histology: Squamous gender: F race: Caucasian tobacco history: Y final patient stage: IIIA date of birth: 1938-08-28 date of surgery: 2007-10-15 vital statistics: D last follow-up survival: 2008-03-09 recurrence: Y last follow-up recurrence: 2008-02-15
Treatment protocol
None
Growth protocol
None
Extracted molecule
total RNA
Extraction protocol
After homogenization, total RNA was extracted using TRI Reagent (Life Technologies, Grand Island, NY) according to manufacturer’s protocol. The nanodrop spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE) was used to estimate the concentration of RNA and the quality of the RNA (RIN number) was assessed on Nano Series II RNA LAB-chips using Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Santa Clara, CA)
Label
biotin
Label protocol
500 ng of total RNA was used to label the cRNA probes by Ambion Illumina TotalPrep RNA Amplification kit (Cat# IL1791)
Hybridization protocol
1.5 ug of the amplified and labeled cRNA probes was hybridized to the chip overnight at 58 degree C, then washed, blocked and detected by streptavidin-Cy3 per manufacturer's protocol.
Scan protocol
The chips were scanned by Illumina iScan system.
Data processing
Bead-level data were processed with the MBCB algorithm (Ding et al, Nucl Acids Res, 36:e58, 2008), which is a background-correction and summarization method, then quantile-normalized and log2-transformed
