|
| Status |
Public on May 14, 2014 |
| Title |
Hep3B Cells 1.5% Oxygen, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Hep3B cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Hep3B Hepatoma Cell Line
oxygen concentration: 1.5% (H4)
|
| Treatment protocol |
Prior to hypoxia treatment, 25 mM HEPES was added to growth media and cells were incubated under normoxia (21% O2) or hypoxia (1.5% O2) for 12-16 hrs.
|
| Growth protocol |
Hep3B cells were cultured at 30-50% confluency in MEM/EBSS (Hyclone) containing 10% FBS, 2 mM L-glutamine, 1 mM sodium pyruvate, 100,000 units/L Penicillin/Streptomycin, 1.5 g/L sodium bicarbonate, and 1X non-essential amino acids (NEAA). Prior to hypoxia treatment, 25 mM HEPES was added to growth media and cells were incubated under normoxia (21% O2) or hypoxia (1.5% O2) for 12-16 hrs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using a Qiagen RNeasy Plus RNA extraction kit.
|
| Label |
biotin
|
| Label protocol |
Standard Affymetrix protocol
|
| |
|
| Hybridization protocol |
Standard Affymetrix protocol
|
| Scan protocol |
Standard Affymetrix protocol
|
| Description |
Hypoxia:hu_4_H2.CEL
|
| Data processing |
To assess alternative splicing events, raw CEL files were imported into Altanalyze (version 2.0.7) using RMA normalization through Affymetrix Power Tools and Alternative Splicing was summarized at the exon level for Alternative Exons, filtering for probes with DABG P<0.05 or expression below 1. FIRMA and Splicing Index was calculated by comparing the hypoxia samples (H) to the normoxia (N) controls.
HuEx-1_0-st-v2.r2.pgf
|
| |
|
| Submission date |
May 13, 2014 |
| Last update date |
May 14, 2014 |
| Contact name |
Cheng-Jun Hu |
| E-mail(s) |
cheng-jun.hu@ucdenver.edu
|
| Phone |
3037244574
|
| Organization name |
University of Colorado Denver
|
| Department |
Craniofacial Biology
|
| Lab |
Cheng-Jun Hu
|
| Street address |
E. 17th Ave
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL10520 |
| Series (1) |
| GSE57613 |
Hypoxia regulates alternative splicing of HIF and non-HIF target genes |
|
