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
32858,SRR29482326,SRX24993370,SRS21694834,SRP515140,PRJNA1126247,Specific oncogene activation of the cell of origin in mucosal melanoma [SORT seq],GSE270356,Other,Mucosal melanoma MM is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics  we develop a zebrafish model in which all melanocytes experience CCND1 expression and loss of PTEN and TP53. Surprisingly  melanoma only develops from melanocytes lining internal organs  analogous to the location of patient MM. We find that zebrafish MMs have a unique chromatin landscape from cutaneous melanoma. Internal melanocytes are labeled using a MM specific transcriptional enhancer. Normal zebrafish internal melanocytes share a gene expression signature with MMs. Patient and zebrafish MMs show increased migratory neural crest gene and decreased antigen presentation gene expression  consistent with the increased metastatic behavior and decreased immunotherapy sensitivity of MM. Our work suggests the cell state of the originating melanocyte influences the behavior of derived melanomas. Our animal model phenotypically and transcriptionally mimics patient tumors  allowing this model to be used for MM therapeutic discovery. As this is a non MAPK driven genetically engineered model of melanoma  our work also has implications for the 15% of cutaneous melanoma patients who lack MAPK driving mutations.  Overall design: Single cell RNA sequencing was done on internal vs. external normal adult zebrafish melanocytes using the SORT seq platform.,,,,Internal melanocytes,GSM8340241,,source name:Internal melanocytes|tissue:Internal melanocytes|cell type:melanocytes|genotype:mitfa / ; roy /  fish injected with mitfa:GFP|geo loc name:missing|collection date:missing,Internal melanocytes,BWA was used to align paired end read to danRer11. Count tables were generated using MapAndGo. Count tables were corrected using UMI to remove duplicate reads. Transcript counts were adjusted using Poissonian counting statistics to yield the number of UMIs detected per cell. Counts were imported into R using the Seurat suite version 3.0 Assembly: danRer11 Supplementary files format and content: .tsv file contains count matrix file used for data normalization and visualization using Seurat Library strategy: SORT seq,Internal melanocytes,,Respective tissues were mechanically dissociated  digested in TrypLE for 45 min Invitrogen  12563011  40uM filtered  spun down  and resuspended in FACs buffer dPBS Mg+/Ca+ free  with 2% FBS  pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification  library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.,mitfa / ; roy /  zebrafish injected with mitfa:GFP were Raised to maturity to obtain tissues,tissue:Internal melanocytes|cell type:melanocytes|genotype:mitfa / ; roy /  fish injected with mitfa:GFP,GSM8340241,GSM8340241: Internal melanocytes; Danio rerio; OTHER,GSM8340241 r1,GSM8340241,1,Respective tissues were mechanically dissociated  digested in TrypLE for 45 min Invitrogen  12563011  40uM filtered  spun down  and resuspended in FACs buffer dPBS Mg+/Ca+ free  with 2% FBS  pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification  library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP515140,,,HAR-MI-002_H5GCWBGXF_R2.fastq.gz HAR-MI-002_H5GCWBGXF_R1.fastq.gz,fastq fastq,2957975418.0,34395063.0,GSM8340241 r1,0:26 1:60,A:738954503;C:560052455;G:520746060;T:1137116132;N:1106268,26,60,,,738954503,560052455,520746060,1137116132,1106268,SRX24993370,SRS21694834,SRA1904773,"Insco Lab, Medical Oncology, Dana Farber Cancer Institute","Insco Lab, Medical Oncology, Dana Farber Cancer Institute",2,0.11637,0.84116,0.10894,0.31188,0.98851,0.71526,0.6688,0.60221,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,United States,2024-06-20,Undetermined,Adult,Skin,Surface Structure
32859,SRR29482327,SRX24993369,SRS21694833,SRP515140,PRJNA1126247,Specific oncogene activation of the cell of origin in mucosal melanoma [SORT seq],GSE270356,Other,Mucosal melanoma MM is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics  we develop a zebrafish model in which all melanocytes experience CCND1 expression and loss of PTEN and TP53. Surprisingly  melanoma only develops from melanocytes lining internal organs  analogous to the location of patient MM. We find that zebrafish MMs have a unique chromatin landscape from cutaneous melanoma. Internal melanocytes are labeled using a MM specific transcriptional enhancer. Normal zebrafish internal melanocytes share a gene expression signature with MMs. Patient and zebrafish MMs show increased migratory neural crest gene and decreased antigen presentation gene expression  consistent with the increased metastatic behavior and decreased immunotherapy sensitivity of MM. Our work suggests the cell state of the originating melanocyte influences the behavior of derived melanomas. Our animal model phenotypically and transcriptionally mimics patient tumors  allowing this model to be used for MM therapeutic discovery. As this is a non MAPK driven genetically engineered model of melanoma  our work also has implications for the 15% of cutaneous melanoma patients who lack MAPK driving mutations.  Overall design: Single cell RNA sequencing was done on internal vs. external normal adult zebrafish melanocytes using the SORT seq platform.,,,,Cutaneous melanocytes,GSM8340240,,source name:Cutaneous melanocytes|tissue:Cutaneous melanocytes|cell type:melanocytes|genotype:mitfa / ; roy /  fish injected with mitfa:GFP|geo loc name:missing|collection date:missing,Cutaneous melanocytes,BWA was used to align paired end read to danRer11. Count tables were generated using MapAndGo. Count tables were corrected using UMI to remove duplicate reads. Transcript counts were adjusted using Poissonian counting statistics to yield the number of UMIs detected per cell. Counts were imported into R using the Seurat suite version 3.0 Assembly: danRer11 Supplementary files format and content: .tsv file contains count matrix file used for data normalization and visualization using Seurat Library strategy: SORT seq,Cutaneous melanocytes,,Respective tissues were mechanically dissociated  digested in TrypLE for 45 min Invitrogen  12563011  40uM filtered  spun down  and resuspended in FACs buffer dPBS Mg+/Ca+ free  with 2% FBS  pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification  library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.,mitfa / ; roy /  zebrafish injected with mitfa:GFP were Raised to maturity to obtain tissues,tissue:Cutaneous melanocytes|cell type:melanocytes|genotype:mitfa / ; roy /  fish injected with mitfa:GFP,GSM8340240,GSM8340240: Cutaneous melanocytes; Danio rerio; OTHER,GSM8340240 r1,GSM8340240,1,Respective tissues were mechanically dissociated  digested in TrypLE for 45 min Invitrogen  12563011  40uM filtered  spun down  and resuspended in FACs buffer dPBS Mg+/Ca+ free  with 2% FBS  pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification  library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP515140,,,HAR-MI-001_H5GCWBGXF_R2.fastq.gz HAR-MI-001_H5GCWBGXF_R1.fastq.gz,fastq fastq,2680460212.0,31168142.0,GSM8340240 r1,0:26 1:60,A:704357434;C:519158361;G:467098420;T:988838604;N:1007393,26,60,,,704357434,519158361,467098420,988838604,1007393,SRX24993369,SRS21694833,SRA1904773,"Insco Lab, Medical Oncology, Dana Farber Cancer Institute","Insco Lab, Medical Oncology, Dana Farber Cancer Institute",2,0.11679,0.81545,0.10693,0.5033,0.9808,0.76404,0.44749,0.57623,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,United States,2024-06-20,Undetermined,Adult,Skin,Surface Structure
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
38078,SRR1531477,SRX665258,SRS670072,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somite stage  secti1d from right to left,GSM1448815,,tissue:whole embryo|Stage:15 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,15 somite stage  secti1d from right to left,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,GSM1448815,GSM1448815: 15 somite stage  secti1d from right to left; Danio rerio; RNA Seq,GSM1448815,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448815,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_15ss_RL_R1.fastq.gz dr_15ss_RL_R2.fastq.gz,fastq fastq,3840123336.0,37648268.0,GSM1448815 r1,0:51 1:51,A:915153174;C:577478134;G:648196113;T:1695635476;N:3660439,51,51,,,915153174,577478134,648196113,1695635476,3660439,SRX665258,SRS670072,SRA177126,GEO,Hubrecht Institute,2,0.05313,0.71589,0.0419,0.15174,0.97717,0.77484,0.5218,0.45828,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38079,SRR1531478,SRX665258,SRS670072,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somite stage  secti1d from right to left,GSM1448815,,tissue:whole embryo|Stage:15 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,15 somite stage  secti1d from right to left,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,GSM1448815,GSM1448815: 15 somite stage  secti1d from right to left; Danio rerio; RNA Seq,GSM1448815,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448815,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_15ss_RL_R1.fastq.gz miseq_dr_15ss_RL_R2.fastq.gz,fastq fastq,619303490.0,1235999.0,GSM1448815 r2,0:251 1:250.06,A:196814024;C:126079066;G:111585151;T:184825248;N:1,251,250,,,196814024,126079066,111585151,184825248,1,SRX665258,SRS670072,SRA177126,GEO,Hubrecht Institute,2,0.37674,0.6743,0.06734,0.08523,0.92516,0.86196,0.56151,0.54745,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38080,SRR1531475,SRX665257,SRS670070,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somite stage  secti1d from left to right,GSM1448814,,tissue:whole embryo|Stage:15 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,15 somite stage  secti1d from left to right,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,GSM1448814,GSM1448814: 15 somite stage  secti1d from left to right; Danio rerio; RNA Seq,GSM1448814,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448814,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_15ss_LR_R2.fastq.gz dr_15ss_LR_R1.fastq.gz,fastq fastq,2077803342.0,20370621.0,GSM1448814 r1,0:51 