|
| Status |
Public on Dec 12, 2023 |
| Title |
Basal population from Patient 2397 [BRCA2-Basal-2397] |
| Sample type |
SRA |
| |
|
| Source name |
Mammary gland
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Mammary gland
genotype: BRCA2
cell type: Basal
patient: 2397
Sex: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiagen's miRNeasy kit and Dnase treated.
A minimum of 10 ng of total RNA was used to construct libraries following Ilumina's recommended protocol for TruSeq RNA Library Prep Kit v2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
BRCA2-Basal-2397
|
| Data processing |
Libraries were sequenced on an Illumina NextSeq 500.
Reads were aligned to the human genome hg38 by the align function of the Rsubread software tool version 1.33.5.
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's inbuilt RefSeq annotation.
Assembly: hg38
Supplementary files format and content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.
|
| |
|
| Submission date |
May 24, 2023 |
| Last update date |
Dec 12, 2023 |
| Contact name |
Yunshun Chen |
| E-mail(s) |
[email protected]
|
| Organization name |
Walter and Eliza Hall Institute of Medical Research
|
| Department |
ACRF Cancer Biology and Stem Cells
|
| Lab |
Chen
|
| Street address |
1G Royal Parade
|
| City |
Parkville |
| State/province |
VIC |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE233307 |
RNA-sequencing of epithelial cell subpopulations from human breast tissue [RNASeq_1_BRCA2] |
| GSE233505 |
Identification of aberrant luminal progenitors and mTORC1 as a potential chemoprevention target in BRCA2 mutation carriers |
|
