{"database": "metadata", "table": "run_metadata", "rows": [[67719, "SRR17247467", "SRX13426485", "SRS11327473", "SRP351089", "PRJNA789478", "Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C", "GSE191029", "Other", "Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood.  Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions.  Dysregulated expression of protein kinase C delta PKC d  encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors.  PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations.  Cxcl8 induced association of PKC d with the focal adhesion complex  activating MEK/ERK signaling and expression of niche factors in human endothelial cells.  Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow.  Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.", null, "pubmed:37209097", null, "zfish km july2020 prkcda 1 gex", "GSM5737709", null, "source name:zebrafish kidney marrow|Stage:adult|class:prkcda|tissue:kidney marrow|geo loc name:missing|collection date:missing", "zfish km july2020 prkcda 1 gex", "scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11  GRCh38 Supplementary files format and content: scRNAseq:  hdf5 file format containing gene cell barcode matrices.  scATACseq:  hdf5 file format containing peak cell barcode matrices.  RNA seq:  Normalized abundance table from RSEM with TPM  FPKM and other metrics per gene.  ATAC seq:  bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.", "zebrafish kidney marrow", "No treatments", "Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.", "Fish were maintained on a recirculating water system at 28C.", "Stage:adult|class:prkcda|tissue:kidney marrow", "GSM5737709", "GSM5737709: zfish km july2020 prkcda 1 gex; Danio rerio; RNA Seq", "GSM5737709 r1", "GSM5737709", "1", "Fish were euthanized and kidney marrow was dissected  RBC lysis was performed and single cells were isolated using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP351089", null, null, "prkcda_1_gex_S1_L001_R1_001.fastq.gz prkcda_1_gex_S1_L001_R2_001.fastq.gz", "fastq fastq", 14142779894.0, 46830397.0, "GSM5737709 r1", "0:151 1:151", "A:3803907364;C:2547631786;G:2315347877;T:5475620885;N:271982", 151, 151, null, null, 3803907364, 2547631786, 2315347877, 5475620885, 271982, "SRX13426485", "SRS11327473", "SRA1347311", "Blaser Lab, Comprehensive Cancer Center, Ohio State University", "Blaser Lab, Comprehensive Cancer Center, Ohio State University", 2, 0.02414, 0.84338, 0.00622, 0.11548, 0.99097, 0.8144, 0.62514, 0.57188, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-12-16", "Adult", "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": ["67719"], "units": {}, "query_ms": 8.28945199464215}