{"database": "metadata", "table": "run_metadata", "rows": [[59872, "SRR12055987", "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.", null, "pubmed:33377867", null, "scRNA seq zebrafish 4dpf  neuromast hair cells", "GSM4628143", null, "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\u2019s 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\u00a0were 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\u00b0C. The dissociated cells were filtered with 40 \u03bcm 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\u00b0C. 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\u2019s 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", null, "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\u00b0C. The dissociated cells were filtered with 40 \u03bcm 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\u00b0C. 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", null, "SRP268040", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=ZM4 S1 L003 I1 001.fastq.gz   read2PairFiles=ZM4 S1 L003 R1 001.fastq.gz   read3PairFiles=ZM4 S1 L003 R2 001.fastq.gz", "ZM4_S1_L003_I1_001.fastq.gz ZM4_S1_L003_R1_001.fastq.gz ZM4_S1_L003_R2_001.fastq.gz", "fastq fastq fastq", 5589739452.0, 42346511.0, "GSM4628143 r3", "0:8 1:26 2:98", "A:1586134828;C:1202961360;G:1215543516;T:1584245728;N:854020", 8, 26, 98, null, 1586134828, 1202961360, 1215543516, 1584245728, 854020, "SRX8584378", "SRS6875885", "SRA1089164", "GEO", "Molecular Biology, NIDCD", 1, 0.93749, null, 0.12195, null, 0.82286, null, 0.41205, null, 98, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-06-19", "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": ["59872"], "units": {}, "query_ms": 9.352260000014212}