cell line: SW480 treatment: scrambled siRNA control biological replicate: 2
Extracted molecule
total RNA
Extraction protocol
RNA was isolated from SW480sicontrol and SW480siKrasV12 cells utilizing the RNeasy Mini Prep Kit per manufacturer’s instructions (Qiagen, Valencia, CA).
Label
biotin
Label protocol
Per Affymetrix Protocol
Hybridization protocol
Array hybridization were performed per recommended specifications (Asuragen, Austin, TX).
Scan protocol
Scanning were performed per recommended specifications (Asuragen, Austin, TX).
Data processing
Genechip PrimeView Human Arrays were utilized (Affymetrix, Santa Clara, CA). CEL files were analyzed utilizing R/Bioconductor package, oneChannelGUI. Briefly, normalization of expression values was performed utilizing the “Expresso” option, selecting “RMA” as the background correction, “quantiles” as normalization, “pmonly” as the PM correction, and “MAS” as the expression. Probes were filtered with IQR settings of 0.25. P values were calculated using a two-tailed Student’s t-test.
