|
| Status |
Public on Oct 12, 2012 |
| Title |
cell line HT29 8 hour hypoxia timepoint |
| Sample type |
RNA |
| |
|
| Source name |
cancer cell line (HT29)
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: hypoxia
time point (hr): 8
|
| Treatment protocol |
The cells were then transferred to a hypoxic chamber (MACS VA500, Don Whitley Scientific, West-Yorkshire, UK) with atmosphere composition of 5% H2, 5% CO2, 0.0% O2 and residual N2. Cells were exposed to normoxia (time-point 0 hours) and different times of severe hypoxia (1, 2, 4, 8, 12, 16 and 24 hours, respectively).
|
| Growth protocol |
Exponentially growing prostate (DU145), colon (HT29) and breast (MCF7) carcinoma cells were seeded on glass dishes in McCoy, DMEM or RPMI media, respectively with 10% FCS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated for each time-point using RNeasy (Qiagen, Hilden, Germany) following manufacturer’s specifications. RNA quantity/quality was determined using an ND-1000 spectrometer (NanoDrop Technologies, Wilmington, DE) and RNA Nano LabChip kit on the 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA).
|
| Label |
biotin
|
| Label protocol |
Twenty ng pooled RNA was processed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA) for 2-cycle amplification and samples were hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips.
|
| |
|
| Hybridization protocol |
standard Affymetrix protocol
|
| Scan protocol |
standard Affymetrix protocol
|
| Description |
The platform is identical to GPL570 but a custom CDF environment was used to extract data [Brainarray Version 13.0.0, HGU133Plus2_Hs_ENTREZG]. CDF and other files can be downloaded at: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/13.0.0/entrezg.asp
|
| Data processing |
All analyses were performed in R (v2.11.1). Data processing was performed for each cell line separately using RMA (affy package, v1.26.1) for pre-processing, and updated Entrez GeneID annotation (hgu133plus2hsentrezgcdf package, v13.0.0).
|
| |
|
| Submission date |
Oct 11, 2012 |
| Last update date |
Oct 12, 2012 |
| Contact name |
Kenneth Chung-kan Chu |
| E-mail(s) |
kenneth.chungkan.chu@gmail.com
|
| Organization name |
Ontario Institute for Cancer Research
|
| Street address |
101 College Street, Suite 800
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 0A3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL14877 |
| Series (1) |
| GSE41491 |
Hypoxia transcriptomic time-series data in three different cancer cell lines |
|