1:51,A:487276259;C:320933398;G:342175116;T:925418636;N:1999933,51,51,,,487276259,320933398,342175116,925418636,1999933,SRX665257,SRS670070,SRA177126,GEO,Hubrecht Institute,2,0.04544,0.77533,0.03741,0.15439,0.98435,0.77662,0.56397,0.57005,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38081,SRR1531476,SRX665257,SRS670070,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somite stage  secti1d from left to right,GSM1448814,,tissue:whole embryo|Stage:15 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,15 somite stage  secti1d from left to right,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,GSM1448814,GSM1448814: 15 somite stage  secti1d from left to right; Danio rerio; RNA Seq,GSM1448814,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448814,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_15ss_LR_R1.fastq.gz miseq_dr_15ss_LR_R2.fastq.gz,fastq fastq,648479770.0,1294232.0,GSM1448814 r2,0:251 1:250.05,A:208271519;C:133135452;G:114142609;T:192930139;N:51,251,250,,,208271519,133135452,114142609,192930139,51,SRX665257,SRS670070,SRA177126,GEO,Hubrecht Institute,2,0.34992,0.64011,0.08713,0.16967,0.92103,0.83853,0.54292,0.52547,251,250,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38082,SRR1531473,SRX665256,SRS670071,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somite stage  secti1d from dorsal to ventral end,GSM1448813,,tissue:whole embryo|Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,15 somite stage  secti1d from dorsal to ventral end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,GSM1448813,GSM1448813: 15 somite stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq,GSM1448813,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448813,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_15ss_DV_R1.fastq.gz dr_15ss_DV_R2.fastq.gz,fastq fastq,2516804610.0,24674555.0,GSM1448813 r1,0:51 1:51,A:579818006;C:406550753;G:379205422;T:1129932140;N:21298289,51,51,,,579818006,406550753,379205422,1129932140,21298289,SRX665256,SRS670071,SRA177126,GEO,Hubrecht Institute,2,0.04189,0.74891,0.03368,0.12625,0.98695,0.78423,0.46823,0.53429,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38083,SRR1531474,SRX665256,SRS670071,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somite stage  secti1d from dorsal to ventral end,GSM1448813,,tissue:whole embryo|Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,15 somite stage  secti1d from dorsal to ventral end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,GSM1448813,GSM1448813: 15 somite stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq,GSM1448813,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448813,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_15ss_DV_R1.fastq.gz miseq_dr_15ss_DV_R2.fastq.gz,fastq fastq,1831352383.0,3654695.0,GSM1448813 r2,0:251 1:250.10,A:593055798;C:392880040;G:312965357;T:532451118;N:70,251,250,,,593055798,392880040,312965357,532451118,70,SRX665256,SRS670071,SRA177126,GEO,Hubrecht Institute,2,0.27976,0.58087,0.05423,0.08127,0.93943,0.88868,0.51246,0.50653,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38084,SRR1531471,SRX665255,SRS670069,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somite stage  secti1d from ventral to dorsal end,GSM1448812,,tissue:whole embryo|Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,15 somite stage  secti1d from ventral to dorsal end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448812,GSM1448812: 15 somite stage  secti1d from ventral to dorsal end; Danio rerio; RNA Seq,GSM1448812,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448812,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_15ss_VD_R1.fastq.gz dr_15ss_VD_R2.fastq.gz,fastq fastq,1673808678.0,16409889.0,GSM1448812 r1,0:51 1:51,A:397744759;C:269067687;G:250815180;T:740808813;N:15372239,51,51,,,397744759,269067687,250815180,740808813,15372239,SRX665255,SRS670069,SRA177126,GEO,Hubrecht Institute,2,0.05917,0.69313,0.0499,0.19364,0.98364,0.78232,0.54626,0.5434,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38085,SRR1531472,SRX665255,SRS670069,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somite stage  secti1d from ventral to dorsal end,GSM1448812,,tissue:whole embryo|Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,15 somite stage  secti1d from ventral to dorsal end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448812,GSM1448812: 15 somite stage  secti1d from ventral to dorsal end; Danio rerio; RNA Seq,GSM1448812,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448812,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_15ss_VD_R2.fastq.gz miseq_dr_15ss_VD_R1.fastq.gz,fastq fastq,587520609.0,1172567.0,GSM1448812 r2,0:251 1:250.06,A:194391951;C:123162952;G:98682047;T:171283648;N:11,251,250,,,194391951,123162952,98682047,171283648,11,SRX665255,SRS670069,SRA177126,GEO,Hubrecht Institute,2,0.25906,0.51091,0.10052,0.13544,0.94274,0.90015,0.54255,0.53365,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38086,SRR1531470,SRX665254,SRS670068,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somite stage  secti1d from posterior to anterior end,GSM1448811,,tissue:whole embryo|Stage:15 somites|sectioning direction:posterior anterior|section thickness:18 µm|embedding strategy:intact embryo,15 somite stage  secti1d from posterior to anterior end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:posterior anterior|section thickness:18 µm|embedding strategy:intact embryo,GSM1448811,GSM1448811: 15 somite stage  secti1d from posterior to anterior end; Danio rerio; RNA Seq,GSM1448811,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448811,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_15ss_PA_R2.fastq.gz dr_15ss_PA_R1.fastq.gz,fastq fastq,2483143794.0,24344547.0,GSM1448811 r1,0:51 1:51,A:563038776;C:400378151;G:372280878;T:1126633332;N:20812657,51,51,,,563038776,400378151,372280878,1126633332,20812657,SRX665254,SRS670068,SRA177126,GEO,Hubrecht Institute,2,0.04278,0.78001,0.03367,0.11539,0.98727,0.77865,0.49734,0.53041,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38087,SRR1531469,SRX665253,SRS670067,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,15 somite stage  secti1d from anterior to posterior end,GSM1448810,,tissue:whole embryo|Stage:15 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,15 somite stage  secti1d from anterior to posterior end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:15 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,GSM1448810,GSM1448810: 15 somite stage  secti1d from anterior to posterior end; Danio rerio; RNA Seq,GSM1448810,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448810,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_15ss_AP_R2.fastq.gz dr_15ss_AP_R1.fastq.gz,fastq fastq,3436281570.0,33689035.0,GSM1448810 r1,0:51 1:51,A:794842891;C:552474558;G:514289189;T:1545720661;N:28954271,51,51,,,794842891,552474558,514289189,1545720661,28954271,SRX665253,SRS670067,SRA177126,GEO,Hubrecht Institute,2,0.04616,0.72787,0.03714,0.11902,0.98636,0.78372,0.50428,0.54252,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38088,SRR1531468,SRX665252,SRS670066,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,10 somite stage  secti1d from right to left,GSM1448809,,tissue:whole embryo|Stage:10 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,10 somite stage  secti1d from right to left,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:10 somites|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,GSM1448809,GSM1448809: 10 somite stage  secti1d from right to left; Danio rerio; RNA Seq,GSM1448809,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448809,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_10ss_RL_R2.fastq.gz dr_10ss_RL_R1.fastq.gz,fastq fastq,2058025848.0,20176724.0,GSM1448809 r1,0:51 1:51,A:466388690;C:327195544;G:324646168;T:921984274;N:17811172,51,51,,,466388690,327195544,324646168,921984274,17811172,SRX665252,SRS670066,SRA177126,GEO,Hubrecht Institute,2,0.03352,0.82842,0.02775,0.10176,0.99019,0.7878,0.56827,0.53664,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38089,SRR1531467,SRX665251,SRS670065,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,10 somite stage  secti1d from left to right,GSM1448808,,tissue:whole embryo|Stage:10 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,10 somite stage  secti1d from left to right,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:10 somites|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,GSM1448808,GSM1448808: 10 somite stage  secti1d from left to right; Danio rerio; RNA Seq,GSM1448808,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448808,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_10ss_LR_R1.fastq.gz dr_10ss_LR_R2.fastq.gz,fastq fastq,2372600886.0,23260793.0,GSM1448808 r1,0:51 1:51,A:539978604;C:369014393;G:373430985;T:1069557826;N:20619078,51,51,,,539978604,369014393,373430985,1069557826,20619078,SRX665251,SRS670065,SRA177126,GEO,Hubrecht Institute,2,0.04947,0.82594,0.04114,0.11817,0.98703,0.77727,0.5181,0.46105,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38090,SRR1531465,SRX665250,SRS670064,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,10 somite stage  secti1d from dorsal to ventral end,GSM1448807,,tissue:whole embryo|Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,10 somite stage  secti1d from dorsal to ventral end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,GSM1448807,GSM1448807: 10 somite stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq,GSM1448807,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448807,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_10ss_DV_R1.fastq.gz dr_10ss_DV_R2.fastq.gz,fastq fastq,4808137200.0,47138600.0,GSM1448807 r1,0:51 1:51,A:1069537756;C:773357615;G:788490520;T:2131916220;N:44835089,51,51,,,1069537756,773357615,788490520,2131916220,44835089,SRX665250,SRS670064,SRA177126,GEO,Hubrecht Institute,2,0.05336,0.7348,0.04376,0.11098,0.98311,0.78829,0.55869,0.5169,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38091,SRR1531466,SRX665250,SRS670064,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,10 somite stage  secti1d from dorsal to ventral end,GSM1448807,,tissue:whole embryo|Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,10 somite stage  secti1d from dorsal to