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,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,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,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,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,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
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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
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,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,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,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,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,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,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,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,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,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,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
55361,SRR10321292,SRX7032109,SRS5552215,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 A,GSM4134188,,source name:Tgmyl7:GFP 2dpf embryo|Stage:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo,LG A,"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,GSM4134188,GSM4134188: LG A; Danio rerio; RNA Seq,GSM4134188,,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:GSM4134188,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP226527,,,LG-A_HF2K3BGXC_S7_L001_R1_001.fastq.gz LG-A_HF2K3BGXC_S7_L001_R2_001.fastq.gz,fastq fastq,718764350.0,8357725.0,GSM4134188 r1,0:26 1:60,A:175945701;C:132625850;G:132781182;T:277212457;N:199160,26,60,,,175945701,132625850,132781182,277212457,199160,SRX7032109,SRS5552215,SRA982819,GEO,"Bakkers, Hubrecht Institute",2,0.11716,0.82752,0.10489,0.34715,0.97686,0.77423,0.57648,0.4889,26,60,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
55362,SRR10321293,SRX7032109,SRS5552215,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 A,GSM4134188,,source name:Tgmyl7:GFP 2dpf embryo|Stage:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo,LG A,"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,GSM4134188,GSM4134188: LG A; Danio rerio; RNA Seq,GSM4134188,,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:GSM4134188,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP226527,,,LG-A_HF2K3BGXC_S7_L002_R1_001.fastq.gz LG-A_HF2K3BGXC_S7_L002_R2_001.fastq.gz,fastq fastq,706043402.0,8209807.0,GSM4134188 r2,0:26 1:60,A:171617783;C:129365895;G:133886696;T:270994479;N:178549,26,60,,,171617783,129365895,133886696,270994479,178549,SRX7032109,SRS5552215,SRA982819,GEO,"Bakkers, Hubrecht Institute",2,0.11469,0.82025,0.10321,0.34365,0.97853,0.77358,0.5514,0.49163,26,60,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
55363,SRR10321294,SRX7032109,SRS5552215,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 A,GSM4134188,,source name:Tgmyl7:GFP 2dpf embryo|Stage:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo,LG A,"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,GSM4134188,GSM4134188: LG A; Danio rerio; RNA Seq,GSM4134188,,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:GSM4134188,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP226527,,,LG-A_HF2K3BGXC_S7_L003_R1_001.fastq.gz LG-A_HF2K3BGXC_S7_L003_R2_001.fastq.gz,fastq fastq,724780910.0,8427685.0,GSM4134188 r3,0:26 1:60,A:177259308;C:133737279;G:134127261;T:279526553;N:130509,26,60,,,177259308,133737279,134127261,279526553,130509,SRX7032109,SRS5552215,SRA982819,GEO,"Bakkers, Hubrecht Institute",2,0.11681,0.82709,0.10477,0.3456,0.97743,0.77555,0.5658,0.47721,26,60,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
55364,SRR10321295,SRX7032109,SRS5552215,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 A,GSM4134188,,source name:Tgmyl7:GFP 2dpf embryo|Stage:2dpf|line:Tgmyl7:GFP|tissue:2dpf zebrafish embryo,LG A,"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,GSM4134188,GSM4134188: LG A; Danio rerio; RNA Seq,GSM4134188,,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:GSM4134188,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP226527,,,LG-A_HF2K3BGXC_S7_L004_R1_001.fastq.gz LG-A_HF2K3BGXC_S7_L004_R2_001.fastq.gz,fastq fastq,710625138.0,8263083.0,GSM4134188 r4,0:26 1:60,A:172737690;C:130422622;G:134392616;T:272953106;N:119104,26,60,,,172737690,130422622,134392616,272953106,119104,SRX7032109,SRS5552215,SRA982819,GEO,"Bakkers, Hubrecht Institute",2,0.11478,0.82425,0.10243,0.34317,0.97796,0.77425,0.53983,0.48743,26,60,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
61999,SRR13115089,SRX9557302,SRS7769186,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNI160317 P1 8,GSM4930061,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,ZNI160317 P1 8,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,GSM4930061,GSM4930061: ZNI160317 P1 8; Danio rerio; RNA Seq,GSM4930061,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930061,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNI160317_P1_8_R1.fastq.gz ZNI160317_P1_8_R2.fastq.gz,fastq fastq,1337385100.0,13373851.0,GSM4930061 r1,0:30 1:70,A:347006359;C:234653057;G:234033243;T:521283652;N:408789,30,70,,,347006359,234653057,234033243,521283652,408789,SRX9557302,SRS7769186,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.43417,0.78388,0.40203,0.40818,0.99299,0.77843,0.50945,0.55316,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
