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| Status |
Public on Nov 18, 2021 |
| Title |
CND_cKit_P_DDR2_P |
| Sample type |
SRA |
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| Source name |
CND_cKit_P_DDR2_P
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| Organism |
Mus musculus |
| Characteristics |
cell type: cardiac interstitial cells
cell subtype: cKit+/DDR2+/CD45+
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Briefly, heart samples were mechanically minced into 1-mm3 pieces and digested in collagenase II (150 U mg/mL, Worthington, LS004174) followed by brief low-speed (850 rpm for 2 minutes) centrifugation to remove cardiomyocytes and tissue debris. After removing cardiomyocytes by cell strainers, cKit +/-DDR2 +/- cardiac interstitial cells were obtained by FACS sorting with cKit antibody and DDR2 antibody and surface depletion of CD45 in the double positive population.
The Chromium Single Cell 3' Library & Gel Bead Kit v3.1 (PN- 1000268), Chromium Single Cell 3' Chip G kit v2 (PN-1000120) and Dual Index Kit TT Set A, (PN-1000215) were used according to the manufacturers instructions in the Chromium Single Cell 3' Reagents Kits V3.1 User Guide.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The raw data was processed with the Cell Ranger pipeline (10X Genomics; version 3.0.1). Reads were aligned to the 10x mouse genome mm10.
Preparations derived from cell surface sorting strategy yielded 12286 barcoded cells for analysis, from which 3603 corresponded to cKit+DDR2-, 2755 corresponded to cKit-DDR2+, 4546 corresponded to cKit+DDR2+, and 1382 corresponded to cKit+DDR2+CD45-. Final removal of unwanted sources of variation and batch effect corrections was performed using Seurat R Package (v4.0.4)
Sequenced reads were aligned to the human reference genome mm-10
Genome_build: mm-10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: comma separated values of digital expression matrix; rows are genes; columns are cells with cell barcode
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| Submission date |
Nov 15, 2021 |
| Last update date |
Nov 18, 2021 |
| Contact name |
Oscar E Echeagaray |
| E-mail(s) |
oscar.echeagaray@gmail.com
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| Organization name |
San Diego State University
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| Department |
Biology
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| Lab |
Sussman Lab
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| Street address |
5500 Campanile Drive
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| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92182 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE188804 |
"Youthful" Phenotype of c-Kit+ Cardiac Fibroblasts [DDR2_cKit] |
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| Relations |
| BioSample |
SAMN23150732 |
| SRA |
SRX13138422 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5690362_CND_cKit_P_DDR2_P.txt.gz |
95.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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