|
| Status |
Public on Jan 14, 2022 |
| Title |
C4-2-tet-shRB-DMSO_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
C4-2 cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: prostate cancer cell line
medium condition: In RPMI 1640 medium with 5% charcoal-stripped FBS (CSS)
cell line: C4-2-tet-shRB
treatment: untreated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Rneasy Mini Kit (QIAGEN) following manufacturer’s protocol.
RNA-seq libraries of both C4-2-tet-shRB (DHT) and LNCaP cells were performed by using TruSeq® Strnd Total RNA LT (Illumina). RNA-seq libraries of VCaP cells and C4-2-tet-shRB (GSK) were performed by using TruSeq® Stranded mRNA (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
C42shRB_Dox_GSK_count_table.txt.gz
C42shRB_2_S2_L001
|
| Data processing |
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were aligned to the human reference genome (hg19) using STAR (version 2.7.2) followed by counting with featureCounts (version 1.6.4) from GRCh37 Ensembl reference.
Genome_build: hg19
Supplementary_files_format_and_content: txt file forraw counts of sequence reads
|
| |
|
| Submission date |
Jun 08, 2021 |
| Last update date |
Jan 14, 2022 |
| Contact name |
Changmeng Cai |
| E-mail(s) |
changmeng.cai@umb.edu
|
| Organization name |
University of Massachusetts Boston
|
| Street address |
100 William T Morrissey Blvd
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02125 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE176403 |
RB1 loss promotes a noncanonical activator function of LSD1 and sensitizes castration-resistant prostate cancer to LSD1 inhibition [RNA-seq] |
| GSE176404 |
RB1 loss promotes a noncanonical activator function of LSD1 and sensitizes castration-resistant prostate cancer to LSD1 inhibition |
|
| Relations |
| BioSample |
SAMN19608179 |
| SRA |
SRX11094495 |