62000,SRR13115088,SRX9557301,SRS7763907,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNI160317 P1 7,GSM4930060,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,ZNI160317 P1 7,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,GSM4930060,GSM4930060: ZNI160317 P1 7; Danio rerio; RNA Seq,GSM4930060,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930060,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNI160317_P1_7_R1.fastq.gz ZNI160317_P1_7_R2.fastq.gz,fastq fastq,1279888600.0,12798886.0,GSM4930060 r1,0:30 1:70,A:326535111;C:229909698;G:228370251;T:494684312;N:389228,30,70,,,326535111,229909698,228370251,494684312,389228,SRX9557301,SRS7763907,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.48745,0.80016,0.46063,0.38614,0.99097,0.78147,0.46969,0.58779,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
62001,SRR13115087,SRX9557300,SRS7770578,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNI160317 P1 6,GSM4930059,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,ZNI160317 P1 6,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,GSM4930059,GSM4930059: ZNI160317 P1 6; Danio rerio; RNA Seq,GSM4930059,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930059,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNI160317_P1_6_R1.fastq.gz ZNI160317_P1_6_R2.fastq.gz,fastq fastq,1356342900.0,13563429.0,GSM4930059 r1,0:30 1:70,A:379084008;C:226360122;G:228552139;T:521934821;N:411810,30,70,,,379084008,226360122,228552139,521934821,411810,SRX9557300,SRS7770578,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.44737,0.74966,0.42078,0.34194,0.9934,0.79091,0.84735,0.42938,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
62002,SRR13115086,SRX9557299,SRS7758037,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNI160317 P1 5,GSM4930058,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,ZNI160317 P1 5,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,GSM4930058,GSM4930058: ZNI160317 P1 5; Danio rerio; RNA Seq,GSM4930058,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930058,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNI160317_P1_5_R1.fastq.gz ZNI160317_P1_5_R2.fastq.gz,fastq fastq,1167185600.0,11671856.0,GSM4930058 r1,0:30 1:70,A:281862692;C:225836593;G:215293596;T:443836278;N:356441,30,70,,,281862692,225836593,215293596,443836278,356441,SRX9557299,SRS7758037,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.40867,0.83648,0.37699,0.32708,0.99048,0.78938,0.83594,0.51462,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
62003,SRR13115085,SRX9557298,SRS7758574,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNI130317 D3 8,GSM4930057,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,ZNI130317 D3 8,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,GSM4930057,GSM4930057: ZNI130317 D3 8; Danio rerio; RNA Seq,GSM4930057,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930057,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNI130317_D3_8_R1.fastq.gz ZNI130317_D3_8_R2.fastq.gz,fastq fastq,2604566100.0,26045661.0,GSM4930057 r1,0:30 1:70,A:675108201;C:476173471;G:445286652;T:1007719103;N:278673,30,70,,,675108201,476173471,445286652,1007719103,278673,SRX9557298,SRS7758574,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.35348,0.7674,0.33767,0.54152,0.98362,0.77975,0.76003,0.66589,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Larval,Larval,Embryo Imprecise,All anatomical structures
62004,SRR13115084,SRX9557297,SRS7773180,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNI130317 D3 7,GSM4930056,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,ZNI130317 D3 7,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,GSM4930056,GSM4930056: ZNI130317 D3 7; Danio rerio; RNA Seq,GSM4930056,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930056,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNI130317_D3_7_R1.fastq.gz ZNI130317_D3_7_R2.fastq.gz,fastq fastq,2213102100.0,22131021.0,GSM4930056 r1,0:30 1:70,A:576371932;C:403154890;G:384156998;T:849195962;N:222318,30,70,,,576371932,403154890,384156998,849195962,222318,SRX9557297,SRS7773180,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.4685,0.7605,0.4456,0.5035,0.98397,0.77952,0.68687,0.43992,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Larval,Larval,Embryo Imprecise,All anatomical structures
62005,SRR13115083,SRX9557296,SRS7771026,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNI130317 D3 6,GSM4930055,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,ZNI130317 D3 6,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,GSM4930055,GSM4930055: ZNI130317 D3 6; Danio rerio; RNA Seq,GSM4930055,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930055,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNI130317_D3_6_R1.fastq.gz ZNI130317_D3_6_R2.fastq.gz,fastq fastq,2981646200.0,29816462.0,GSM4930055 r1,0:30 1:70,A:778866100;C:536844713;G:508978814;T:1156648935;N:307638,30,70,,,778866100,536844713,508978814,1156648935,307638,SRX9557296,SRS7771026,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.29676,0.76913,0.28115,0.54055,0.98504,0.77082,0.79461,0.64154,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Larval,Larval,Embryo Imprecise,All anatomical structures
62006,SRR13115082,SRX9557295,SRS7772891,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNI130317 D3 5,GSM4930054,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,ZNI130317 D3 5,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,GSM4930054,GSM4930054: ZNI130317 D3 5; Danio rerio; RNA Seq,GSM4930054,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930054,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNI130317_D3_5_R1.fastq.gz ZNI130317_D3_5_R2.fastq.gz,fastq fastq,370600.0,3706.0,GSM4930054 r1,0:30 1:70,A:103174;C:82663;G:82368;T:102335;N:60,30,70,,,103174,82663,82368,102335,60,SRX9557295,SRS7772891,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.00286,0.00114,0.00285,0.00085,1.0,0.99997,,1.0,30,70,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Larval,Larval,Embryo Imprecise,All anatomical structures
