:207473 26 60     305572355 230224915 236268214 480774305 207473 SRX7032110 SRS5552216 SRA982819 GEO Bakkers, Hubrecht Institute 2 0.11724 0.86376 0.10408 0.336 0.97522 0.77273 0.53004 0.4873 26 60 T B sc-like readlen illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2019-10-21 Hatching Embryo Embryo Imprecise All anatomical structures

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