ventral end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,GSM1448807,GSM1448807: 10 somite stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq,GSM1448807,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448807,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_10ss_DV_R1.fastq.gz miseq_dr_10ss_DV_R2.fastq.gz,fastq fastq,981031778.0,1957880.0,GSM1448807 r2,0:251 1:250.07,A:318017696;C:204637111;G:170546834;T:287830124;N:13,251,250,,,318017696,204637111,170546834,287830124,13,SRX665250,SRS670064,SRA177126,GEO,Hubrecht Institute,2,0.28421,0.5957,0.04748,0.07361,0.93917,0.88298,0.53618,0.53493,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38092,SRR1531463,SRX665249,SRS670063,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,10 somite stage  secti1d from ventral to dorsal end,GSM1448806,,tissue:whole embryo|Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,10 somite stage  secti1d from ventral to dorsal end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448806,GSM1448806: 10 somite stage  secti1d from ventral to dorsal end; Danio rerio; RNA Seq,GSM1448806,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448806,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_10ss_VD_R1.fastq.gz dr_10ss_VD_R2.fastq.gz,fastq fastq,4042242048.0,39629824.0,GSM1448806 r1,0:51 1:51,A:880941046;C:636899286;G:642176352;T:1845085169;N:37140195,51,51,,,880941046,636899286,642176352,1845085169,37140195,SRX665249,SRS670063,SRA177126,GEO,Hubrecht Institute,2,0.04898,0.80518,0.04234,0.10309,0.99044,0.78437,0.4974,0.53264,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38093,SRR1531464,SRX665249,SRS670063,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,10 somite stage  secti1d from ventral to dorsal end,GSM1448806,,tissue:whole embryo|Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,10 somite stage  secti1d from ventral to dorsal end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448806,GSM1448806: 10 somite stage  secti1d from ventral to dorsal end; Danio rerio; RNA Seq,GSM1448806,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448806,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_10ss_VD_R1.fastq.gz miseq_dr_10ss_VD_R2.fastq.gz,fastq fastq,738071470.0,1473056.0,GSM1448806 r2,0:251 1:250.05,A:241662059;C:148514183;G:127467910;T:220427298;N:20,251,250,,,241662059,148514183,127467910,220427298,20,SRX665249,SRS670063,SRA177126,GEO,Hubrecht Institute,2,0.33554,0.65168,0.04798,0.07375,0.93334,0.87121,0.53425,0.51721,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38094,SRR1531461,SRX665248,SRS670062,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,10 somite stage  secti1d from posterior to anterior end,GSM1448805,,tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,10 somite stage  secti1d from posterior to anterior end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,GSM1448805,GSM1448805: 10 somite stage  secti1d from posterior to anterior end; Danio rerio; RNA Seq,GSM1448805,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448805,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_10ss_PA_R1.fastq.gz dr_10ss_PA_R2.fastq.gz,fastq fastq,4759203720.0,46658860.0,GSM1448805 r1,0:51 1:51,A:1044025561;C:745846492;G:761494052;T:2164007108;N:43830507,51,51,,,1044025561,745846492,761494052,2164007108,43830507,SRX665248,SRS670062,SRA177126,GEO,Hubrecht Institute,2,0.04594,0.81204,0.0388,0.10992,0.98938,0.78244,0.51272,0.52639,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38095,SRR1531462,SRX665248,SRS670062,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,10 somite stage  secti1d from posterior to anterior end,GSM1448805,,tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,10 somite stage  secti1d from posterior to anterior end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,GSM1448805,GSM1448805: 10 somite stage  secti1d from posterior to anterior end; Danio rerio; RNA Seq,GSM1448805,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448805,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_10ss_PA_R2.fastq.gz miseq_dr_10ss_PA_R1.fastq.gz,fastq fastq,923948352.0,1843960.0,GSM1448805 r2,0:251 1:250.07,A:301981474;C:189568545;G:157916393;T:274481921;N:19,251,250,,,301981474,189568545,157916393,274481921,19,SRX665248,SRS670062,SRA177126,GEO,Hubrecht Institute,2,0.33803,0.65569,0.05131,0.07917,0.93419,0.87355,0.4399,0.52526,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38096,SRR1531460,SRX665247,SRS670061,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,10 somite stage  secti1d from anterior to posterior end  replicate,GSM1448804,,tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,10 somite stage  secti1d from anterior to posterior end  replicate,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,GSM1448804,GSM1448804: 10 somite stage  secti1d from anterior to posterior end  replicate; Danio rerio; RNA Seq,GSM1448804,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448804,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_10ss_AP2_R1.fastq.gz dr_10ss_AP2_R2.fastq.gz,fastq fastq,2096761878.0,20556489.0,GSM1448804 r1,0:51 1:51,A:486131317;C:330426143;G:323887100;T:938024368;N:18292950,51,51,,,486131317,330426143,323887100,938024368,18292950,SRX665247,SRS670061,SRA177126,GEO,Hubrecht Institute,2,0.0484,0.78914,0.0396,0.12303,0.9866,0.78234,0.53395,0.53422,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38097,SRR1531458,SRX665246,SRS670060,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,10 somite stage  secti1d from anterior to posterior end,GSM1448803,,tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,10 somite stage  secti1d from anterior to posterior end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,GSM1448803,GSM1448803: 10 somite stage  secti1d from anterior to posterior end; Danio rerio; RNA Seq,GSM1448803,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448803,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_10ss_AP_R2.fastq.gz dr_10ss_AP_R1.fastq.gz,fastq fastq,3873169500.0,37972250.0,GSM1448803 r1,0:51 1:51,A:844434990;C:614503150;G:615061181;T:1763736099;N:35434080,51,51,,,844434990,614503150,615061181,1763736099,35434080,SRX665246,SRS670060,SRA177126,GEO,Hubrecht Institute,2,0.0354,0.81065,0.02893,0.12263,0.98944,0.77386,0.52631,0.52007,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38098,SRR1531459,SRX665246,SRS670060,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,10 somite stage  secti1d from anterior to posterior end,GSM1448803,,tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,10 somite stage  secti1d from anterior to posterior end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 µm|embedding strategy:intact embryo,GSM1448803,GSM1448803: 10 somite stage  secti1d from anterior to posterior end; Danio rerio; RNA Seq,GSM1448803,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448803,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_10ss_AP_R1.fastq.gz miseq_dr_10ss_AP_R2.fastq.gz,fastq fastq,496084013.0,990096.0,GSM1448803 r2,0:251 1:250.05,A:161790706;C:99237964;G:85634725;T:149420610;N:8,251,250,,,161790706,99237964,85634725,149420610,8,SRX665246,SRS670060,SRA177126,GEO,Hubrecht Institute,2,0.35483,0.66804,0.06659,0.09269,0.92699,0.86113,0.53381,0.51797,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Segmentation,Embryo,Whole Organism,All anatomical structures
38099,SRR1531457,SRX665245,SRS670059,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from dorsal to ventral end  replicate,GSM1448802,,tissue:whole embryo|Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from dorsal to ventral end  replicate,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,GSM1448802,GSM1448802: shield stage  secti1d from dorsal to ventral end  replicate; Danio rerio; RNA Seq,GSM1448802,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448802,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_DV2_R2.fastq.gz dr_shield_DV2_R1.fastq.gz,fastq fastq,2735350014.0,26817157.0,GSM1448802 r1,0:51 1:51,A:650077339;C:412458828;G:411687121;T:1237686190;N:23440536,51,51,,,650077339,412458828,411687121,1237686190,23440536,SRX665245,SRS670059,SRA177126,GEO,Hubrecht Institute,2,0.02556,0.75175,0.01912,0.10697,0.99076,0.79819,0.54093,0.55229,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38100,SRR1531455,SRX665244,SRS670058,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from dorsal to ventral end,GSM1448801,,tissue:whole embryo|Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from dorsal to ventral end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,GSM1448801,GSM1448801: shield stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq,GSM1448801,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448801,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_DV_R1.fastq.gz dr_shield_DV_R2.fastq.gz,fastq fastq,1605318738.0,15738419.0,GSM1448801 r1,0:51 1:51,A:361176217;C:248822696;G:253372108;T:726629351;N:15318366,51,51,,,361176217,248822696,253372108,726629351,15318366,SRX665244,SRS670058,SRA177126,GEO,Hubrecht Institute,2,0.02633,0.68496,0.02344,0.10104,0.99638,0.80006,0.46031,0.57655,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38101,SRR1531456,SRX665244,SRS670058,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from dorsal to ventral end,GSM1448801,,tissue:whole embryo|Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from dorsal to ventral end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,GSM1448801,GSM1448801: shield stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq,GSM1448801,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448801,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_shield_DV_R1.fastq.gz miseq_dr_shield_DV_R2.fastq.gz,fastq fastq,114907294.0,229320.0,GSM1448801 r2,0:251 1:250.08,A:37813553;C:24168661;G:19441624;T:33483456;N:0,251,250,,,37813553,24168661,19441624,33483456,0,SRX665244,SRS670058,SRA177126,GEO,Hubrecht Institute,2,0.26022,0.46204,0.03083,0.05933,0.94627,0.89301,0.56728,0.55478,251,250,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38102,SRR1531453,SRX665243,SRS670056,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from ventral to dorsal end,GSM1448800,,tissue:whole embryo|Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from