62007,SRR13115081,SRX9557294,SRS7758850,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC181016 12,GSM4930053,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,ZNC181016 12,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,GSM4930053,GSM4930053: ZNC181016 12; Danio rerio; RNA Seq,GSM4930053,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930053,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC181016_12_R1.fastq.gz ZNC181016_12_R2.fastq.gz,fastq fastq,476005400.0,4760054.0,GSM4930053 r1,0:30 1:70,A:124538753;C:84143341;G:82570226;T:184169560;N:583520,30,70,,,124538753,84143341,82570226,184169560,583520,SRX9557294,SRS7758850,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.42712,0.77974,0.39704,0.48771,0.99389,0.86135,0.73235,0.64741,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
62008,SRR13115080,SRX9557293,SRS7765456,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC181016 11,GSM4930052,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,ZNC181016 11,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,GSM4930052,GSM4930052: ZNC181016 11; Danio rerio; RNA Seq,GSM4930052,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930052,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC181016_11_R1.fastq.gz ZNC181016_11_R2.fastq.gz,fastq fastq,786776600.0,7867766.0,GSM4930052 r1,0:30 1:70,A:213121780;C:142546342;G:132623188;T:297537196;N:948094,30,70,,,213121780,142546342,132623188,297537196,948094,SRX9557293,SRS7765456,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.41249,0.76451,0.39753,0.55115,0.99086,0.84307,0.62648,0.41771,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
62009,SRR13115079,SRX9557292,SRS7762461,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC181016 10,GSM4930051,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,ZNC181016 10,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,GSM4930051,GSM4930051: ZNC181016 10; Danio rerio; RNA Seq,GSM4930051,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930051,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC181016_10_R1.fastq.gz ZNC181016_10_R2.fastq.gz,fastq fastq,497840900.0,4978409.0,GSM4930051 r1,0:30 1:70,A:137854508;C:86121616;G:83106652;T:190153177;N:604947,30,70,,,137854508,86121616,83106652,190153177,604947,SRX9557292,SRS7762461,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.43691,0.74632,0.41151,0.5336,0.99324,0.84906,0.82241,0.65847,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
62010,SRR13115078,SRX9557291,SRS7771620,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC181016 9,GSM4930050,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,ZNC181016 9,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,GSM4930050,GSM4930050: ZNC181016 9; Danio rerio; RNA Seq,GSM4930050,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930050,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC181016_9_R1.fastq.gz ZNC181016_9_R2.fastq.gz,fastq fastq,932985500.0,9329855.0,GSM4930050 r1,0:30 1:70,A:250634435;C:162916909;G:167128292;T:351161628;N:1144236,30,70,,,250634435,162916909,167128292,351161628,1144236,SRX9557291,SRS7771620,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.54048,0.54987,0.52828,0.36431,0.99362,0.86535,0.61298,0.67072,30,70,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
62011,SRR13115077,SRX9557290,SRS7763268,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC160317 P1 4,GSM4930049,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,ZNC160317 P1 4,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,GSM4930049,GSM4930049: ZNC160317 P1 4; Danio rerio; RNA Seq,GSM4930049,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930049,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC160317_P1_4_R1.fastq.gz ZNC160317_P1_4_R2.fastq.gz,fastq fastq,1307869800.0,13078698.0,GSM4930049 r1,0:30 1:70,A:317290751;C:239429367;G:234943406;T:515801063;N:405213,30,70,,,317290751,239429367,234943406,515801063,405213,SRX9557290,SRS7763268,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.33232,0.8203,0.31733,0.37763,0.98985,0.77374,0.71932,0.58771,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
62012,SRR13115076,SRX9557289,SRS7768293,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC160317 P1 3,GSM4930048,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,ZNC160317 P1 3,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,GSM4930048,GSM4930048: ZNC160317 P1 3; Danio rerio; RNA Seq,GSM4930048,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930048,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC160317_P1_3_R1.fastq.gz ZNC160317_P1_3_R2.fastq.gz,fastq fastq,457462200.0,4574622.0,GSM4930048 r1,0:30 1:70,A:108644216;C:83870596;G:86397141;T:178408097;N:142150,30,70,,,108644216,83870596,86397141,178408097,142150,SRX9557289,SRS7768293,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.50502,0.8447,0.46926,0.30821,0.98748,0.78955,0.52537,0.59534,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
