{"database": "metadata", "table": "run_metadata", "rows": [[71059, "SRR21152617", "SRX17164236", "SRS14735585", "SRP393251", "PRJNA871903", "Single cell transcriptomic profiling of the zebrafish inner ear reveals molecularly distinct hair cell and supporting cell subtypes", "GSE211728", "Transcriptome Analysis", "A major cause of human deafness and vestibular dysfunction is permanent loss of the mechanosensory hair cells of the inner ear. In non mammalian vertebrates such as zebrafish  regeneration of missing hair cells can occur throughout life. While a comparative approach has the potential to reveal the basis of such differential regenerative ability  the degree to which the inner ears of fish and mammals share common hair and supporting cell types remains unresolved. Here we perform single cell RNA sequencing of the zebrafish inner ear at embryonic through adult stages to catalog the diversity of hair and non sensory supporting cells. We identify a putative progenitor population for hair and supporting cells  as well as distinct hair and supporting cell types in the maculae versus cristae. The hair and supporting cell types differ from those described for the lateral line  a distributed mechanosensory organ in zebrafish in which most studies of hair cell regeneration have been conducted. In the maculae  we identify two subtypes of hair cells that share gene expression with mammalian striolar or extrastriolar hair cells. In situ hybridization reveals that these hair cell subtypes occupy distinct spatial domains within the two major macular organs  the utricle and saccule  consistent with the reported distinct electrophysiological properties of hair cells within these domains. These findings suggest that primitive specialization of spatially distinct striolar and extrastriolar hair cells likely arose in the last common ancestor of fish and mammals. The similarities of inner ear cell type composition between fish and mammals also support using zebrafish as a relevant model for understanding inner ear specific hair cell function and regeneration. Overall design: Inner ears were dissected from the Sox10Cre;UbiSwitch zebrafish at 14dpf n=35 and 12mpf n=6. Converted cells were isolated by Fluorescence activated cell sorting FACS according to the presence or absence of mCherry signal and analyzed using 10x genomics based scRNAseq. Reads were aligned to danRer11 using the Cellranger pipeline", null, "pubmed:36598134", null, "14dpf Sox10CreUbiswitch ear", "GSM6500163", null, "source name:inner ear|tissue:inner ear|cell type:mixed|genotype:Sox10:Cre; ubb:LOXP EGFP LOXP mCherry|age:14 dpf", "14dpf Sox10CreUbiswitch ear", "Base calling and sample were demultiplexed by bcl2fastq performed by the single cell sequencing and CyTOF core at Chilren's Hospital Los Angeles Sequences were alinged to danRer11 and UMI counts were created using cellranger count v6.0.0 14dpf or cellranger arc count v2.0.0 12mpf Downstream analysis was performed in R and Python Assembly: danRer11 Supplementary files format and content: .csv files filtered barcode feature count matrix for each individual library Supplementary files format and content: .rds file of Seurat Object containing raw count matrix of integrated libraries  including the two libraries here and other published data", "inner ear", null, "For 14 dpf animals  heads from converted Sox10:Cre; ubb:LOXP EGFP LOXP mCherry fish were decapitated at the level of the pectoral fin with eyes and brains removed. For 12 mpf animals  utricle  saccule  and lagena were extracted from converted Sox10:Cre; ubb:LOXP EGFP LOXP mCherry fish post brains and otolith crystals were removed. Dissected heads and otic sensory patches were then incubated in fresh Ringer\u2019s solution for 5\u201310\u2009min  followed by mechanical and enzymatic dissociation by pipetting every 5\u2009min in protease solution 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS and incubated at 28.5\u2009\u00b0C for 20\u201330\u2009min or until full dissociation. Reaction was stopped by adding 6\u00d7 stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 376\u2009\u00d7\u2009g  5\u2009min  4\u2009\u00b0C and resuspended in suspension media 1% FBS  0.8\u2009mM CaCl2  50\u2009U/mL penicillin  and 0.05\u2009mg/mL streptomycin Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies twice. Final volumes of 500\u2009\u03bcL resuspended cells were placed on ice and fluorescence activated cell sorted FACS to isolate live cells that excluded the nuclear stain DAPI 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.3.1 dpf 14 dpf or Single Cell Multiome ATAC + Gene Expression kit 12 mpf", null, "tissue:inner ear|cell type:mixed|genotype:Sox10:Cre; ubb:LOXP EGFP LOXP mCherry|age:14 dpf", "GSM6500163", "GSM6500163: 14dpf Sox10CreUbiswitch ear; Danio rerio; RNA Seq", "GSM6500163 r1", "GSM6500163", "1", "For 14 dpf animals  heads from converted Sox10:Cre; ubb:LOXP EGFP LOXP mCherry fish were decapitated at the level of the pectoral fin with eyes and brains removed. For 12 mpf animals  utricle  saccule  and lagena were extracted from converted Sox10:Cre; ubb:LOXP EGFP LOXP mCherry fish post brains and otolith crystals were removed. Dissected heads and otic sensory patches were then incubated in fresh Ringer's solution for 5\u201310\u2009min  followed by mechanical and enzymatic dissociation by pipetting every 5\u2009min in protease solution 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS and incubated at 28.5\u2009\u00b0C for 20\u201330\u2009min or until full dissociation. Reaction was stopped by adding 6\u00d7 stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 376\u2009\u00d7\u2009g  5\u2009min  4\u2009\u00b0C and resuspended in suspension media 1% FBS  0.8\u2009mM CaCl2  50\u2009U/mL penicillin  and 0.05\u2009mg/mL streptomycin Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500\u2009\u03bcL resuspended cells were placed on ice and fluorescence activated cell sorted FACS to isolate live cells that excluded the nuclear stain DAPI 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.3.1 dpf 14 dpf or Single Cell Multiome ATAC + Gene Expression kit 12 mpf", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP393251", null, "loader:fastq load.py", "sox10CreUbiSwitch_14dpf_ear_S1_L001_R1_001.fastq.gz sox10CreUbiSwitch_14dpf_ear_S1_L001_R2_001.fastq.gz", "fastq fastq", 66312808744.0, 512252644.0, "GSM6500163 r1", "0:29 1:100.45", "A:19003048692;C:14320898403;G:14949837823;T:17995908285;N:43115541", 29, 100, null, null, 19003048692, 14320898403, 14949837823, 17995908285, 43115541, "SRX17164236", "SRS14735585", "SRA1480233", "University of Southern California", "University of Southern California", 2, 0.0023, 0.91017, 0.00102, 0.17968, 0.99642, 0.78338, 0.36213, 0.5439, 29, 101, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-08-21", "Larval", "Larval", "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": ["71059"], "units": {}, "query_ms": 9.327731997473165}