ventral to dorsal end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448800,GSM1448800: shield stage  secti1d from ventral to dorsal end; Danio rerio; RNA Seq,GSM1448800,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448800,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_VD_R1.fastq.gz dr_shield_VD_R2.fastq.gz,fastq fastq,1840839492.0,18047446.0,GSM1448800 r1,0:51 1:51,A:421253850;C:292045914;G:295175858;T:814744774;N:17619096,51,51,,,421253850,292045914,295175858,814744774,17619096,SRX665243,SRS670056,SRA177126,GEO,Hubrecht Institute,2,0.01815,0.6287,0.01468,0.09567,0.99452,0.80975,0.5259,0.58926,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38103,SRR1531454,SRX665243,SRS670056,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from ventral to dorsal end,GSM1448800,,tissue:whole embryo|Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from ventral to dorsal end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448800,GSM1448800: shield stage  secti1d from ventral to dorsal end; Danio rerio; RNA Seq,GSM1448800,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448800,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_shield_VD_R2.fastq.gz miseq_dr_shield_VD_R1.fastq.gz,fastq fastq,158531701.0,316379.0,GSM1448800 r2,,,,,,,,,,,,SRX665243,SRS670056,SRA177126,GEO,Hubrecht Institute,2,0.06803,0.1733,0.00916,0.026,0.94085,0.88899,0.58254,0.5723,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38104,SRR1531451,SRX665242,SRS670055,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from right to left,GSM1448799,,tissue:whole embryo|Stage:shield stage|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from right to left,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,GSM1448799,GSM1448799: shield stage  secti1d from right to left; Danio rerio; RNA Seq,GSM1448799,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448799,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_RL_R1.fastq.gz dr_shield_RL_R2.fastq.gz,fastq fastq,2003076918.0,19638009.0,GSM1448799 r1,0:51 1:51,A:457537608;C:308292947;G:312973612;T:905317961;N:18954790,51,51,,,457537608,308292947,312973612,905317961,18954790,SRX665242,SRS670055,SRA177126,GEO,Hubrecht Institute,2,0.02111,0.7573,0.01656,0.11316,0.99364,0.8005,0.4501,0.59142,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38105,SRR1531452,SRX665242,SRS670055,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from right to left,GSM1448799,,tissue:whole embryo|Stage:shield stage|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from right to left,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,GSM1448799,GSM1448799: shield stage  secti1d from right to left; Danio rerio; RNA Seq,GSM1448799,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448799,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_shield_RL_R1.fastq.gz miseq_dr_shield_RL_R2.fastq.gz,fastq fastq,154180181.0,307695.0,GSM1448799 r2,0:251 1:250.08,A:50801230;C:32293099;G:25917988;T:45167860;N:4,251,250,,,50801230,32293099,25917988,45167860,4,SRX665242,SRS670055,SRA177126,GEO,Hubrecht Institute,2,0.31553,0.64085,0.03613,0.06829,0.94101,0.8938,0.60272,0.58117,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38106,SRR1531449,SRX665241,SRS670053,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from left to right,GSM1448798,,tissue:whole embryo|Stage:shield stage|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from left to right,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,GSM1448798,GSM1448798: shield stage  secti1d from left to right; Danio rerio; RNA Seq,GSM1448798,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448798,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_LR_R1.fastq.gz dr_shield_LR_R2.fastq.gz,fastq fastq,1755442542.0,17210221.0,GSM1448798 r1,0:51 1:51,A:401133098;C:265688355;G:264899378;T:807011867;N:16709844,51,51,,,401133098,265688355,264899378,807011867,16709844,SRX665241,SRS670053,SRA177126,GEO,Hubrecht Institute,2,0.02829,0.71918,0.02455,0.14486,0.99484,0.79866,0.50383,0.57925,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38107,SRR1531450,SRX665241,SRS670053,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from left to right,GSM1448798,,tissue:whole embryo|Stage:shield stage|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from left to right,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,GSM1448798,GSM1448798: shield stage  secti1d from left to right; Danio rerio; RNA Seq,GSM1448798,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448798,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_shield_LR_R1.fastq.gz miseq_dr_shield_LR_R2.fastq.gz,fastq fastq,139755993.0,278913.0,GSM1448798 r2,0:251 1:250.07,A:46536591;C:28346077;G:23036783;T:41836538;N:4,251,250,,,46536591,28346077,23036783,41836538,4,SRX665241,SRS670053,SRA177126,GEO,Hubrecht Institute,2,0.27443,0.57858,0.06346,0.09954,0.94194,0.89522,0.55896,0.56169,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38108,SRR1531448,SRX665240,SRS670054,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from vegetal to animal pole  replicate,GSM1448797,,tissue:whole embryo|Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from vegetal to animal pole  replicate,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448797,GSM1448797: shield stage  secti1d from vegetal to animal pole  replicate; Danio rerio; RNA Seq,GSM1448797,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448797,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_VA2_R1.fastq.gz dr_shield_VA2_R2.fastq.gz,fastq fastq,1962884532.0,19243966.0,GSM1448797 r1,0:51 1:51,A:449529690;C:292065368;G:287973067;T:916330652;N:16985755,51,51,,,449529690,292065368,287973067,916330652,16985755,SRX665240,SRS670054,SRA177126,GEO,Hubrecht Institute,2,0.04512,0.77455,0.03997,0.11233,0.99293,0.78488,0.50931,0.5171,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38109,SRR1531446,SRX665239,SRS670057,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from vegetal to animal pole,GSM1448796,,tissue:whole embryo|Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from vegetal to animal pole,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448796,GSM1448796: shield stage  secti1d from vegetal to animal pole; Danio rerio; RNA Seq,GSM1448796,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448796,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_VA_R2.fastq.gz dr_shield_VA_R1.fastq.gz,fastq fastq,2367839934.0,23214117.0,GSM1448796 r1,0:51 1:51,A:544061124;C:369321045;G:383489434;T:1047897582;N:23070749,51,51,,,544061124,369321045,383489434,1047897582,23070749,SRX665239,SRS670057,SRA177126,GEO,Hubrecht Institute,2,0.02284,0.57831,0.0199,0.08251,0.99579,0.81653,0.4451,0.5792,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38110,SRR1531447,SRX665239,SRS670057,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from vegetal to animal pole,GSM1448796,,tissue:whole embryo|Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from vegetal to animal pole,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448796,GSM1448796: shield stage  secti1d from vegetal to animal pole; Danio rerio; RNA Seq,GSM1448796,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448796,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_shield_VA_R1.fastq.gz miseq_dr_shield_VA_R2.fastq.gz,fastq fastq,139677889.0,278764.0,GSM1448796 r2,0:251 1:250.06,A:45877333;C:29821713;G:24032460;T:39946380;N:3,251,250,,,45877333,29821713,24032460,39946380,3,SRX665239,SRS670057,SRA177126,GEO,Hubrecht Institute,2,0.21444,0.33364,0.02489,0.04529,0.95156,0.901,0.56549,0.55749,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38111,SRR1531444,SRX665238,SRS670052,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from animal to vegetal pole,GSM1448795,,tissue:whole embryo|Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from animal to vegetal pole,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448795,GSM1448795: shield stage  secti1d from animal to vegetal pole; Danio rerio; RNA Seq,GSM1448795,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448795,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_AV_R1.fastq.gz dr_shield_AV_R2.fastq.gz,fastq fastq,2059615110.0,20192305.0,GSM1448795 r1,0:51 1:51,A:487942041;C:328047311;G:336282927;T:886836259;N:20506572,51,51,,,487942041,328047311,336282927,886836259,20506572,SRX665238,SRS670052,SRA177126,GEO,Hubrecht Institute,2,0.01633,0.50842,0.0136,0.07269,0.99541,0.82183,0.51242,0.59281,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38112,SRR1531445,SRX665238,SRS670052,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from animal to vegetal pole,GSM1448795,,tissue:whole embryo|Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from animal to vegetal pole,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448795,GSM1448795: shield stage  secti1d from animal to vegetal pole; Danio rerio; RNA Seq,GSM1448795,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448795,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_shield_AV_R1.fastq.gz miseq_dr_shield_AV_R2.fastq.gz,fastq fastq,176530873.0,352271.0,GSM1448795 r2,0:251 1:250.12,A:57029265;C:38838035;G:30065677;T:50597891;N:5,251,250,,,57029265,38838035,30065677,50597891,5,SRX665238,SRS670052,SRA177126,GEO,Hubrecht Institute,2,0.20318,0.26844,0.02342,0.03751,0.95499,0.9069,0.4325,0.57102,251,251,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
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
