|
| Status |
Public on Jun 24, 2019 |
| Title |
DMSO-rep2 |
| Sample type |
SRA |
| |
|
| Source name |
prostate cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: prostate cancer cell line
cell line: LNCaP
treatment: DMSO
|
| Treatment protocol |
LNCaP cells were treated with vehicle control or 10 uM of each PARP inhibitors for 24 hours. And for gene knockdown experiments, LNCaP cells were transfected with indicated siRNA for 72 hours.
|
| Growth protocol |
LNCaP cells were maintaned in RPMI 1640 medium supplemented with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
RNA-Seq libraries were prepared using NEBNext Ultra RNA Library Prep Kit (New England BioLabs; E7530) according to the manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file: PARPi.csv
|
| Data processing |
bcl2fastq v2.18 used for base calling with default parameters
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Tophat2 (v2.1.0) with default setting.
Raw counts (counts per million, cpm) were generated by HTseq (v0.6.1) using the union method with default parameters. Genes that had at least 1 read per million in at least half of the samples were kept for further analysis.
The number of reads were normalized using the EdgeR package (3.12.0) for R.
Genome_build: hg19
Supplementary_files_format_and_content: Comma-delimited csv files include normalized counts per million for each Sample
|
| |
|
| Submission date |
May 10, 2018 |
| Last update date |
Jun 24, 2019 |
| Contact name |
Li Jia |
| E-mail(s) |
ljia@bwh.harvard.edu
|
| Organization name |
Brigham and Women's Hospital
|
| Department |
Surgery
|
| Lab |
Thorn 1529
|
| Street address |
20 Shattuck Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE114273 |
Gene expression profilings for prostate cancer cells after inhibition of PARP1 or PARP2 using pharmaceutical or siRNA-based approaches |
| GSE114275 |
Selective Targeting of PARP2 Inhibits Androgen Receptor Signaling and Prostate Cancer Growth Through Disruption of FOXA1 Function |
|
| Relations |
| BioSample |
SAMN09104576 |
| SRA |
SRX4062862 |
