|
| Status |
Public on Mar 16, 2013 |
| Title |
MDA-MB-453 siCtrl-DHT |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-453 cells transfected with control siRNA followed by DHT treatment
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-453
cell type: breast cancer
|
| Treatment protocol |
The MDA-MB-453 cells were transfected with siRNA and then grown in the phenol red-free medium supplemented with 5% charcoal/dextran-treated fetal bovine serum for 48 h, followed by treatment of vehicle or 10 nM DHT for 6 h.
|
| Growth protocol |
The MDA-MB-453 cells were maintained in DMEM supplemented with 10% fetal bovinw serum at 37oC incubator
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was prepared using RNeasy Mini Kit (Qiagen) according to the manufacturer's instruction. The polyadenylated mRNA was purified using oligo d(T)25 beads (NEB).
1 ng of mRNA was used for library preparation using Encore Complete RNA-seq kit (NuGEN) according to the manufacturer's instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA-seq
|
| Data processing |
Basecalls performed using CASAVA version 1.9
RNA-seq reads were aligned to hg19 using TopHat v2.0.4
Differential expression was characterized using Cuffdiff (version 0.0.5).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each condition
|
| |
|
| Submission date |
Mar 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Yiwen Chen |
| E-mail(s) |
ychen26@mdanderson.org
|
| Organization name |
University of Texas MD Anderson Cancer Center
|
| Department |
Bioinformatics and Computational Biology
|
| Lab |
Yiwen Chen
|
| Street address |
1400 Pressler Street
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE45202 |
Amplitude modulation of androgen signaling by c-MYC [RNA-Seq] |
| GSE45203 |
Amplitude modulation of androgen signaling by c-MYC |
|
| Relations |
| SRA |
SRX250098 |
| BioSample |
SAMN01978927 |
