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Sample GSM6133973 Query DataSets for GSM6133973
Status Public on Nov 22, 2022
Title epicardial cells, scRNA-seq
Sample type SRA
 
Source name heart (ventricle)
Organism Danio rerio
Characteristics cell type: epicardial cells
tissue: heart (ventricle)
strain: EK (tcf21:nucEGFP)
age: 6 months
treatment: no treatment
Treatment protocol Heart amputation injury
Growth protocol Standard zebrafish breeding conditions
Extracted molecule total RNA
Extraction protocol Hearts were dissociated into single cells and the epicardial cells were isolated by FACS as described previously (PMID 26657776).
Library prep was performed according to the manufacturer’s instructions (single cell 3' v3 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, amplified by PCR and the appropriate sized fragments were selected 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.
Single Cell 3' GEM (Gel Bead Kit v3, Chromium Single Cell B Chip Kit)
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description 10x Genomics
Data processing Demultiplexing, barcoded processing, gene counting and aggregation done with Cell Ranger software v3.0.2
Sample integration (batch correction), expression value normalization, clustering, cell type annotation and so on were done with SCTransform, scater, and scran. For more details and the cell type annotation information, see https://github.com/abcwcm/Cao_Epicardium
Assembly: GRCz10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)
 
Submission date May 12, 2022
Last update date Nov 22, 2022
Contact name Friederike Dündar
E-mail(s) frd2007@med.cornell.edu
Organization name Weill Cornell Medicine
Department Physiology & Biophysics
Lab Applied Bioinformatics Core
Street address 1300 York Ave
City New York
State/province New York
ZIP/Postal code 10065
Country USA
 
Platform ID GPL21741
Series (1)
GSE202836 An injury-associated transient progenitor state in the epicardium mediates heart regeneration
Relations
BioSample SAMN28204117
SRA SRX15241415

Supplementary file Size Download File type/resource
GSM6133973_Ctrl-epi_barcodes.tsv.gz 27.2 Kb (ftp)(http) TSV
GSM6133973_Ctrl-epi_features.tsv.gz 301.2 Kb (ftp)(http) TSV
GSM6133973_Ctrl-epi_matrix.mtx.gz 22.7 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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