62013,SRR13115075,SRX9557288,SRS7776259,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC160317 P1 2,GSM4930047,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,ZNC160317 P1 2,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,GSM4930047,GSM4930047: ZNC160317 P1 2; Danio rerio; RNA Seq,GSM4930047,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930047,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC160317_P1_2_R1.fastq.gz ZNC160317_P1_2_R2.fastq.gz,fastq fastq,1340603100.0,13406031.0,GSM4930047 r1,0:30 1:70,A:322845512;C:246499562;G:249678813;T:521170210;N:409003,30,70,,,322845512,246499562,249678813,521170210,409003,SRX9557288,SRS7776259,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.35361,0.84311,0.33033,0.35892,0.98725,0.7723,0.63118,0.58869,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
62014,SRR13115074,SRX9557287,SRS7772244,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC160317 P1 1,GSM4930046,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,ZNC160317 P1 1,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,GSM4930046,GSM4930046: ZNC160317 P1 1; Danio rerio; RNA Seq,GSM4930046,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930046,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC160317_P1_1_R1.fastq.gz ZNC160317_P1_1_R2.fastq.gz,fastq fastq,532291500.0,5322915.0,GSM4930046 r1,0:30 1:70,A:127478940;C:97180307;G:100496111;T:206975403;N:160739,30,70,,,127478940,97180307,100496111,206975403,160739,SRX9557287,SRS7772244,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.50083,0.83039,0.4776,0.33992,0.98589,0.78255,0.59541,0.59566,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
62015,SRR13115073,SRX9557286,SRS7771774,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC151116 12,GSM4930045,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,ZNC151116 12,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,GSM4930045,GSM4930045: ZNC151116 12; Danio rerio; RNA Seq,GSM4930045,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930045,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC151116_12_R1.fastq.gz ZNC151116_12_R2.fastq.gz,fastq fastq,1207658000.0,12076580.0,GSM4930045 r1,0:30 1:70,A:297106318;C:212194469;G:224350366;T:473097329;N:909518,30,70,,,297106318,212194469,224350366,473097329,909518,SRX9557286,SRS7771774,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.42243,0.66493,0.4018,0.15026,0.9949,0.85701,0.69732,0.72078,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
62016,SRR13115072,SRX9557285,SRS7762982,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC151116 11,GSM4930044,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,ZNC151116 11,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,GSM4930044,GSM4930044: ZNC151116 11; Danio rerio; RNA Seq,GSM4930044,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930044,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC151116_11_R1.fastq.gz ZNC151116_11_R2.fastq.gz,fastq fastq,1264736000.0,12647360.0,GSM4930044 r1,0:30 1:70,A:305172802;C:225250825;G:234261405;T:499104109;N:946859,30,70,,,305172802,225250825,234261405,499104109,946859,SRX9557285,SRS7762982,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.58354,0.87807,0.56642,0.15401,0.99364,0.8412,0.63236,0.70146,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
62017,SRR13115071,SRX9557284,SRS7764916,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC151116 10,GSM4930043,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,ZNC151116 10,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,GSM4930043,GSM4930043: ZNC151116 10; Danio rerio; RNA Seq,GSM4930043,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930043,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC151116_10_R1.fastq.gz ZNC151116_10_R2.fastq.gz,fastq fastq,1177857100.0,11778571.0,GSM4930043 r1,0:30 1:70,A:285930811;C:206559699;G:218627577;T:465859304;N:879709,30,70,,,285930811,206559699,218627577,465859304,879709,SRX9557284,SRS7764916,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.45186,0.88321,0.43175,0.19229,0.9946,0.83169,0.80603,0.72758,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
62018,SRR13115070,SRX9557283,SRS7764847,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC151116 9,GSM4930042,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,ZNC151116 9,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:2 dpf,GSM4930042,GSM4930042: ZNC151116 9; Danio rerio; RNA Seq,GSM4930042,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930042,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC151116_9_R1.fastq.gz ZNC151116_9_R2.fastq.gz,fastq fastq,1261452300.0,12614523.0,GSM4930042 r1,0:30 1:70,A:305810580;C:222719536;G:231761383;T:500202963;N:957838,30,70,,,305810580,222719536,231761383,500202963,957838,SRX9557283,SRS7764847,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.62185,0.88423,0.58866,0.19394,0.99318,0.81602,0.59672,0.71811,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Hatching,Embryo,Embryo Imprecise,All anatomical structures
62019,SRR13115069,SRX9557282,SRS7769259,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC150518 D3 12,GSM4930041,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,ZNC150518 D3 12,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,GSM4930041,GSM4930041: ZNC150518 D3 12; Danio rerio; RNA Seq,GSM4930041,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930041,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC150518_D3_12_R1.fastq.gz ZNC150518_D3_12_R2.fastq.gz,fastq fastq,2298421350.0,15322809.0,GSM4930041 r1,0:75 1:75,A:545919146;C:363966133;G:364434887;T:1023925692;N:175492,75,75,,,545919146,363966133,364434887,1023925692,175492,SRX9557282,SRS7769259,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.23981,0.79945,0.1958,0.38716,0.99095,0.84701,0.21462,0.79358,75,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Larval,Larval,Embryo Imprecise,All anatomical structures