40164,SRR2921973,SRX1432516,SRS1163508,SRP066192,PRJNA302179,Genome–wide transcriptional profiling with spatial resolution identifies Bone Morphogenetic Protein signaling as essential regulator of zebrafish cardiomyocyte regeneration.,GSE74652,Transcriptome Analysis,In contrast to mammals  zebrafish regenerate heart injuries via proliferation of cardiomyocytes located at the wound border. Here  we show that tomo seq can be used to identify whole genome transcriptional profiles of the injury zone  the border zone and the healthy myocardium. Interestingly  the border zone is characterized by the re expression of embryonic cardiac genes that are also activated post myocardial infarction in mouse and human  including targets of Bone Morphogenetic Protein BMP signaling. Endogenous BMP signaling has been reported to be detrimental to mammalian cardiac repair. In contrast  we find that genetic or chemical inhibition of BMP signaling in zebrafish reduces cardiomyocyte dedifferentiation and proliferation  ultimately compromising myocardial regeneration  while bmp2b overexpression is sufficient to enhance it. Our results provide a resource for further studies on the molecular regulation of cardiac regeneration and reveal intriguing differential cellular responses of cardiomyocytes to a conserved signaling pathway in regenerative versus non regenerative hearts. Overall design: To generate spatially resolved RNA seq data for injured zebrafish hearts 3 and 7 xxx post injury  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 NextSeq  using 75bp paired end sequencing.,,pubmed:26748692,,zebrafish heart WT 7dpi #1,GSM1924888,,source name:cryoinjured ventricle of the heart|tissue:adult heart|sectioning direction:injury area   uninjured  remote myocardium|sectioning thickness:12 µm|embedding strategy:extracted heart at 7 days post cryoinjury,zebrafish heart WT 7dpi #1,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. 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: 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 sections,cryoinjured ventricle of the heart,Unfixed ventricle was embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see: Junker et al.  2014  Cell,,tissue:adult heart|sectioning direction:injury area   uninjured  remote myocardium|sectioning thickness:12 µm|embedding strategy:extracted heart at 7 days post cryoinjury,GSM1924888,GSM1924888: zebrafish heart WT 7dpi #1; Danio rerio; RNA Seq,GSM1924888,,1,RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see: Junker et al.  2014  Cell,GEO Accession:GSM1924888,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP066192,,,FKHEART7_R1.fastq.gz FKHEART7_R2.fastq.gz,fastq fastq,3128649900.0,20745605.0,GSM1924888 r1,0:75.43 1:75.38,A:1025473014;C:388501715;G:410501025;T:1304153289;N:20857,75,75,,,1025473014,388501715,410501025,1304153289,20857,SRX1432516,SRS1163508,SRA311639,GEO,"Jeroen Bakkers, Hubrecht Institute",2,0.31194,0.62458,0.26968,0.18109,0.99308,0.89258,0.54708,0.5286,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,celseq,,Netherlands,2015-11-03,Adult,Adult,Heart,Cardiovascular System
40165,SRR2921972,SRX1432515,SRS1163510,SRP066192,PRJNA302179,Genome–wide transcriptional profiling with spatial resolution identifies Bone Morphogenetic Protein signaling as essential regulator of zebrafish cardiomyocyte regeneration.,GSE74652,Transcriptome Analysis,In contrast to mammals  zebrafish regenerate heart injuries via proliferation of cardiomyocytes located at the wound border. Here  we show that tomo seq can be used to identify whole genome transcriptional profiles of the injury zone  the border zone and the healthy myocardium. Interestingly  the border zone is characterized by the re expression of embryonic cardiac genes that are also activated post myocardial infarction in mouse and human  including targets of Bone Morphogenetic Protein BMP signaling. Endogenous BMP signaling has been reported to be detrimental to mammalian cardiac repair. In contrast  we find that genetic or chemical inhibition of BMP signaling in zebrafish reduces cardiomyocyte dedifferentiation and proliferation  ultimately compromising myocardial regeneration  while bmp2b overexpression is sufficient to enhance it. Our results provide a resource for further studies on the molecular regulation of cardiac regeneration and reveal intriguing differential cellular responses of cardiomyocytes to a conserved signaling pathway in regenerative versus non regenerative hearts. Overall design: To generate spatially resolved RNA seq data for injured zebrafish hearts 3 and 7 xxx post injury  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 NextSeq  using 75bp paired end sequencing.,,pubmed:26748692,,zebrafish heart WT 3dpi #1,GSM1924887,,source name:cryoinjured ventricle of the heart|tissue:adult heart|sectioning direction:injury area   uninjured  remote myocardium|sectioning thickness:12 µm|embedding strategy:extracted heart at 3 days post cryoinjury,zebrafish heart WT 3dpi #1,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. 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: 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 sections,cryoinjured ventricle of the heart,Unfixed ventricle was embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see: Junker et al.  2014  Cell,,tissue:adult heart|sectioning direction:injury area   uninjured  remote myocardium|sectioning thickness:12 µm|embedding strategy:extracted heart at 3 days post cryoinjury,GSM1924887,GSM1924887: zebrafish heart WT 3dpi #1; Danio rerio; RNA Seq,GSM1924887,,1,RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see: Junker et al.  2014  Cell,GEO Accession:GSM1924887,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP066192,,,FKHEART3_R1.fastq.gz FKHEART3_R2.fastq.gz,fastq fastq,784558404.0,5209213.0,GSM1924887 r1,0:75.22 1:75.39,A:291009319;C:102718146;G:111606154;T:279144074;N:80711,75,75,,,291009319,102718146,111606154,279144074,80711,SRX1432515,SRS1163510,SRA311639,GEO,"Jeroen Bakkers, Hubrecht Institute",2,0.12872,0.82031,0.12623,0.08476,0.99997,0.82828,0.0,0.566,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,celseq,,Netherlands,2015-11-03,Adult,Adult,Heart,Cardiovascular System
40599,SRR3231354,SRX1637105,SRS1342922,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate4.1,GSM2090871,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090871,GSM2090871: 8hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090871,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate4.1_R1_001.fastq.gz 8hpf_wt_Plate4.1_R2_001.fastq.gz,fastq fastq,2340114249.0,31038332.0,GSM2090871 r1,0:75.50 1:75.29,A:719873895;C:416010081;G:472221417;T:731461092;N:547764,75,75,,,719873895,416010081,472221417,731461092,547764,SRX1637105,SRS1342922,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",1,0.00529,,0.00355,,0.99655,,0.52173,,76,,T,,under 1.2% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40600,SRR3231355,SRX1637105,SRS1342922,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate4.1,GSM2090871,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090871,GSM2090871: 8hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090871,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate4.2_R1_001.fastq.gz 8hpf_wt_Plate4.2_R2_001.fastq.gz,fastq fastq,2340187687.0,31038332.0,GSM2090871 r2,0:75.50 1:75.29,A:718375391;C:414519064;G:478873036;T:728401149;N:19047,75,75,,,718375391,414519064,478873036,728401149,19047,SRX1637105,SRS1342922,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",1,0.00524,,0.00333,,0.99634,,0.47321,,76,,T,,under 1.2% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40601,SRR3231356,SRX1637105,SRS1342922,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate4.1,GSM2090871,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090871,GSM2090871: 8hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090871,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate4.3_R1_001.fastq.gz 8hpf_wt_Plate4.3_R2_001.fastq.gz,fastq fastq,2331948832.0,15464230.0,GSM2090871 r3,0:75.51 1:75.29,A:710801790;C:413559417;G:478178818;T:728790143;N:618664,75,75,,,710801790,413559417,478178818,728790143,618664,SRX1637105,SRS1342922,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00263,0.00843,0.0023,0.00555,0.99955,0.99437,0.37837,0.52459,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40602,SRR3231357,SRX1637105,SRS1342922,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate4.1,GSM2090871,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090871,GSM2090871: 8hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090871,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate4_R1_001.fastq.gz 8hpf_wt_Plate4_R2_001.fastq.gz,fastq fastq,2346532249.0,15562065.0,GSM2090871 r4,0:75.50 1:75.29,A:726362504;C:417435976;G:471522192;T:731180603;N:30974,75,75,,,726362504,417435976,471522192,731180603,30974,SRX1637105,SRS1342922,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0024,0.00837,0.00209,0.00548,0.99975,0.99409,0.2,0.53439,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40603,SRR3231350,SRX1637104,SRS1342923,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate3.1,GSM2090870,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090870,GSM2090870: 8hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090870,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate3.1_R2_001.fastq.gz 8hpf_wt_Plate3.1_R1_001.fastq.gz,fastq fastq,1401297283.0,9290433.0,GSM2090870 r1,0:75.49 1:75.34,A:419635887;C:271951633;G:296507210;T:413191086;N:11467,75,75,,,419635887,271951633,296507210,413191086,11467,SRX1637104,SRS1342923,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00163,0.00616,0.00116,0.00341,0.99951,0.99425,0.125,0.59722,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40604,SRR3231351,SRX1637104,SRS1342923,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate3.1,GSM2090870,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090870,GSM2090870: 8hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090870,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate3.2_R1_001.fastq.gz 8hpf_wt_Plate3.2_R2_001.fastq.gz,fastq fastq,1401701707.0,9293054.0,GSM2090870 r2,0:75.50 1:75.34,A:422173594;C:272799681;G:292195265;T:414209404;N:323763,75,75,,,422173594,272799681,292195265,414209404,323763,SRX1637104,SRS1342923,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00183,0.0057,0.00134,0.00307,0.99959,0.9948,0.18965,0.59402,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40605,SRR3231352,SRX1637104,SRS1342923,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate3.1,GSM2090870,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090870,GSM2090870: 8hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090870,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate3.3_R1_001.fastq.gz 8hpf_wt_Plate3.3_R2_001.fastq.gz,fastq fastq,1395747908.0,9253276.0,GSM2090870 r3,0:75.50 