{"database": "metadata", "table": "run_metadata", "rows": [[72589, "SRR22838795", "SRX18797976", "SRS16231609", "SRP414185", "PRJNA914428", "Single cell RNA sequencing scRNA seq of GFP+cells isolated from TgBrn3c:mGFP 6 days zebrafish with GFP expression in all hair cells.", "GSE221471", "Other", "Hair cells play key roles in hearing and balance  and hair cell loss would result in hearing loss or vestibular dysfunction. Zebrafsh  owing to their hair cell enriched organs  have been widely applied in hair cell related research worldwide. In this study  we analyzed the GFP+cells isolated from TgBrn3c:mGFP larvae with GFP expression in all hair cells using single cell RNA sequencing scRNA seq. Three subtypes of hair cells  namely macula hair cell MHC  crista hair cell CHC  and neuromast hair cell NHC  were characterized and validated by whole mount in situ hybridization analysis of marker genes. The hair cell scRNA seq data revealed hair cell specifc genes  including hearing loss genes that have been identifed in humans and novel genes potentially involved in hair cell formation and function. Overall design: Zebrafsh were maintained at 28.5 \u00b0C. The TgBrn3c:mGFP transgenic zebrafsh larvae at 6 dpf dpf were anesthetized and then treated with 0.25% trypsin to dissociate into single cells  which were divided into GFP positive and GFP negative cells through the fuorescent activated cell sorter  and the RNA expressed in GFP positive cells were then obtained and sequenced using the 10\u00d7Genomics platform", null, "pubmed:35753015", null, "GFP+  scRNAseq", "GSM6873779", null, "tissue:GFP+cells from TgBrn3c:mGFP zebrafish|cell type:hair cell|age:6 days", "GFP+  scRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: FASTQ", "GFP+cells from TgBrn3c:mGFP zebrafish", null, "The TgBrn3c:mGFP transgenic zebrafsh larvae at 6 dpf dpf were anesthetized and then treated with 0.25% trypsin to dissociate into single cells  which were divided into GFP positive and GFP negative cells through the fuorescent activated cell sorter  and the RNA expressed in GFP positive cells were then obtained and sequenced using the 10\u00d7Genomics platform. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "cell type:hair cell|age:6 days", "GSM6873779", "GSM6873779: GFP+  scRNAseq; Danio rerio; RNA Seq", "GSM6873779 r1", "GSM6873779", "1", "The TgBrn3c:mGFP transgenic zebrafsh larvae at 6 dpf dpf were anesthetized and then treated with 0.25% trypsin to dissociate into single cells  which were divided into GFP positive and GFP negative cells through the fuorescent activated cell sorter  and the RNA expressed in GFP positive cells were then obtained and sequenced using the 10\u00d7Genomics platform. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP414185", null, null, "brn3c6dpf_R1.fq.gz brn3c6dpf_R2.fq.gz", "fastq fastq", 201407352000.0, 671357840.0, "GSM6873779 r1", "0:150 1:150", "A:47653455771;C:37496314066;G:61110504409;T:55144480424;N:2597330", 150, 150, null, null, 47653455771, 37496314066, 61110504409, 55144480424, 2597330, "SRX18797976", "SRS16231609", "SRA1563296", "Nantong University", "Nantong University", 2, 0.0, 0.90004, 0.0, 0.18176, 1.0, 0.76794, null, 0.55523, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-12-20", "Larval", "Larval", "Undetermined", "Undetermined"]], "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": ["72589"], "units": {}, "query_ms": 14.120021995040588}