62020,SRR13115068,SRX9557281,SRS7766227,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC150518 D3 11,GSM4930040,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,ZNC150518 D3 11,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,GSM4930040,GSM4930040: ZNC150518 D3 11; Danio rerio; RNA Seq,GSM4930040,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930040,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC150518_D3_11_R1.fastq.gz ZNC150518_D3_11_R2.fastq.gz,fastq fastq,3199504350.0,21330029.0,GSM4930040 r1,0:75 1:75,A:748258719;C:507211088;G:514998852;T:1428788005;N:247686,75,75,,,748258719,507211088,514998852,1428788005,247686,SRX9557281,SRS7766227,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.25242,0.81595,0.20841,0.36846,0.99097,0.85967,0.18463,0.82302,75,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Larval,Larval,Embryo Imprecise,All anatomical structures
62021,SRR13115067,SRX9557280,SRS7768833,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC150518 D3 10,GSM4930039,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,ZNC150518 D3 10,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,GSM4930039,GSM4930039: ZNC150518 D3 10; Danio rerio; RNA Seq,GSM4930039,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930039,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC150518_D3_10_R1.fastq.gz ZNC150518_D3_10_R2.fastq.gz,fastq fastq,2658831450.0,17725543.0,GSM4930039 r1,0:75 1:75,A:625534082;C:417705892;G:426157752;T:1189229752;N:203972,75,75,,,625534082,417705892,426157752,1189229752,203972,SRX9557280,SRS7768833,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.23113,0.80915,0.18421,0.36927,0.98999,0.8564,0.20942,0.82095,75,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Larval,Larval,Embryo Imprecise,All anatomical structures
62022,SRR13115066,SRX9557279,SRS7766135,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC150518 D3 9,GSM4930038,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,ZNC150518 D3 9,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,GSM4930038,GSM4930038: ZNC150518 D3 9; Danio rerio; RNA Seq,GSM4930038,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930038,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC150518_D3_9_R1.fastq.gz ZNC150518_D3_9_R2.fastq.gz,fastq fastq,2430204300.0,16201362.0,GSM4930038 r1,0:75 1:75,A:564592499;C:391377408;G:394850295;T:1079194135;N:189963,75,75,,,564592499,391377408,394850295,1079194135,189963,SRX9557279,SRS7766135,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.23779,0.82277,0.19359,0.35691,0.99052,0.84782,0.19244,0.82522,75,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Larval,Larval,Embryo Imprecise,All anatomical structures
62023,SRR13115065,SRX9557278,SRS7770977,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC Day3 8 cdh17,GSM4930037,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,ZNC Day3 8 cdh17,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,GSM4930037,GSM4930037: ZNC Day3 8 cdh17; Danio rerio; RNA Seq,GSM4930037,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930037,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC_Day3_8_Cdh17_R1.fastq.gz ZNC_Day3_8_Cdh17_R2.fastq.gz,fastq fastq,2759354100.0,18395694.0,GSM4930037 r1,0:75 1:75,A:633904086;C:422853685;G:442214525;T:1260362836;N:18968,75,75,,,633904086,422853685,442214525,1260362836,18968,SRX9557278,SRS7770977,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.18316,0.81253,0.14356,0.39781,0.98981,0.79088,0.15253,0.71003,75,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Larval,Larval,Embryo Imprecise,All anatomical structures
62024,SRR13115064,SRX9557277,SRS7767884,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC Day3 8,GSM4930036,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,ZNC Day3 8,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,GSM4930036,GSM4930036: ZNC Day3 8; Danio rerio; RNA Seq,GSM4930036,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930036,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC_Day3_8_R1.fastq.gz ZNC_Day3_8_R2.fastq.gz,fastq fastq,1626486900.0,16264869.0,GSM4930036 r1,0:30 1:70,A:415111245;C:288158602;G:286216834;T:636912014;N:88205,30,70,,,415111245,288158602,286216834,636912014,88205,SRX9557277,SRS7767884,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.41941,0.8262,0.39771,0.35346,0.99328,0.83303,0.81573,0.8154,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Larval,Larval,Embryo Imprecise,All anatomical structures
62025,SRR13115063,SRX9557276,SRS7770407,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC Day3 7 cdh17,GSM4930035,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,ZNC Day3 7 cdh17,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,GSM4930035,GSM4930035: ZNC Day3 7 cdh17; Danio rerio; RNA Seq,GSM4930035,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930035,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC_Day3_7_Cdh17_R1.fastq.gz ZNC_Day3_7_Cdh17_R2.fastq.gz,fastq fastq,2424094950.0,16160633.0,GSM4930035 r1,0:75 1:75,A:569330755;C:376795082;G:392500564;T:1085451652;N:16897,75,75,,,569330755,376795082,392500564,1085451652,16897,SRX9557276,SRS7770407,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.19495,0.80133,0.15558,0.41834,0.98612,0.78626,0.19164,0.71458,75,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Larval,Larval,Embryo Imprecise,All anatomical structures
