run_metadata: 71059

This data as json

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
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		pubmed:36598134		14dpf Sox10CreUbiswitch ear	GSM6500163		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		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 5–10 min followed by mechanical and enzymatic dissociation by pipetting every 5 min in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS and incubated at 28.5 °C for 20–30 min or until full dissociation. Reaction was stopped by adding 6× stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 376 × g 5 min 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/mL penicillin and 0.05 mg/mL streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies twice. Final volumes of 500 μL 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′ Library and Gel Bead Kit v.3.1 dpf 14 dpf or Single Cell Multiome ATAC + Gene Expression kit 12 mpf		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 5–10 min followed by mechanical and enzymatic dissociation by pipetting every 5 min in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS and incubated at 28.5 °C for 20–30 min or until full dissociation. Reaction was stopped by adding 6× stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 376 × g 5 min 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/mL penicillin and 0.05 mg/mL streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 μL 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′ Library and Gel Bead Kit v.3.1 dpf 14 dpf or Single Cell Multiome ATAC + Gene Expression kit 12 mpf		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP393251		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			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		United States	2022-08-21	Larval	Larval	Multi-tissue	Multi-system