|
| Status |
Public on Sep 26, 2013 |
| Title |
T47D,shXBP1,Hypoxia+Glucose deprivation,biological rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
T47D cell line under treated condition with XBP1 knockdown
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: T47D
|
| Treatment protocol |
For all hypoxia experiments, cells were maintained in an anaerobic chamber (Coy laboratory) with 0.1% O2. For glucose deprivation experiments, cells were maintained in DMEM without glucose medium (Gibco) with 10% FBS (Gibco) and 50 units/ml of penicillin/streptomycin. MDA-MB-231/T47D cells infected with control shRNA or XBP1 shRNA lentiviruses grown in glucose free medium were treated in 0.1% O2 in a hypoxia chamber for 24h.
|
| Growth protocol |
All breast cancer cells were cultured according to Neve et al (Cancer Cell 2006). Following retroviral or lentiviral infection, cells were maintained in the presence of puromycin (2 ug/ml) (Sigma).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by using RNeasy mini kit with on column DNase digestion (QIAGEN).
|
| Label |
biotin
|
| Label protocol |
Biotin labeled cRNA was prepared from 1 ug of total RNA according to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
The biotin labeled cRNA was fragmented, and hybridized to Affymetrix human U133 plus 2.0 expression array according to the standard Affymetrix protocol.
|
| Scan protocol |
Standard Affymetrix protocol.
|
| Description |
Gene expression data from T47D cell line under treated condition with XBP1 knockdown
|
| Data processing |
Raw gene expression values were obtained using Affymetrix GeneChip software and further analyzed using the Robust Multichip Average (RMA) algorithm in the Bioconductor affy package 1.30.0.
|
| |
|
| Submission date |
Aug 18, 2013 |
| Last update date |
Sep 26, 2013 |
| Contact name |
Xiaole Shirley Liu |
| E-mail(s) |
xsliu.dfci@gmail.com
|
| Phone |
(617) 632-2472
|
| Organization name |
Dana-Farber Cancer Institute, Harvard School of Public Health
|
| Department |
Department of Biostatistics and Computational Biology
|
| Street address |
450 Brookline Avenue, CLS 11007
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215-5450 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE49953 |
Expression data from two breast cancer cell lines |
| GSE49955 |
Genome-wide maps of XBP1 binding sites in different breast cancer cell lines. |
|