1:75.34,A:416176386;C:270989429;G:295563056;T:412655214;N:363823,75,75,,,416176386,270989429,295563056,412655214,363823,SRX1637104,SRS1342923,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00148,0.0058,0.00112,0.00312,0.99969,0.99476,0.16279,0.54093,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40606,SRR3231353,SRX1637104,SRS1342923,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate3.1,GSM2090870,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090870,GSM2090870: 8hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090870,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate3_R1_001.fastq.gz 8hpf_wt_Plate3_R2_001.fastq.gz,fastq fastq,1407551761.0,9332199.0,GSM2090870 r4,0:75.49 1:75.34,A:425795996;C:274090898;G:292401737;T:415244521;N:18609,75,75,,,425795996,274090898,292401737,415244521,18609,SRX1637104,SRS1342923,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00196,0.00615,0.00142,0.00325,0.99926,0.99403,0.39682,0.57712,74,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40607,SRR3231346,SRX1637103,SRS1342924,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate2.1,GSM2090869,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090869,GSM2090869: 8hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090869,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate2.1_R1_001.fastq.gz 8hpf_wt_Plate2.1_R2_001.fastq.gz,fastq fastq,952595024.0,6315631.0,GSM2090869 r1,0:75.47 1:75.36,A:302137554;C:151875219;G:168962721;T:329611160;N:8370,75,75,,,302137554,151875219,168962721,329611160,8370,SRX1637103,SRS1342924,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00829,0.04086,0.00683,0.01381,0.99898,0.97133,0.21481,0.68244,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40608,SRR3231347,SRX1637103,SRS1342924,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate2.1,GSM2090869,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090869,GSM2090869: 8hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090869,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate2.2_R1_001.fastq.gz 8hpf_wt_Plate2.2_R2_001.fastq.gz,fastq fastq,946451815.0,6274940.0,GSM2090869 r2,0:75.47 1:75.36,A:302374789;C:151074230;G:165028305;T:327758585;N:215906,75,75,,,302374789,151074230,165028305,327758585,215906,SRX1637103,SRS1342924,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00869,0.03997,0.00704,0.01272,0.99888,0.97183,0.24342,0.68028,75,74,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40609,SRR3231348,SRX1637103,SRS1342924,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate2.1,GSM2090869,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090869,GSM2090869: 8hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090869,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate2.3_R2_001.fastq.gz 8hpf_wt_Plate2.3_R1_001.fastq.gz,fastq fastq,947126047.0,6279272.0,GSM2090869 r3,0:75.48 1:75.36,A:299035197;C:150983123;G:168162807;T:328697140;N:247780,75,75,,,299035197,150983123,168162807,328697140,247780,SRX1637103,SRS1342924,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00868,0.03867,0.00717,0.01319,0.99864,0.97356,0.29285,0.66677,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40610,SRR3231349,SRX1637103,SRS1342924,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate2.1,GSM2090869,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090869,GSM2090869: 8hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090869,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate2_R1_001.fastq.gz 8hpf_wt_Plate2_R2_001.fastq.gz,fastq fastq,948028451.0,6285580.0,GSM2090869 r4,0:75.47 1:75.36,A:304286797;C:151414365;G:164490323;T:327824187;N:12779,75,75,,,304286797,151414365,164490323,327824187,12779,SRX1637103,SRS1342924,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0086,0.04012,0.00712,0.01343,0.99888,0.97177,0.29411,0.66575,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40611,SRR3231342,SRX1637102,SRS1342925,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate1.1,GSM2090868,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090868,GSM2090868: 8hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090868,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate1.1_R1_001.fastq.gz 8hpf_wt_Plate1.1_R2_001.fastq.gz,fastq fastq,1189452130.0,7888435.0,GSM2090868 r1,0:75.47 1:75.32,A:375847699;C:199289576;G:245818831;T:368358068;N:137956,75,75,,,375847699,199289576,245818831,368358068,137956,SRX1637102,SRS1342925,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00377,0.02162,0.00304,0.01018,0.99931,0.9848,0.29032,0.61771,75,73,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40612,SRR3231343,SRX1637102,SRS1342925,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate1.1,GSM2090868,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090868,GSM2090868: 8hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090868,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate1.2_R1_001.fastq.gz 8hpf_wt_Plate1.2_R2_001.fastq.gz,fastq fastq,1238856894.0,8215764.0,GSM2090868 r2,0:75.47 1:75.32,A:389215255;C:208182440;G:256176425;T:385173832;N:108942,75,75,,,389215255,208182440,256176425,385173832,108942,SRX1637102,SRS1342925,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00375,0.02269,0.00298,0.01135,0.99928,0.98423,0.40579,0.61686,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40613,SRR3231344,SRX1637102,SRS1342925,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate1.1,GSM2090868,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090868,GSM2090868: 8hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090868,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate1.3_R1_001.fastq.gz 8hpf_wt_Plate1.3_R2_001.fastq.gz,fastq fastq,1240573542.0,8227185.0,GSM2090868 r3,0:75.47 1:75.32,A:389703162;C:207657187;G:257329681;T:385780094;N:103418,75,75,,,389703162,207657187,257329681,385780094,103418,SRX1637102,SRS1342925,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00354,0.02325,0.00287,0.01111,0.99922,0.98309,0.47368,0.60449,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40614,SRR3231345,SRX1637102,SRS1342925,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate1.1,GSM2090868,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090868,GSM2090868: 8hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090868,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate1_R1_001.fastq.gz 8hpf_wt_Plate1_R2_001.fastq.gz,fastq fastq,1215460175.0,8061085.0,GSM2090868 r4,0:75.46 1:75.32,A:382475416;C:204057930;G:251490776;T:377293780;N:142273,75,75,,,382475416,204057930,251490776,377293780,142273,SRX1637102,SRS1342925,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00394,0.02131,0.00309,0.0101,0.99928,0.98472,0.34285,0.61368,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40615,SRR3231338,SRX1637101,SRS1342933,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate4.1,GSM2090867,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090867,GSM2090867: 8hpf Tdrd6a :  Plate4.1; Danio rerio; RNA Seq,GSM2090867,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate4.1_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate4.1_R2_001.fastq.gz,fastq fastq,660308475.0,4377096.0,GSM2090867 r1,0:75.49 1:75.36,A:203051507;C:115872485;G:122313924;T:219064434;N:6125,75,75,,,203051507,115872485,122313924,219064434,6125,SRX1637101,SRS1342933,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00239,0.00751,0.00191,0.00364,0.99941,0.99385,0.5625,0.71067,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40616,SRR3231339,SRX1637101,SRS1342933,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate4.1,GSM2090867,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090867,GSM2090867: 8hpf Tdrd6a :  Plate4.1; Danio rerio; RNA Seq,GSM2090867,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate4.2_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate4.2_R2_001.fastq.gz,fastq fastq,659386859.0,4370960.0,GSM2090867 r2,0:75.50 1:75.36,A:204037715;C:116060649;G:120151402;T:218981853;N:155240,75,75,,,204037715,116060649,120151402,218981853,155240,SRX1637101,SRS1342933,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00303,0.00736,0.00246,0.00371,0.99941,0.99429,0.45614,0.65738,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40617,SRR3231340,SRX1637101,SRS1342933,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate4.1,GSM2090867,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090867,GSM2090867: 8hpf Tdrd6a :  Plate4.1; Danio rerio; RNA Seq,GSM2090867,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate4.3_R2_001.fastq.gz 8hpf_Tdrd6a-:-_Plate4.3_R1_001.fastq.gz,fastq fastq,656929514.0,4354565.0,GSM2090867 r3,0:75.50 1:75.36,A:200970859;C:115371071;G:121921931;T:218498053;N:167600,75,75,,,200970859,115371071,121921931,218498053,167600,SRX1637101,SRS1342933,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00267,0.00746,0.00211,0.00354,0.99926,0.99371,0.58181,0.66467,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40618,SRR3231341,SRX1637101,SRS1342933,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate4.1,GSM2090867,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090867,GSM2090867: 8hpf Tdrd6a :  Plate4.1; Danio rerio; RNA Seq,GSM2090867,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate4_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate4_R2_001.fastq.gz,fastq fastq,659750831.0,4373567.0,GSM2090867 r4,0:75.49 1:75.36,A:205228191;C:116070031;G:119659384;T:218783801;N:9424,75,75,,,205228191,116070031,119659384,218783801,9424,SRX1637101,SRS1342933,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00286,0.00728,0.00232,0.00355,0.99945,0.99439,0.47169,0.69696,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40619,SRR3231334,SRX1637100,SRS1342932,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate3.1,GSM2090866,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090866,GSM2090866: 8hpf Tdrd6a :  Plate3.1; Danio rerio; RNA Seq,GSM2090866,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate3.1_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate3.1_R2_001.fastq.gz,fastq fastq,991807830.0,6574461.0,GSM2090866 r1,0:75.50 