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| Status |
Public on Nov 22, 2022 |
| Title |
7-days post amputation, epicardial cells, scRNA-seq |
| Sample type |
SRA |
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| Source name |
heart (ventricle)
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| Organism |
Danio rerio |
| Characteristics |
cell type: epicardial cells
tissue: heart (ventricle)
strain: EK (tcf21:nucEGFP)
age: 6 months
treatment: partial ventricular amputation
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| Treatment protocol |
Heart amputation injury
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| Growth protocol |
Standard zebrafish breeding conditions
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| 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)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
10x Genomics
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| 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)
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| Submission date |
May 12, 2022 |
| Last update date |
Nov 22, 2022 |
| Contact name |
Friederike Dündar |
| E-mail(s) |
frd2007@med.cornell.edu
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| Organization name |
Weill Cornell Medicine
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| Department |
Physiology & Biophysics
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| Lab |
Applied Bioinformatics Core
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| Street address |
1300 York Ave
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL21741 |
| Series (1) |
| GSE202836 |
An injury-associated transient progenitor state in the epicardium mediates heart regeneration |
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| Relations |
| BioSample |
SAMN28204118 |
| SRA |
SRX15241414 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6133972_7dpa-epi_barcodes.tsv.gz |
35.5 Kb |
(ftp)(http) |
TSV |
| GSM6133972_7dpa-epi_features.tsv.gz |
301.2 Kb |
(ftp)(http) |
TSV |
| GSM6133972_7dpa-epi_matrix.mtx.gz |
35.3 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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