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Status |
Public on Sep 26, 2013 |
Title |
MDA-MB-231,shCtrl,Hypoxia+Glucose deprivation,biological rep 1 |
Sample type |
RNA |
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Source name |
MDA-MB-231 cell line under treated condition without XBP1 knockdown
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Organism |
Homo sapiens |
Characteristics |
cell line: MDA-MB-231
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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.
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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).
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted by using RNeasy mini kit with on column DNase digestion (QIAGEN).
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Label |
biotin
|
Label protocol |
Biotin labeled cRNA was prepared from 1 ug of total RNA according to the standard Affymetrix protocol.
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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.
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Scan protocol |
Standard Affymetrix protocol.
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Description |
Gene expression data from MDA-MB-231 cell line under treated condition without XBP1 knockdown
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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.
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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
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Organization name |
Dana-Farber Cancer Institute, Harvard School of Public Health
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Department |
Department of Biostatistics and Computational Biology
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Street address |
450 Brookline Avenue, CLS 11007
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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. |
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