1:75.35,A:306057776;C:164673747;G:183621348;T:337443425;N:11534,75,75,,,306057776,164673747,183621348,337443425,11534,SRX1637100,SRS1342932,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00573,0.01848,0.00474,0.0066,0.99918,0.98362,0.36274,0.59804,75,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40620,SRR3231335,SRX1637100,SRS1342932,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate3.1,GSM2090866,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090866,GSM2090866: 8hpf Tdrd6a :  Plate3.1; Danio rerio; RNA Seq,GSM2090866,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate3.2_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate3.2_R2_001.fastq.gz,fastq fastq,985873592.0,6535185.0,GSM2090866 r2,0:75.50 1:75.35,A:306272693;C:164036011;G:179508984;T:335829272;N:226632,75,75,,,306272693,164036011,179508984,335829272,226632,SRX1637100,SRS1342932,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00561,0.0179,0.00465,0.00654,0.99918,0.98437,0.31,0.63328,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40621,SRR3231336,SRX1637100,SRS1342932,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate3.1,GSM2090866,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090866,GSM2090866: 8hpf Tdrd6a :  Plate3.1; Danio rerio; RNA Seq,GSM2090866,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate3.3_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate3.3_R2_001.fastq.gz,fastq fastq,985261576.0,6530964.0,GSM2090866 r3,0:75.51 1:75.35,A:302874779;C:163594572;G:182423657;T:336116219;N:252349,75,75,,,302874779,163594572,182423657,336116219,252349,SRX1637100,SRS1342932,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0057,0.01777,0.00484,0.00661,0.99926,0.98482,0.3146,0.64967,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40622,SRR3231337,SRX1637100,SRS1342932,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate3.1,GSM2090866,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090866,GSM2090866: 8hpf Tdrd6a :  Plate3.1; Danio rerio; RNA Seq,GSM2090866,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate3_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate3_R2_001.fastq.gz,fastq fastq,988364061.0,6551921.0,GSM2090866 r4,0:75.50 1:75.35,A:308483971;C:164508093;G:179109944;T:336245723;N:16330,75,75,,,308483971,164508093,179109944,336245723,16330,SRX1637100,SRS1342932,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00558,0.0188,0.00462,0.00684,0.99912,0.98354,0.38775,0.62734,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40623,SRR3231330,SRX1637099,SRS1342934,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate2.1,GSM2090865,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090865,GSM2090865: 8hpf Tdrd6a :  Plate2.1; Danio rerio; RNA Seq,GSM2090865,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090865,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate2.1_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate2.1_R2_001.fastq.gz,fastq fastq,1347558297.0,8935001.0,GSM2090865 r1,0:75.49 1:75.32,A:428692990;C:233467157;G:260154804;T:425229674;N:13672,75,75,,,428692990,233467157,260154804,425229674,13672,SRX1637099,SRS1342934,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00717,0.02482,0.00583,0.01367,0.9977,0.98301,0.54347,0.62642,74,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40624,SRR3231331,SRX1637099,SRS1342934,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate2.1,GSM2090865,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090865,GSM2090865: 8hpf Tdrd6a :  Plate2.1; Danio rerio; RNA Seq,GSM2090865,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090865,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate2.2_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate2.2_R2_001.fastq.gz,fastq fastq,1347477358.0,8934352.0,GSM2090865 r2,0:75.50 1:75.32,A:431085993;C:234267083;G:255942417;T:425873702;N:308163,75,75,,,431085993,234267083,255942417,425873702,308163,SRX1637099,SRS1342934,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00723,0.02422,0.00571,0.01316,0.99748,0.9825,0.4935,0.61373,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40625,SRR3231332,SRX1637099,SRS1342934,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate2.1,GSM2090865,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090865,GSM2090865: 8hpf Tdrd6a :  Plate2.1; Danio rerio; RNA Seq,GSM2090865,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090865,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate2.3_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate2.3_R2_001.fastq.gz,fastq fastq,1342511024.0,8901101.0,GSM2090865 r3,0:75.50 1:75.32,A:424536537;C:232976344;G:259737347;T:424897714;N:363082,75,75,,,424536537,232976344,259737347,424897714,363082,SRX1637099,SRS1342934,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00707,0.02424,0.00579,0.01341,0.99788,0.98277,0.3897,0.60237,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40626,SRR3231333,SRX1637099,SRS1342934,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate2.1,GSM2090865,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090865,GSM2090865: 8hpf Tdrd6a :  Plate2.1; Danio rerio; RNA Seq,GSM2090865,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090865,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate2_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate2_R2_001.fastq.gz,fastq fastq,1349985043.0,8951395.0,GSM2090865 r4,0:75.49 1:75.32,A:433870230;C:234813106;G:255398294;T:425882927;N:20486,75,75,,,433870230,234813106,255398294,425882927,20486,SRX1637099,SRS1342934,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00663,0.02406,0.00536,0.01336,0.99772,0.98281,0.48872,0.63184,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40627,SRR3231326,SRX1637098,SRS1342905,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate1.1,GSM2090864,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090864,GSM2090864: 8hpf Tdrd6a :  Plate1.1; Danio rerio; RNA Seq,GSM2090864,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090864,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate1.1_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate1.1_R2_001.fastq.gz,fastq fastq,2529086421.0,16774294.0,GSM2090864 r1,0:75.43 1:75.34,A:796779684;C:413533280;G:487547543;T:830919763;N:306151,75,75,,,796779684,413533280,487547543,830919763,306151,SRX1637098,SRS1342905,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.05805,0.15018,0.04986,0.07872,0.98729,0.92443,0.5,0.46925,76,76,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40628,SRR3231327,SRX1637098,SRS1342905,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate1.1,GSM2090864,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090864,GSM2090864: 8hpf Tdrd6a :  Plate1.1; Danio rerio; RNA Seq,GSM2090864,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090864,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate1.2_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate1.2_R2_001.fastq.gz,fastq fastq,2629569381.0,17440212.0,GSM2090864 r2,0:75.43 1:75.34,A:823719446;C:431439564;G:506909577;T:867265650;N:235144,75,75,,,823719446,431439564,506909577,867265650,235144,SRX1637098,SRS1342905,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0575,0.1556,0.04944,0.08069,0.98648,0.92245,0.5,0.58664,76,76,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40629,SRR3231328,SRX1637098,SRS1342905,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate1.1,GSM2090864,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090864,GSM2090864: 8hpf Tdrd6a :  Plate1.1; Danio rerio; RNA Seq,GSM2090864,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090864,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate1.3_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate1.3_R2_001.fastq.gz,fastq fastq,2626839769.0,17422028.0,GSM2090864 r3,0:75.43 1:75.35,A:822264952;C:429448970;G:507899334;T:867005630;N:220883,75,75,,,822264952,429448970,507899334,867005630,220883,SRX1637098,SRS1342905,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.05904,0.1574,0.05085,0.08206,0.98685,0.92133,0.50407,0.58481,75,75,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40630,SRR3231329,SRX1637098,SRS1342905,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate1.1,GSM2090864,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090864,GSM2090864: 8hpf Tdrd6a :  Plate1.1; Danio rerio; RNA Seq,GSM2090864,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090864,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate1_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate1_R2_001.fastq.gz,fastq fastq,2592347629.0,17194377.0,GSM2090864 r4,0:75.43 1:75.34,A:813940505;C:424856630;G:499860954;T:853378694;N:310846,75,75,,,813940505,424856630,499860954,853378694,310846,SRX1637098,SRS1342905,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0589,0.14612,0.05081,0.07706,0.98756,0.92829,0.52503,0.46498,75,75,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40631,SRR3231322,SRX1637097,SRS1342906,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8and24hpf wt Plate1.1,GSM2090863,,tissue:Germ cells|cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8and24hpf wt Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090863,GSM2090863: 8and24hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090863,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090863,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8and24hpf_wt_Plate1.1_R1_001.fastq.gz 8and24hpf_wt_Plate1.1_R2_001.fastq.gz,fastq fastq,354951269.0,2354572.0,GSM2090863 r1,0:75.37 1:75.38,A:109255676;C:46649925;G:56800706;T:142212324;N:32638,75,75,,,109255676,46649925,56800706,142212324,32638,SRX1637097,SRS1342906,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.08814,0.58586,0.05414,0.12777,0.98236,0.8253,0.52224,0.5333,75,55,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40632,SRR3231323,SRX1637097,SRS1342906,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8and24hpf wt Plate1.1,GSM2090863,,tissue:Germ cells|cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8and24hpf wt Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090863,GSM2090863: 8and24hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090863,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090863,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8and24hpf_wt_Plate1.2_R1_001.fastq.gz 8and24hpf_wt_Plate1.2_R2_001.fastq.gz,fastq fastq,373175186.0,2475371.0,GSM2090863 