62026,SRR13115062,SRX9557275,SRS7763168,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC Day3 7,GSM4930034,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,ZNC Day3 7,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,GSM4930034,GSM4930034: ZNC Day3 7; Danio rerio; RNA Seq,GSM4930034,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930034,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC_Day3_7_R1.fastq.gz ZNC_Day3_7_R2.fastq.gz,fastq fastq,1549364000.0,15493640.0,GSM4930034 r1,0:30 1:70,A:414205106;C:269572178;G:270299745;T:595203829;N:83142,30,70,,,414205106,269572178,270299745,595203829,83142,SRX9557275,SRS7763168,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.52133,0.78351,0.49589,0.42266,0.99026,0.84494,0.70819,0.83054,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Larval,Larval,Embryo Imprecise,All anatomical structures
62027,SRR13115061,SRX9557274,SRS7762079,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC Day3 6 cdh17,GSM4930033,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,ZNC Day3 6 cdh17,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,GSM4930033,GSM4930033: ZNC Day3 6 cdh17; Danio rerio; RNA Seq,GSM4930033,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930033,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC_Day3_6_Cdh17_R1.fastq.gz ZNC_Day3_6_Cdh17_R2.fastq.gz,fastq fastq,2642399850.0,17615999.0,GSM4930033 r1,0:75 1:75,A:599469339;C:414117498;G:431827804;T:1196967848;N:17361,75,75,,,599469339,414117498,431827804,1196967848,17361,SRX9557274,SRS7762079,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.17331,0.82507,0.13368,0.35409,0.99097,0.80906,0.15443,0.79756,75,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Larval,Larval,Embryo Imprecise,All anatomical structures
62028,SRR13115060,SRX9557273,SRS7759143,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC Day3 6,GSM4930032,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,ZNC Day3 6,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,GSM4930032,GSM4930032: ZNC Day3 6; Danio rerio; RNA Seq,GSM4930032,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930032,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC_Day3_6_R1.fastq.gz ZNC_Day3_6_R2.fastq.gz,fastq fastq,1731099900.0,17310999.0,GSM4930032 r1,0:30 1:70,A:448536306;C:307872161;G:305369329;T:669226814;N:95290,30,70,,,448536306,307872161,305369329,669226814,95290,SRX9557273,SRS7759143,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.51243,0.83279,0.48297,0.33603,0.99437,0.86109,0.8427,0.87097,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Larval,Larval,Embryo Imprecise,All anatomical structures
62029,SRR13115059,SRX9557272,SRS7759454,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC Day3 5 cdh17,GSM4930031,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,ZNC Day3 5 cdh17,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,GSM4930031,GSM4930031: ZNC Day3 5 cdh17; Danio rerio; RNA Seq,GSM4930031,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930031,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC_Day3_5_Cdh17_R1.fastq.gz ZNC_Day3_5_Cdh17_R2.fastq.gz,fastq fastq,2694776550.0,17965177.0,GSM4930031 r1,0:75 1:75,A:638503692;C:412528735;G:438711717;T:1205014811;N:17595,75,75,,,638503692,412528735,438711717,1205014811,17595,SRX9557272,SRS7759454,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.17601,0.78883,0.14121,0.4155,0.98987,0.79894,0.18689,0.72642,75,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Larval,Larval,Embryo Imprecise,All anatomical structures
62030,SRR13115058,SRX9557271,SRS7768399,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC Day3 5,GSM4930030,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,ZNC Day3 5,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,GSM4930030,GSM4930030: ZNC Day3 5; Danio rerio; RNA Seq,GSM4930030,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930030,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC_Day3_5_R1.fastq.gz ZNC_Day3_5_R2.fastq.gz,fastq fastq,1855905300.0,18559053.0,GSM4930030 r1,0:30 1:70,A:480683585;C:329517881;G:331272380;T:714329711;N:101743,30,70,,,480683585,329517881,331272380,714329711,101743,SRX9557271,SRS7768399,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.57343,0.81165,0.5499,0.3557,0.99202,0.84713,0.78354,0.85858,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Larval,Larval,Embryo Imprecise,All anatomical structures
62031,SRR13115057,SRX9557270,SRS7765052,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC Day1 4 cdh17,GSM4930029,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf,ZNC Day1 4 cdh17,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf,GSM4930029,GSM4930029: ZNC Day1 4 cdh17; Danio rerio; RNA Seq,GSM4930029,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930029,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC_Day1_4_Cdh17_R1.fastq.gz ZNC_Day1_4_Cdh17_R2.fastq.gz,fastq fastq,2620130250.0,17467535.0,GSM4930029 r1,0:75 1:75,A:586017099;C:400844453;G:419358801;T:1213892274;N:17623,75,75,,,586017099,400844453,419358801,1213892274,17623,SRX9557270,SRS7765052,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.20536,0.8052,0.14853,0.34732,0.9918,0.80466,0.12586,0.67366,75,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
62032,SRR13115056,SRX9557269,SRS7758083,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC Day1 4,GSM4930028,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf,ZNC Day1 4,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf,GSM4930028,GSM4930028: ZNC Day1 4; Danio rerio; RNA Seq,GSM4930028,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930028,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC_Day1_4_R1.fastq.gz ZNC_Day1_4_R2.fastq.gz,fastq fastq,1824990500.0,18249905.0,GSM4930028 r1,0:30 1:70,A:473976672;C:320918108;G:324168670;T:705832460;N:94590,30,70,,,473976672,320918108,324168670,705832460,94590,SRX9557269,SRS7758083,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.44709,0.76785,0.42343,0.45478,0.98894,0.82479,0.8491,0.78301,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
