|
| Status |
Public on Jul 21, 2017 |
| Title |
EV JQ1 RNASeq rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Prostate cells_EV_JQ1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: C4-2
genotype: wildtype
passages: 25-28
|
| Treatment protocol |
C4-2 stable cells were treated with 1 µm JQ1 for 24 hours.
|
| Growth protocol |
C4-2 stable cells were routinely generated by regular cultures (typically 2–3 × 10^6 cells into a T75 flask) on uncoated plastic in RPMI1640 medium (Gibco, USA) supplemented with Charcoal stripped serum (Gibco, USA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted using RNeasy Mini Kit.
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Clinic sequence core using the pipeline Cassava 1.7
Reads aligned to human reference genome (hg19) using Tophat (v2.0.6) with default parameters
Raw count and RPKM were calcualted using RSeQC (v2.3.6) with parameters "-d '1+-,1-+,2++,2--' -r hg19.refseq.bed12"
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bigWig file
|
| |
|
| Submission date |
Feb 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhenqing Ye |
| E-mail(s) |
[email protected]
|
| Organization name |
UT Health San Antonio
|
| Department |
6Department of Population Health Sciences
|
| Street address |
8403 Floyd Curl Dr
|
| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE78213 |
SPOP mutation confers intrinsic BET inhibitor resistance in prostate cancer (BRD4_JQ1_RNA-seq) |
| GSE88872 |
SPOP mutation confers intrinsic BET inhibitor resistance in prostate cancer |
|
| Relations |
| BioSample |
SAMN04510494 |
| SRA |
SRX1597609 |
