{"database": "metadata", "table": "run_metadata", "rows": [[50724, "SRR8270601", "SRX5087287", "SRS4099390", "SRP171998", "PRJNA507898", "Single cell RNA Seq reveals Fgf signaling dynamics during sensory hair cell regeneration", "GSE123241", "Transcriptome Analysis", "Loss of sensory hair cells leads to deafness and balance deficiencies. In contrast to mammalian hair cells  zebrafish ear and lateral line hair cells regenerate from poorly characterized  proliferating support cells. Equally ill defined is the gene regulatory network underlying the progression of support cells to cycling hair cell progenitors and differentiated hair cells. We used single cell RNA Sequencing scRNA Seq of lateral line sensory organs and uncovered five different support cell types  including quiescent and activated stem cells. In silico ordering of support cells along a developmental trajectory identified cells that self renew and new groups of genes required for hair cell differentiation. scRNA Seq analyses of fgf3 mutants  in which hair cell regeneration is increased demonstrates that Fgf and Notch signaling inhibit proliferation of support cells in parallel by inhibiting Wnt signaling. Our scRNA Seq analyses set the foundation for mechanistic studies of sensory organ regeneration and is crucial for identifying factors to trigger hair cell production in mammals. Overall design: Single cell RNA sequecing on FACS sorted cells from the zebrafish neuromast in 5df embryos in 3 different samples: wild type  fgf3 mutants  and fgf3 siblings.", null, "pubmed:30681411;pubmed:31488837", null, "fgf3 sibling", "GSM3498553", null, "source name:neuromast|age:5dpf|tissue:neuromast|genotype:fgf3+/ |strain:fgf3^t26212; ETkrt4:EGFPSqGw57A; Tgpou4f3:GAP GFPs356t", "fgf3 sibling", "Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Genome build: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.", "neuromast", null, "Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq", null, "age:5dpf|tissue:neuromast|genotype:fgf3+/ |strain:fgf3^t26212;ETkrt4:EGFPSqGw57A;Tgpou4f3:GAP GFPs356t", "GSM3498553", "GSM3498553: fgf3 sibling; Danio rerio; RNA Seq", "GSM3498553", null, "1", "Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq", "GEO Accession:GSM3498553", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP171998", null, null, "possorted_genome_bam_fgf3_sib.bam", "10X Genomics bam file", 15833733894.0, 159936706.0, "GSM3498553 r1", "0:99", "A:4876827108;C:3036857735;G:3248946665;T:4560644612;N:110457774", 99, null, null, null, 4876827108, 3036857735, 3248946665, 4560644612, 110457774, "SRX5087287", "SRS4099390", "SRA817952", "GEO", "Stowers Institute", 1, 0.89735, null, 0.21699, null, 0.80409, null, 0.4894, null, 99, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2018-12-02", "Larval", "Larval", "Lateral Line", "Sensory 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": ["50724"], "units": {}, "query_ms": 7.135182000638451}