r2,0:75.37 1:75.38,A:114080796;C:49251081;G:59964869;T:149836843;N:41597,75,75,,,114080796,49251081,59964869,149836843,41597,SRX1637097,SRS1342906,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0895,0.59282,0.05309,0.12622,0.9811,0.82185,0.51449,0.52518,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40633,SRR3231324,SRX1637097,SRS1342906,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8and24hpf wt Plate1.1,GSM2090863,,tissue:Germ cells|cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8and24hpf wt Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090863,GSM2090863: 8and24hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090863,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090863,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8and24hpf_wt_Plate1.3_R1_001.fastq.gz 8and24hpf_wt_Plate1.3_R2_001.fastq.gz,fastq fastq,376796544.0,2499144.0,GSM2090863 r3,0:75.38 1:75.39,A:114262594;C:49685044;G:61341084;T:151464220;N:43602,75,75,,,114262594,49685044,61341084,151464220,43602,SRX1637097,SRS1342906,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.08885,0.60874,0.05444,0.12569,0.98177,0.81233,0.51071,0.53112,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40634,SRR3231325,SRX1637097,SRS1342906,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8and24hpf wt Plate1.1,GSM2090863,,tissue:Germ cells|cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8and24hpf wt Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8and24hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090863,GSM2090863: 8and24hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090863,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090863,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8and24hpf_wt_Plate1_R1_001.fastq.gz 8and24hpf_wt_Plate1_R2_001.fastq.gz,fastq fastq,370852802.0,2459988.0,GSM2090863 r4,0:75.37 1:75.38,A:113706258;C:48924259;G:59523739;T:148663433;N:35113,75,75,,,113706258,48924259,59523739,148663433,35113,SRX1637097,SRS1342906,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.08962,0.59214,0.05376,0.12667,0.98226,0.82142,0.53851,0.52744,75,32,T,B,mate1 technical by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Pharyngula,Embryo,Gonad,Reproductive System
40635,SRR3231318,SRX1637096,SRS1342907,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate5.1,GSM2090862,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090862,GSM2090862: 3.5hpf wt Plate5.1; Danio rerio; RNA Seq,GSM2090862,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090862,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate5.1_R1_001.fastq.gz 3.5hpf_wt_Plate5.1_R2_001.fastq.gz,fastq fastq,465283988.0,3083951.0,GSM2090862 r1,0:75.46 1:75.41,A:131913263;C:74557873;G:91090052;T:167720369;N:2431,75,75,,,131913263,74557873,91090052,167720369,2431,SRX1637096,SRS1342907,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00196,0.01756,0.00174,0.00396,0.99981,0.97512,0.4375,0.58617,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40636,SRR3231319,SRX1637096,SRS1342907,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate5.1,GSM2090862,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090862,GSM2090862: 3.5hpf wt Plate5.1; Danio rerio; RNA Seq,GSM2090862,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090862,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate5.2_R1_001.fastq.gz 3.5hpf_wt_Plate5.2_R2_001.fastq.gz,fastq fastq,492787533.0,3266133.0,GSM2090862 r2,0:75.46 1:75.41,A:138920634;C:79266412;G:96252502;T:178340643;N:7342,75,75,,,138920634,79266412,96252502,178340643,7342,SRX1637096,SRS1342907,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00175,0.01711,0.00149,0.00417,0.99965,0.9754,0.28571,0.59079,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40637,SRR3231320,SRX1637096,SRS1342907,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate5.1,GSM2090862,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090862,GSM2090862: 3.5hpf wt Plate5.1; Danio rerio; RNA Seq,GSM2090862,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090862,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate5.3_R1_001.fastq.gz 3.5hpf_wt_Plate5.3_R2_001.fastq.gz,fastq fastq,478302056.0,3170122.0,GSM2090862 r3,0:75.46 1:75.41,A:134552769;C:76719834;G:94014994;T:173009599;N:4860,75,75,,,134552769,76719834,94014994,173009599,4860,SRX1637096,SRS1342907,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0018,0.01735,0.00154,0.00386,0.99967,0.97429,0.23809,0.55019,75,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40638,SRR3231321,SRX1637096,SRS1342907,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate5.1,GSM2090862,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate5.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090862,GSM2090862: 3.5hpf wt Plate5.1; Danio rerio; RNA Seq,GSM2090862,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090862,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate5_R1_001.fastq.gz 3.5hpf_wt_Plate5_R2_001.fastq.gz,fastq fastq,487978460.0,3234287.0,GSM2090862 r4,0:75.46 1:75.41,A:138127249;C:78568068;G:95022582;T:176256804;N:3757,75,75,,,138127249,78568068,95022582,176256804,3757,SRX1637096,SRS1342907,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00178,0.01711,0.00155,0.00374,0.99975,0.97457,0.38888,0.54467,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40639,SRR3231314,SRX1637095,SRS1342908,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate4.1,GSM2090861,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090861,GSM2090861: 3.5hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090861,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090861,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate4.1_R1_001.fastq.gz 3.5hpf_wt_Plate4.1_R2_001.fastq.gz,fastq fastq,1165572863.0,7724698.0,GSM2090861 r1,0:75.47 1:75.42,A:341597187;C:187300441;G:218487967;T:418181251;N:6017,75,75,,,341597187,187300441,218487967,418181251,6017,SRX1637095,SRS1342908,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0024,0.05972,0.00175,0.01107,0.99894,0.93363,0.46268,0.54466,75,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40640,SRR3231315,SRX1637095,SRS1342908,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate4.1,GSM2090861,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090861,GSM2090861: 3.5hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090861,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090861,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate4.2_R1_001.fastq.gz 3.5hpf_wt_Plate4.2_R2_001.fastq.gz,fastq fastq,1231311328.0,8160147.0,GSM2090861 r2,0:75.48 1:75.42,A:359044176;C:198664662;G:229959438;T:443624264;N:18788,75,75,,,359044176,198664662,229959438,443624264,18788,SRX1637095,SRS1342908,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0022,0.06116,0.00155,0.01128,0.99888,0.93229,0.40298,0.54742,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40641,SRR3231316,SRX1637095,SRS1342908,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate4.1,GSM2090861,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090861,GSM2090861: 3.5hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090861,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090861,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate4.3_R1_001.fastq.gz 3.5hpf_wt_Plate4.3_R2_001.fastq.gz,fastq fastq,1197590912.0,7936665.0,GSM2090861 r3,0:75.48 1:75.42,A:348626376;C:192686213;G:225139549;T:431126048;N:12726,75,75,,,348626376,192686213,225139549,431126048,12726,SRX1637095,SRS1342908,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00247,0.06111,0.00168,0.01107,0.9987,0.9318,0.41176,0.55782,75,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40642,SRR3231317,SRX1637095,SRS1342908,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate4.1,GSM2090861,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090861,GSM2090861: 3.5hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090861,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090861,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate4_R1_001.fastq.gz 3.5hpf_wt_Plate4_R2_001.fastq.gz,fastq fastq,1224213980.0,8113208.0,GSM2090861 r4,0:75.48 1:75.42,A:358299358;C:197501927;G:228122097;T:440281285;N:9313,75,75,,,358299358,197501927,228122097,440281285,9313,SRX1637095,SRS1342908,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00255,0.06199,0.00181,0.0116,0.9989,0.93326,0.48684,0.54385,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40643,SRR3231310,SRX1637094,SRS1342909,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate3.1,GSM2090860,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090860,GSM2090860: 3.5hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090860,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090860,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate3.1_R1_001.fastq.gz 3.5hpf_wt_Plate3.1_R2_001.fastq.gz,fastq fastq,626596035.0,4155091.0,GSM2090860 r1,0:75.44 1:75.37,A:192353640;C:87072147;G:109704935;T:237462123;N:3190,75,75,,,192353640,87072147,109704935,237462123,3190,SRX1637094,SRS1342909,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00677,0.07893,0.00548,0.01598,0.99898,0.92987,0.43902,0.58089,73,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System
40644,SRR3231311,SRX1637094,SRS1342909,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,3.5hpf wt Plate3.1,GSM2090860,,tissue:Germ cells|cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,3.5hpf wt Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:3.5hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090860,GSM2090860: 3.5hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090860,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090860,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,3.5hpf_wt_Plate3.2_R1_001.fastq.gz 3.5hpf_wt_Plate3.2_R2_001.fastq.gz,fastq fastq,662952483.0,4396049.0,GSM2090860 r2,0:75.44 1:75.37,A:202110673;C:92410890;G:116053839;T:252366901;N:10180,75,75,,,202110673,92410890,116053839,252366901,10180,SRX1637094,SRS1342909,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00616,0.08027,0.00497,0.01696,0.99896,0.9277,0.50649,0.58134,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Blastula,Embryo,Gonad,Reproductive System