run_metadata: 41687
This data as json
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| 41687 | SRR5120132 | SRX2435375 | SRS1870362 | SRP095338 | PRJNA358049 | Transcriptomic Analysis of Adult Zebrafish Inner Ear Hair Cells | GSE92559 | Transcriptome Analysis | To understand the basic biological property of hair cells HCs from lower vertebrates we examined transcriptomes of adult zebrafish HCs. GFP labeled HCs were isolated from the utricle saccule and lagena the three inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. 2 000 HCs and 2 000 non sensory cells from the inner ear were individually collected by suction pipet technique. RNA sequencing was performed and the resulting sequences were mapped analyzed and compared. Comparisons allow us to identify enriched genes in HCs which may underlie HC specialization. Overall design: Examination of transcriptomes of adult zebrafish inner ear hair cells and surrounding cells individually collected and sorted using pou4f3 promoter driven GFP marking hair cells. | pubmed:29406519 | GFP+ Hair Cells Biological Replicate 2 Technical 2 | GSM2432253 | tissue:2 000 Inner ear hair cells|cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t | GFP+ Hair Cells Biological Replicate 2 Technical 2 | CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Expression data was exported from CLC Genomics Workbench in the form of Microsoft Excel Spreadsheets. | 2 000 Inner ear hair cells | Qiagen miRNeasy mini plus kit Clontech Smart Seq | cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t | GSM2432253 | GSM2432253: GFP+ Hair Cells Biological Replicate 2 Technical 2; Danio rerio; RNA Seq | GSM2432253 | 1 | Qiagen miRNeasy mini plus kit Clontech Smart Seq | GEO Accession:GSM2432253 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP095338 | zhc_AGGCAGAA-_L002_R1_001.fastq.gz | fastq | 6093457260.0 | 60331260.0 | GSM2432253 r1 | 0:101 | A:1471320441;C:1109536878;G:1119505740;T:1436533942;N:956560259 | 101 | 1471320441 | 1109536878 | 1119505740 | 1436533942 | 956560259 | SRX2435375 | SRS1870362 | SRA505331 | GEO | Department of Biomedical Sciences, Creighton University | 1 | 0.64117 | 0.14727 | 0.78145 | 0.5689 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | United States | 2016-12-19 | Adult | Adult | Ear | Sensory System |