|
| Status |
Public on Jul 13, 2023 |
| Title |
Mouse_HOMER_LV_4 |
| Sample type |
SRA |
| |
|
| Source name |
left vetricular tissue
|
| Organism |
Mus musculus |
| Characteristics |
Sex: male
tissue: left vetricular tissue
cell type: non-cardiomyocytes
group: HOMER
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Viable (DAPI-), metabolically active (Calcein+), nucleated (VDR+), single cells were FACS-purified from digested left ventricular tissues, and subsequently loaded on a 10X Genomics Chromium Single Cell B chip as outlined by the 10X Genomics Chromium Single Cell 3’ Reagent Kits v3 user guide.
Libraries were prepared as outlined by the 10X Genomics Chromium Single Cell 3’ Reagent Kits v3 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics). Constructed libraries were validated and quantified with the Agilent High Sensitivity DNA chip and by real-time qPCR, and subsequently sequenced on an Illumina NextSeq 500 in high-output mode.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
FACS-purfied left ventricular non-cardiomyocytes
|
| Data processing |
10X Genomics Cell Ranger ( version 3.0.2) was used to demultiplex raw base call files from the Illumina sequencer to produce fastq files.
Cell Ranger was used to align the reads, filter out background-associated-barcodes, count barcodes and UMIs, and generate gene-barcode matrices.
Assembly: mm10
Supplementary files format and content: Count matrices in Market Exchange Format for sparse matrices and gzipped tsv files for genes and barcodes corresponding to row and column indices of the count matrices
|
| |
|
| Submission date |
Feb 20, 2023 |
| Last update date |
Jul 13, 2023 |
| Contact name |
I-Hsiu Lee |
| Organization name |
Mass General Hospital/Harvard University
|
| Department |
Center for Systems Biology
|
| Street address |
185 Cambridge Street
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE224959 |
The role of stromal and immune cells in atrial disease |
| GSE225671 |
The role of stromal and immune cells in atrial disease [III] |
|
| Relations |
| BioSample |
SAMN33386166 |
| SRA |
SRX19447775 |