62033,SRR13115055,SRX9557268,SRS7764288,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC Day1 3 cdh17,GSM4930027,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf,ZNC Day1 3 cdh17,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf,GSM4930027,GSM4930027: ZNC Day1 3 cdh17; Danio rerio; RNA Seq,GSM4930027,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930027,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC_Day1_3_Cdh17_R1.fastq.gz ZNC_Day1_3_Cdh17_R2.fastq.gz,fastq fastq,2466426750.0,16442845.0,GSM4930027 r1,0:75 1:75,A:559197003;C:370596624;G:396798736;T:1139817899;N:16488,75,75,,,559197003,370596624,396798736,1139817899,16488,SRX9557268,SRS7764288,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.17575,0.7187,0.13208,0.34663,0.9918,0.80296,0.13918,0.68008,75,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
62034,SRR13115054,SRX9557267,SRS7774800,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC Day1 3,GSM4930026,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf,ZNC Day1 3,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf,GSM4930026,GSM4930026: ZNC Day1 3; Danio rerio; RNA Seq,GSM4930026,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930026,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC_Day1_3_R1.fastq.gz ZNC_Day1_3_R2.fastq.gz,fastq fastq,1440247000.0,14402470.0,GSM4930026 r1,0:30 1:70,A:379463608;C:250428466;G:257147695;T:553131395;N:75836,30,70,,,379463608,250428466,257147695,553131395,75836,SRX9557267,SRS7774800,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.53596,0.7764,0.50896,0.41848,0.99015,0.8294,0.73219,0.81152,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
62035,SRR13115053,SRX9557266,SRS7768946,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC Day1 2 cdh17,GSM4930025,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf,ZNC Day1 2 cdh17,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf,GSM4930025,GSM4930025: ZNC Day1 2 cdh17; Danio rerio; RNA Seq,GSM4930025,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930025,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC_Day1_2_Cdh17_R1.fastq.gz ZNC_Day1_2_Cdh17_R2.fastq.gz,fastq fastq,3627307650.0,24182051.0,GSM4930025 r1,0:75 1:75,A:815949074;C:553523601;G:584584461;T:1673224749;N:25765,75,75,,,815949074,553523601,584584461,1673224749,25765,SRX9557266,SRS7768946,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.1809,0.7971,0.13159,0.32692,0.99145,0.79912,0.15023,0.70213,75,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
62036,SRR13115052,SRX9557265,SRS7758099,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC Day1 2,GSM4930024,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf,ZNC Day1 2,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf,GSM4930024,GSM4930024: ZNC Day1 2; Danio rerio; RNA Seq,GSM4930024,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930024,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC_Day1_2_R1.fastq.gz ZNC_Day1_2_R2.fastq.gz,fastq fastq,1672787100.0,16727871.0,GSM4930024 r1,0:30 1:70,A:440596558;C:289991094;G:295797683;T:646312700;N:89065,30,70,,,440596558,289991094,295797683,646312700,89065,SRX9557265,SRS7758099,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.45459,0.7826,0.43209,0.43388,0.9904,0.82471,0.7902,0.78112,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
62037,SRR13115051,SRX9557264,SRS7760515,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC Day1 1 cdh17,GSM4930023,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf,ZNC Day1 1 cdh17,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf,GSM4930023,GSM4930023: ZNC Day1 1 cdh17; Danio rerio; RNA Seq,GSM4930023,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930023,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC_Day1_1_Cdh17_R1.fastq.gz ZNC_Day1_1_Cdh17_R2.fastq.gz,fastq fastq,4232535600.0,28216904.0,GSM4930023 r1,0:75 1:75,A:1022792924;C:659843704;G:675423200;T:1874448065;N:27707,75,75,,,1022792924,659843704,675423200,1874448065,27707,SRX9557264,SRS7760515,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.17373,0.7926,0.12679,0.32535,0.99354,0.8173,0.15579,0.70536,75,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
62038,SRR13115050,SRX9557263,SRS7763051,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC Day1 1,GSM4930022,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf,ZNC Day1 1,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf,GSM4930022,GSM4930022: ZNC Day1 1; Danio rerio; RNA Seq,GSM4930022,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930022,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC_Day1_1_R1.fastq.gz ZNC_Day1_1_R2.fastq.gz,fastq fastq,1468134100.0,14681341.0,GSM4930022 r1,0:30 1:70,A:390964306;C:252762227;G:257246886;T:567090777;N:69904,30,70,,,390964306,252762227,257246886,567090777,69904,SRX9557263,SRS7763051,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.56006,0.77137,0.5273,0.44146,0.99174,0.848,0.49817,0.83793,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
