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| Status |
Public on Feb 16, 2024 |
| Title |
C57/B6 mice, pooled, cardiac cell suspension |
| Sample type |
SRA |
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| Source name |
Heart
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| Organism |
Mus musculus |
| Characteristics |
tissue: Heart
strain: C57/B6
cell type: Cardiac CD45+CD31- (leukocytes), CD45-CD31- (resident mesenchymal cells), and CD45-CD31+ (endothelial cells)
genotype: Wild Type
treatment: None
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
A single cell suspension was made from fresh cardiac tissue obtained from AC8 overexpressing mice and littermate controls, An equal number of FACS-sorted CD45+CD31- (leukocytes), CD45-CD31- (resident mesenchymal cells), and CD45-CD31+ (endothelial cells) cells were mixed and processed to generate single-cell cDNA libraries.
Using the 10X Genomics platform Cells were sequenced at a target read depth of 75,000 reads/cell using a Novaseq 6000 sequencer (Illumina). Single-cell counts were generated from unaligned reads by sequence alignment and de-multiplexing using Cell Ranger from 10x Genomics.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
NA
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| Data processing |
Cells were sequenced at a target read depth of 75,000 reads/cell using a NovaSeq 6000 sequencer (Illumina). Single-cell counts were generated from unaligned reads by sequence alignment and de-multiplexing using Cell Ranger from 10x Genomics.
Single-cell counts were generated from unaligned reads by sequence alignment and de-multiplexing using Cell Ranger from 10x Genomics. Post-alignment QA/QC performed using single-cell counts suggested that none of the 10,667 cells expressed mitochondrial genes at greater than 5 percent of their total gene expression; cells were not excluded from further analysis.
Normalized cell counts were generated using filter exclude features where value <= 0.0 in at least 99.9 % of the cells, CPM (counts per million), the scale factor of 10000, and log transformation.
Of the 22,441 genes, 13,331 passed these criteria, and the remaining 9,110 were filtered out.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
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| Submission date |
Feb 16, 2024 |
| Last update date |
Feb 16, 2024 |
| Contact name |
Supriyo De |
| Organization name |
NIA-IRP, NIH
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| Department |
Laboratory of Genetics and Genomics
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| Lab |
Computational Biology & Genomics Core
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| Street address |
251 Bayview Blvd
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| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21224 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE255916 |
Cardiomyocyte-specific adenylyl cyclase type-8 overexpression induces cell-autonomous activation of RelA and non-cell-autonomous myocardial and systemic inflammation |
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| Relations |
| BioSample |
SAMN39960523 |
| SRA |
SRX23640266 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8082522_WT_barcodes.tsv.gz |
12.7 Kb |
(ftp)(http) |
TSV |
| GSM8082522_WT_features.tsv.gz |
58.8 Kb |
(ftp)(http) |
TSV |
| GSM8082522_WT_matrix.mtx.gz |
11.4 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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