|
| Status |
Public on Oct 09, 2009 |
| Title |
HepG2 hypoxia (0.5%O2) treatment 0h, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
HepG2 hypoxia (0.5%O2) treatment 0h, biological rep2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2 hepatoma
stress: normoxia
time: control
|
| Treatment protocol |
HepG2 hepatoma, U87 glioma, and MDA-MB231 breast cancer cells were collected under normoxic conditions (~19% O2, 0 hours) and after 4, 8 and 12 hours of hypoxia treatment (0.5% O2).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Accordinging to standard Affymetrix protocol at DFCI Microarray Core.
|
| |
|
| Hybridization protocol |
Accordinging to standard Affymetrix protocol at DFCI Microarray Core.
|
| Scan protocol |
Accordinging to standard Affymetrix protocol at DFCI Microarray Core.
|
| Description |
HepG2_H0-2
|
| Data processing |
We used GcRMA module on Bioconductor with most updated custom CDF (CDF: Hs133P_Hs_REFSEQ_10) (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/cdfreadme.htm) to normalize the microarrays, and MAS5 to get present/absent calls. LIMMA was used to identify probe sets whose expression levels were significantly changed after 4, 8, or 12 hours of hypoxia relative to the normoxic signal. The MAS5 present/absent calls were assigned values of absent=0, marginal=0.5, or present=1. For each probe set, the sum of triplicate samples was partitioned into “present” if sum≥2, and “absent” if sum<2.
|
| |
|
| Submission date |
Oct 09, 2009 |
| Last update date |
Oct 09, 2009 |
| Contact name |
Xiaobo Xia |
| E-mail(s) |
Xiaobo_Xia@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Pediatric Oncology
|
| Lab |
Dr. Andrew Kung
|
| Street address |
44 Binney St, Mayer 649
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL9419 |
| Series (2) |
| GSE18494 |
Expression profiling of hypoxic HepG2 hepatoma, U87 glioma, and MDA-MB231 breast cancer cells: time course |
| GSE18505 |
HepG2 hepatoma and U87 glioma cells: transcriptomic and genomic analyses |
|