62039,SRR13115049,SRX9557262,SRS7759996,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC D3 080518 16,GSM4930021,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,ZNC D3 080518 16,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,GSM4930021,GSM4930021: ZNC D3 080518 16; Danio rerio; RNA Seq,GSM4930021,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930021,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC_D3_080518_16_R1.fastq.gz ZNC_D3_080518_16_R2.fastq.gz,fastq fastq,921652830.0,8777646.0,GSM4930021 r1,0:30 1:75,A:241333121;C:163980216;G:164426120;T:351855419;N:57954,30,75,,,241333121,163980216,164426120,351855419,57954,SRX9557262,SRS7759996,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.3979,0.70843,0.37349,0.6097,0.98575,0.84678,0.70787,0.59963,30,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Larval,Larval,Embryo Imprecise,All anatomical structures
62040,SRR13115048,SRX9557261,SRS7758710,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC D3 080518 15,GSM4930020,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,ZNC D3 080518 15,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,GSM4930020,GSM4930020: ZNC D3 080518 15; Danio rerio; RNA Seq,GSM4930020,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930020,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC_D3_080518_15_R1.fastq.gz ZNC_D3_080518_15_R2.fastq.gz,fastq fastq,919981440.0,8761728.0,GSM4930020 r1,0:30 1:75,A:248798984;C:161884487;G:162776621;T:346462642;N:58706,30,75,,,248798984,161884487,162776621,346462642,58706,SRX9557261,SRS7758710,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.46984,0.67966,0.44578,0.58085,0.98699,0.87146,0.64721,0.61078,30,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Larval,Larval,Embryo Imprecise,All anatomical structures
62041,SRR13115047,SRX9557260,SRS7771725,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC D3 080518 14,GSM4930019,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,ZNC D3 080518 14,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,GSM4930019,GSM4930019: ZNC D3 080518 14; Danio rerio; RNA Seq,GSM4930019,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930019,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC_D3_080518_14_R1.fastq.gz ZNC_D3_080518_14_R2.fastq.gz,fastq fastq,804572055.0,7662591.0,GSM4930019 r1,0:30 1:75,A:215557474;C:136910822;G:146523095;T:305527087;N:53577,30,75,,,215557474,136910822,146523095,305527087,53577,SRX9557260,SRS7771725,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.40462,0.62528,0.38017,0.52239,0.98786,0.87079,0.77915,0.64645,30,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Larval,Larval,Embryo Imprecise,All anatomical structures
62042,SRR13115046,SRX9557259,SRS7761887,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC D3 080518 13,GSM4930018,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,ZNC D3 080518 13,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:3 dpf,GSM4930018,GSM4930018: ZNC D3 080518 13; Danio rerio; RNA Seq,GSM4930018,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930018,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC_D3_080518_13_R1.fastq.gz ZNC_D3_080518_13_R2.fastq.gz,fastq fastq,498833895.0,4750799.0,GSM4930018 r1,0:30 1:75,A:136412426;C:84182094;G:89774672;T:188428798;N:35905,30,75,,,136412426,84182094,89774672,188428798,35905,SRX9557259,SRS7761887,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.45591,0.68087,0.43285,0.56799,0.98912,0.87862,0.69318,0.66501,30,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Larval,Larval,Embryo Imprecise,All anatomical structures
62043,SRR13115045,SRX9557258,SRS7776278,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC D1CTRL 12,GSM4930017,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf,ZNC D1CTRL 12,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf,GSM4930017,GSM4930017: ZNC D1CTRL 12; Danio rerio; RNA Seq,GSM4930017,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930017,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC_D1CTRL_12_R1.fastq.gz ZNC_D1CTRL_12_R2.fastq.gz,fastq fastq,1457792400.0,9718616.0,GSM4930017 r1,0:75 1:75,A:349174227;C:232621187;G:241864815;T:634073664;N:58507,75,75,,,349174227,232621187,241864815,634073664,58507,SRX9557258,SRS7776278,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.18225,0.76763,0.14946,0.4049,0.98675,0.81542,0.28298,0.74865,75,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
62044,SRR13115044,SRX9557257,SRS7761371,SRP293760,PRJNA680334,Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development,GSE162031,Transcriptome Analysis,Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1  2 dpf and 3 dpf zebrafish larvae.,,pubmed:33749326,,ZNC D1CTRL 11,GSM4930016,,source name:Pr1phros|line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf,ZNC D1CTRL 11,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675  2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,Pronephros,The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division  Medical Center Freiburg,line:Tgwt1b:GFP; Tgcdh17:GFP|tissue:pr1phros|age:1 dpf,GSM4930016,GSM4930016: ZNC D1CTRL 11; Danio rerio; RNA Seq,GSM4930016,,1,Pronephric cells were isolated as previously described Yakulov TA et al.  Nat Commun 9: 3660  2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol,GEO Accession:GSM4930016,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP293760,,,ZNC_D1CTRL_11_R1.fastq.gz ZNC_D1CTRL_11_R2.fastq.gz,fastq fastq,1275600900.0,8504006.0,GSM4930016 r1,0:75 1:75,A:309632828;C:204670391;G:213219831;T:548026269;N:51581,75,75,,,309632828,204670391,213219831,548026269,51581,SRX9557257,SRS7761371,SRA1162774,GEO,"Renal Division, Department of Medicine, University Freiburg Medical Center",2,0.17103,0.79111,0.14016,0.382,0.98894,0.83642,0.25652,0.8477,75,75,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2020-11-23,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures