{"database": "metadata", "table": "run_metadata", "rows": [[42689, "SRR5810869", "SRX2989421", "SRS2341344", "SRP111340", "PRJNA393431", "Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart seq]", "GSE100911", "Transcriptome Analysis", "Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here  we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow  constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner  our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs  il2rgaY91fs and double homozygous mutant fish  identifying blood cell losses in T  B  and natural killer cells within specific genetic mutants.  Our analysis also uncovered novel cell types including two classes of natural killer immune cells  classically defined and erythroid primed hematopoietic stem and progenitor cells  mucin secreting kidney cells  and kidney stem/progenitor cells. In total  our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly  we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines  which label distinct blood cell types n = 246 cells total. Secondly  we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked  comprehensive hematopoietic lineage structure within wild type  casper strain zebrafish N=3 animals  n=3 782 cells total. From this  we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly  we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies  including prkdcD3612fs N=3 animals  n=3 201 cells  il2rgaY91fs N=2 animals  n=2 068 cells and prkdcD3612fs  il2rgaY91fs double compound mutant fish N=2 animals  n=2 276 cells. Lastly  we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.", "parent bioproject:PRJNA393415", "pubmed:28878000", null, "rag2 GFP.P2.C01", "GSM2696288", null, "source name:whole kidney marrow|tissue:kidney marrow", "rag2 GFP.P2.C01", "Demultiplexed reads were aligned using STARDobin et al.  2013 to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCountsLiao Y  Smyth GK and Shi W 2014. Genome build: GRCz10 Supplementary files format and content: text file with raw counts", "whole kidney marrow", null, "Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80\u00b0C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.", null, "tissue:kidney marrow", "GSM2696288", "GSM2696288: rag2 GFP.P2.C01; Danio rerio; RNA Seq", "GSM2696288", null, "1", "Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence activated cell sorting into 96 well plates containing 5 ul TCL buffer QIAGEN + 1% BME Bio Rad. Plates were snap frozen and stored in  80\u00b0C before reverse transcription and library construction. Whole transcriptome amplification and library construction were performed on single cells using a modified Smart seq2 protocol adapted by Venteicher et al. PMID 28360267. Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina.", "GEO Accession:GSM2696288", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP111340", null, null, "rag2_GFP.P2.C01.bam", "bam", 79587566.0, 1058811.0, "GSM2696288 r1", "0:37.58 1:37.58", "A:21790575;C:18066457;G:17626457;T:22087840;N:16237", 37, 37, null, null, 21790575, 18066457, 17626457, 22087840, 16237, "SRX2989421", "SRS2341344", "SRA584588", "GEO", "Pathology, Massachusetts General Hospital", 2, 0.9215, 0.92115, 0.19713, 0.19752, 0.9866, 0.98677, 0.49777, 0.49443, 37, 38, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2017-07-07", "Undetermined", "Adult", "Kidney", "Renal System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["42689"], "units": {}, "query_ms": 8.866403994034044}