run_metadata: 59871

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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
59871	SRR12055986	SRX8584378	SRS6875885	SRP268040	PRJNA640655	Emx2 defines bidirectional polarity of neuromasts by changing hair bundle orientation and not hair cell positions	GSE152859	Other	The bidirectional sensitivity of neuromasts to water flow in the zebrafish lateral line system is attributed to the opposite orientation of the hair bundles on top of sensory hair cells HC within a neuromast. post each HC precursor divides to form two nascent HCs HCs of the same bundle orientation are positioned on one side of the neuromast across from HCs with opposite bundle orientation. The transcription factor emx2 is expressed in only one of the sibling HCs. Loss or gain of function of emx2 in HCs causes unidirectional hair bundle orientation in neuromasts. It is not clear whether Emx2 is required specifically in establishing hair bundle orientation post HC formation or Emx2 has an earlier role in HC fate and/or positioning which indirectly changes hair bundle orientation. A phenomenon in which nascent sibling HCs exchange positions with each other has been postulated to be the mechanism for HCs to acquire their designated positions within the neuromast. We asked whether Emx2 is involved in positional acquisition of HCs within the neuromast. Using live imaging and our emx2 reporter we find that the HC rearrangement redefined as two processes named Rock & Roll are required for HCs to acquire their positions. Although Emx2 regulates the duration of the Rock and the frequency of Roll of nascent HCs it is not required for their positional acquisition. Instead Emx2 regulates the morphology of nascent HCs which facilitates the rearrangement process. Overall design: Single cell RNA sequencing on FACS sorted Hair Cells from zebrafish neuromast in 4dpf wild type larvae.		pubmed:33377867		scRNA seq zebrafish 4dpf neuromast hair cells	GSM4628143		tissue:P4 zebrafish hair cell\|genotype/variation:Tgmyo6b:RiboTag\|developmental stage:4 dpf\|cell type:Neuromast hair cells	scRNA seq zebrafish 4dpf neuromast hair cells	Basecalls performed using Illumina’s RTA 2.0.12. Sample demultiplexing alignment and gene counts were performed using the 10X Genomics CellRanger v3.0.1 pipeline using default settings. Secondary analysis was performed using SCANPY version 1.4.4. Genome build: not provided Supplementary files format and content: barcodes.tsv.gz: cell barcodes Supplementary files format and content: features.tsv.gz: gene names Supplementary files format and content: matrix.mtx.gz: expression matrix Supplementary files format and content: filtered feature bc matrix.h5: expression matrix in HDF5 format	P4 zebrafish hair cell	n/a	Zebrafish larvae Tgmyo6b: RiboTag at 4 dpf were dissected to remove the head which included the ear. Approximately 400 dissected bodies in batches of 50 were dissociated by adding 0.5 ml of 0.5% trypsin Gibco cat# 15400054 and triturated with 1 ml pipette tip for 30 seconds at 30°C. The dissociated cells were filtered with 40 μm strainer Pluriselect cat# 43 50040 50 and washed with PBS twice before adding DMEM containing 10% FBS and spun down by centrifugation at 700g rpm for 5 min at 4°C. Cells were resuspended and kept in DMEM before processing for FACS. scRNA seq was carried out with 10X Genomics single cell platform 10X Genomics Pleasanton CA. USA. Approximately 5000 live cells post FACS in a maximum volume of 34 microliters were loaded on a 10X Genomics Chromium Controller 10x Genomics. Chromium Single Cell three prime Library and Gel Bead Kit v2 10X Genomics was used for libraries preparation according to manufacturer’s instructions. Quality of the libraries was evaluated on a Fragment Analyzer instrument Agilent and sequenced on a NextSeq 500 sequencer Illumina with the following paired read lengths: 26 bp Read 1 8 bp I7 Index and 98 bp Read 2.	n/a	genotype/variation:Tgmyo6b:RiboTag\|developmental stage:4 dpf\|cell type:Neuromast hair cells	GSM4628143	GSM4628143: scRNA seq zebrafish 4dpf neuromast hair cells; Danio rerio; RNA Seq	GSM4628143		1	Zebrafish larvae Tgmyo6b: RiboTag at 4 dpf were dissected to remove the head which included the ear. Approximately 400 dissected bodies in batches of 50 were dissociated by adding 0.5 ml of 0.5% trypsin Gibco cat# 15400054 and triturated with 1 ml pipette tip for 30 seconds at 30°C. The dissociated cells were filtered with 40 μm strainer Pluriselect cat# 43 50040 50 and washed with PBS twice before adding DMEM containing 10% FBS and spun down by centrifugation at 700g rpm for 5 min at 4°C. Cells were resuspended and kept in DMEM before processing for FACS. scRNA seq was carried out with 10X Genomics single cell platform 10X Genomics Pleasanton CA. USA. Approximately 5000 live cells post FACS in a maximum volume of 34 microliters were loaded on a 10X Genomics Chromium Controller 10x Genomics. Chromium Single Cell three prime Library and Gel Bead Kit v2 10X Genomics was used for libraries preparation according to manufacturer's instructions. Quality of the libraries was evaluated on a Fragment Analyzer instrument Agilent and sequenced on a NextSeq 500 sequencer Illumina with the following paired read lengths: 26 bp Read 1 8 bp I7 Index and 98 bp Read 2.	GEO Accession:GSM4628143	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP268040		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=ZM4 S1 L002 I1 001.fastq.gz read2PairFiles=ZM4 S1 L002 R1 001.fastq.gz read3PairFiles=ZM4 S1 L002 R2 001.fastq.gz	ZM4_S1_L002_I1_001.fastq.gz ZM4_S1_L002_R1_001.fastq.gz ZM4_S1_L002_R2_001.fastq.gz	fastq fastq fastq	5480072136.0	41515698.0	GSM4628143 r2	0:8 1:26 2:98	A:1556115839;C:1180006462;G:1189325251;T:1553616619;N:1007965	8	26	98		1556115839	1180006462	1189325251	1553616619	1007965	SRX8584378	SRS6875885	SRA1089164	GEO	Molecular Biology, NIDCD	1	0.93811		0.12465		0.8227		0.42538		98		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2020-06-19	Larval	Larval	Multi-tissue	Multi-system