run_metadata: 68951

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
68951	SRR18254620	SRX14395875	SRS12205981	SRP362863	PRJNA813520	Single cell transcriptomic profiling of gill cells of zebrafish Danio rerio exposed to normoxia and hypoxia	GSE198044	Transcriptome Analysis	The fish gill is a multifunctional organ containing a variety of specialized cells including respiratory chemoreceptors neuroepithelial cells NECs. Although the structure function and development of the gill have been studied extensively transcriptomic profiling of individual gill cells is lacking. Using the 10x Genomics Chromium technology we conducted a single transcriptomic study of cells from distal gill filament of ETvmat2:GFP zebrafish acclimated to 14 days of normoxia and hypoxia. Overall approximately 13 000 cells were sequenced with an average depth of 27 000 reads per cell. We identified 16 cell clusters in the gill including NECs neurons pavement cells endothelial cells and mitochondrion rich cells. NECs were identified through expression of vmat2 encoding vesicular monoamine transporter and showed highly differential expressions of tph1a sv2 and mitochondrial proteins implicated in O2 sensing. Differential gene expression analysis showed a shift in transcriptome in NECs following 14 days of acclimation to hypoxia. This study presents a comprehensive cell atlas for the zebrafish gill and provides a framework for future investigations of molecular biology and physiology in gills. Overall design: single cell RNA sequencing of isolated cells from distal gill filament from ETvmat2:GFP zebrafish acclimated to 14 days of normoxia and hypoxia.		pubmed:35710785		Gill tissue combined normoxia and hypoxia	GSM5936455		tissue:Distal gill filament\|genotype:ETvmat2:GFP\|treatment:normoxia and hypoxia samples combined	Gill tissue combined normoxia and hypoxia	Raw sequencing data were processed using the CellRanger v5.0.0 10X Genomics software with default paramters and a custom reference built from the Ensembl release 101 Danio rerio annotation built on the GRCz11 assembly plus an EGFP sequence. FASTQ files were generated using the Cell Ranger mkfastq function and cells were counted using Cell Ranger count. MULTIseq barcodes were processed using the deMULTIplex pipeline to associate cells with their sample of origin Filtered count matrices filtered feature bc matrix were loaded into R as a sparse matrix with the Seurat::Read10X function. Sample barcodes were demultipliexed using the standard deMULTIplex workflow https://github.com/chris mcginnis ucsf/MULTI seq. Data were processed with Seurat to count the percentage of mitochondrial UMIs per cell and data were filtered to retain only cells with <45% mitochondrial UMIs and >100 detected genes. Cell doublets were removed with DoubletFinder assuming a 7.5% doublet formation rate. Raw counts were normalized to depth per 10 000 reads and log normalized. Variable genes were identified and their values Z scaled. The three libraries were merged into a single Seurat object. Dimensional reduction was performed with PCA and cells were projected into UMAP space for visualization; cell clusters were identified with the Seurat FindClusters function. Fastq files from two NextSeq 500 runs were concatenated into a single file for each read for each library. Fastq files are included for both single cell GEX data SC files and MULTI seq barcodes barcode files Genome build: GRCz11 Supplementary files format and content: RDS serialized R object containing data processed with seurat for all three libraries.	Distal gill filament		Distal filaments of gills were trimmed off trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell 3’ Assay. cDNA synthesis and library construction were carried out according to the manufacturer’s protocol and the resulting cDNA libraries were amplified using PCR. Single cell samples were sequenced on a NextSeq 500 sequencing system.		genotype:ETvmat2:GFP\|treatment:normoxia and hypoxia samples combined	GSM5936455	GSM5936455: Gill tissue combined normoxia and hypoxia; Danio rerio; RNA Seq	GSM5936455 r1	GSM5936455	1	Distal filaments of gills were trimmed off trypsinized and mechanically dissociated to isolate individual cells. Cells were processed with the standard Chromium Single Cell three prime Assay. cDNA synthesis and library construction were carried out according to the manufacturer's protocol and the resulting cDNA libraries were amplified using PCR. Single cell samples were sequenced on a NextSeq 500 sequencing system.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP362863		loader:fastq load.py	HN_Barcode_I1.fastq.gz HN_Barcode_R1.fastq.gz HN_Barcode_R2.fastq.gz	fastq fastq fastq	1029719145.0	11315595.0	GSM5936455 r2	0:8 1:28 2:55	A:465061193;C:46504427;G:62910508;T:47445353;N:436244	8	28	55		465061193	46504427	62910508	47445353	436244	SRX14395875	SRS12205981	SRA1392368	Cellular and Molecular Medicine, Bioinformatics, Ottawa Hospital Research Institute, Ontario Genomics Innovation Centre (OGIC)	Cellular and Molecular Medicine, Bioinformatics, Ottawa Hospital Research Institute, Ontario Genomics Innovation Centre (OGIC)	1	0.56414		0.53829		0.99977		0.11976		55		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		Canada	2022-03-07	Undetermined	Undetermined	Gill	Respiratory System