A549 cells were grown in RPMI media and switched to BME+NEAA media with or without serine 24 hours prior to compound treatment (1 uM 16 or DMSO). Samples were harvested in triplicate at 0, 1.5, 6, and 24 hours post compound addition, and hybridized to Affymetrix HG-U219 GeneChips.
Extracted molecule
total RNA
Extraction protocol
Trizol
Label
biotin
Label protocol
standard Affymetix protocol
Hybridization protocol
standard Affymetix protocol
Scan protocol
standard Affymetix protocol
Description
A549_plusSER_1.5hr_compound16_1uM
Data processing
Data were processed using RMA (Gentleman et al., 2004; Irizarry et al., 2003), and differential expression was assessed using the limma package in Bioconductor (Gentleman et al., 2004; Smyth, 2004). Pathway and transcription factor analyses were conducted using the sigpathway algorithm (Tian et al., 2005), Pathway Studio (Ariadne Genomics) and the MetaCore web application (GeneGo Inc).
