|
| Status |
Public on Nov 14, 2022 |
| Title |
C57BL/6J mouse rep3 - Ventral Lobe |
| Sample type |
SRA |
| |
|
| Source name |
prostate
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: prostate
prostate lobe: ventral
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Individual prostate lobes were dissected from 6 month old mice and single-cell RNA-sequencing libraries for each lobe were prepared separately.
Libraries for scRNA-seq were prepared using the 10x Genomics Chromium Single Cell 3’ Library and Gel bead Kit V2 (CG00052_RevF).
single-cell RNA-sequencing 10X Genomics platform
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
single cell RNA-seq
|
| Data processing |
The cDNA libraries were sequenced (150 bp paired-end) on the Illumina HiSeqX platform.
Each sequenced library was demultiplexed to FASTQ files using Cell Ranger (10x Genomics).
Cell Ranger (version 2.2.0) count pipeline was used to align reads to the mm10 mouse transcriptome and create a gene by cell count matrix.
Cell Ranger (version 2.2.0) aggr pipeline was used to aggregate the counts across all the cDNA libraries generated for each mouse prostate lobe.
Genome_build: mm10
Supplementary_files_format_and_content: For each library preparation includes the following files: matrix.mtx, barcodes.tsv, genes.tsv
|
| |
|
| Submission date |
Jan 28, 2021 |
| Last update date |
Nov 16, 2022 |
| Contact name |
Mindy Kim Graham |
| E-mail(s) |
[email protected]
|
| Phone |
4104046391
|
| Organization name |
Northwestern University Feinberg School of Medicine
|
| Department |
Urology
|
| Street address |
303 E. Superior Street Chicago
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE165741 |
Single cell atlas of epithelial and stromal cell heterogeneity by lobe and strain in the mouse prostate |
|
| Relations |
| BioSample |
SAMN17619686 |
| SRA |
SRX9973309 |
