|
| Status |
Public on May 04, 2014 |
| Title |
MCF-7_anoxia |
| Sample type |
RNA |
| |
|
| Source name |
Breast cancer cell line MCF-7
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
oxygen condition: anoxia
|
| Growth protocol |
MCF-7 cells grown in anoxia for 90 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of total RNA was performed using Qiagen Rneasy minikit according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
250 nanograms of total RNA from each sample were used to prepare biotinylated fragmented cRNA according to the GeneChip® Expression. Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA).
|
| |
|
| Hybridization protocol |
Affymetrix GeneChip® expression arrays (GeneChip® Human Gene 2.0 ST Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm.
|
| Scan protocol |
According to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA) the arrays were then washed. and stained using the Fluidics Station 450 and finally scanned using the GeneChip® Scanner 3000 7G.
|
| Description |
Gene expression data from MCF-7 cells grown in anoxia.
|
| Data processing |
The raw data was normalized in the free software Expression Console provided by Affymetrix (affymetrix.com) using the robust multi-array average (RMA) method using default analysis settings.
we only used the probes designated as 'main', and the controls are removed (e.g. control->affx, control->chip, control->bgp->antigenomic, control->bgp->genomic, normgene->exon, normgene->intron and rescue controls etc.).
|
| |
|
| Submission date |
May 16, 2013 |
| Last update date |
May 04, 2014 |
| Contact name |
Mårten Fryknäs |
| E-mail(s) |
marten.fryknas@medsci.uu.se
|
| Organization name |
Uppsala university
|
| Department |
Medical sciencies
|
| Lab |
Clinical pharmacology
|
| Street address |
Akademiska sjh ingång 61
|
| City |
Uppsala |
| ZIP/Postal code |
74185 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL16686 |
| Series (1) |
|
