{"database": "metadata", "table": "run_metadata", "rows": [[10163, "ERR5714657", "ERX5430029", "ERS6251768", "ERP128324", "PRJEB44291", "Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows", "E-MTAB-10360", "Transcriptome Analysis", "Macrophage colony stimulating factor receptor M CSFR/CSF1R signaling is crucial for the differentiation  proliferation  and survival of myeloid cells. Therapeutic targeting of the CSF1R pathway is a promising strategy in many human diseases  including neurological disorders or cancer. Zebrafish are commonly used for human disease modeling and preclinical therapeutic screening. Therefore  it is necessary to understand the proper function of cytokine signaling in zebrafish to reliably model human related diseases. Here  we investigate the roles of zebrafish csf1ra and csf1rb in adult myelopoiesis using single cell RNA sequencing. Our analysis of adult whole kidney marrow WKM hematopoietic cells suggests that csf1rb is expressed mainly by blood and myeloid progenitors and that the expression of csf1ra and csf1rb is non overlapping. We point out differentially expressed genes important in hematopoietic cell differentiation and immune response in selected WKM populations. Our findings could improve the understanding of myeloid cell function and lead to the further study of CSF1R pathway deregulation in disease  mostly in cancerogenesis.", "ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14", null, "Protocols: Whole kidney marrow was collected from 6 mpf zebrafish wt  csf1ra\u03945bp  or csf1rb\u03944bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting  washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further  total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation.", "WT", "SAMEA8567093", "Institute of Molecular Genetics of the Czech Academy of Sciences", "ENA first public:2021 04 24|ENA last update:2021 04 14|External Id:SAMEA8567093|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 04 24T00:22:33Z|INSDC last update:2021 04 14T14:09:18Z|INSDC status:public|Submitter Id:E MTAB 10360:WT|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:head kidney|sample name:E MTAB 10360:WT|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows", "E MTAB 10360:WT p", "WT p", "Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows", "Whole kidney marrow was collected from 6 mpf zebrafish wt  csf1ra\u03945bp  or csf1rb\u03944bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting  washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further  total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3\u02b9 GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation.", "Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP128324", "NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows", "ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14", "WT.bam", "bam", 1041394032.0, 18596322.0, "E MTAB 10360:WT", "0:56", "A:284652376;C:244349479;G:255850754;T:255536179;N:1005244", 56, null, null, null, 284652376, 244349479, 255850754, 255536179, 1005244, "ERX5430029", "ERS6251768", "ERA3959104", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", "Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive", 1, 0.9192, null, 0.10547, null, 0.84782, null, 0.53778, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Czech Republic", "2021-04-14", "Adult", "Adult", "Multi-tissue", "Multi-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": ["10163"], "units": {}, "query_ms": 13.642289995914325}