|
| Status |
Public on Sep 01, 2020 |
| Title |
Patient #2-scRNA |
| Sample type |
SRA |
| |
|
| Source name |
Castration resistant prostate cancer (CRPC) tissue
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Castration resistant prostate cancer (CRPC)
Sex: Male
age: 82
tumor stage: T3
tissue: primary tumor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumor tissues were ressected by biopsy surgery and transported in DMEM/F12 medium on ice to the laboratory within an hour.
For scRNA-seq, the tissues were dissociated into single cells suspensions using digestion buffer (DMEM/F12 Medium+ 2 mg/ml of collagenase IV + 100 IU/ml DNase I), and single cell GEMs were generated by 10X genomics Chromium Controller. cDNA library was constructed following the manufacture’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
CellRanger was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 16bp 10x barcode and the 10bp UMI (bases 17-26).Index contains the sample barcode. Read 2 contains the cDNA information
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized median scaling values for each cell
|
| |
|
| Submission date |
Sep 23, 2019 |
| Last update date |
Sep 02, 2020 |
| Contact name |
Jia Wang |
| E-mail(s) |
wj860520@163.com
|
| Phone |
15821724825
|
| Organization name |
SJTU CHINA
|
| Street address |
Huashan Rd. 1940, build 3. Shanghai,
|
| City |
Shanghai |
| State/province |
Shanghai China |
| ZIP/Postal code |
200017 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE137829 |
Single-cell analysis supports a luminal-neuroendocrine transdifferentiation in human prostate cancer |
|
| Relations |
| BioSample |
SAMN12818420 |
| SRA |
SRX6887740 |
