cell line: MTB;TAN-derived tumor cell line 2, parental recurrent
Treatment protocol
Cells were untreated, parental tumor cell lines of low passage.
Growth protocol
Cell lines were grown to ~80% confluence in standard media prior to RNA harvesting.
Extracted molecule
total RNA
Extraction protocol
Total RNA was extracted according to manufacturer's protocol (Qiagen).
Label
biotin
Label protocol
Ambion MessageAmp Premier labeling
Hybridization protocol
Hybridization targets were prepared from total RNA using a MessageAmp Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX, USA), hybridized to GeneChip™ Mouse 430A Plus 2.0 Array (Affymetrix, Santa Clara, CA, USA) in an Affymetrix GeneChip hybridization Oven 645, washed in Affymetrix GeneChip Fluidics Station 450, and scanned with Affymetrix GeneChip Scanner 7G according to standard Affymetrix GeneChip hybridization, wash, and stain protocols.
Scan protocol
Affymetrix scanning protocol according to manufacturer, Affymetrix GeneChip Command Console Scan Control 3.2.3.1515 and Expression Console version 1.2.0.20
Data processing
CEL files were uploaded into simpleaffy package in R software and GC-RMA normalized. Differential gene expression analysis was determined with limma package in R software, and annotated with annotate package.
