Doxycycline treatment of A375 shBRAF-2 cells. Replicate 2.
Extracted molecule
total RNA
Extraction protocol
RNA obtained using TrizolLS method.
Label
biotin
Label protocol
Biotin labeled cRNA using an IVT kit
Hybridization protocol
Affymterix protocol for hyb and wash on Fludics 450
Scan protocol
Affymetrix protocol for GeneChip scanner 3000
Description
none
Data processing
Data were processed using a program that implemented the recommendations of Choe, et al., Genome Biology, 2005 (PMID: 15693945). Background correction was performed as in the Affymetrix MAS 5.0 application. Probe-level normalization was performed using Quantile Normalization as in the RMA method. Perfect Match and Mismatch probes were contrasted as in the Affymetrix MAS 5.0 application. Multiple probes for each probeset were summarized using the median polish method from the RMA method. These summarized metrics were then further normalized using the Loess method.
