patient identifier: 2 disease state: squamous cell carcinoma of the tongue tissue location: floor of mouth Stage: unknown grade: unknown site: tumor site detail: floor of mouth tumor recurrence: no time.to.recurrence.or.last.follow-up.months: 16.97 site.of.recurrence: NA outcome: ANED
Extracted molecule
total RNA
Extraction protocol
Total RNA was extracted from all tissues using Trizol reagent (Life Technologies, Inc., Burlington, ON, Canada), followed by purification using the Qiagen RNeasy kit/DNase RNase-free set (Qiagen, Valencia, CA, USA), according to manufacturer’s instructions. RNA was quantified by spectrophotometry and its quality was assessed using the 2100 Bioanalyzer (Firmware v.A.01.16, Agilent Technologies, Canada). All samples were of sufficient quantity and quality for arrays and quantitative real-time PCR (QRT-PCR) analyses.
Label
biotin
Label protocol
Amplification and biotin labeling of antisense cRNA was performed using the Enzo BioArray High YieldTM RNA transcript labeling kit (Enzo Diagnostics, Farmingdale, NY, USA), according to the manufacturer’s instructions.
Hybridization protocol
Labeling and hybridization to arrays were performed by The Centre for Applied Genomics, Medical and Related Sciences Centre (MaRS), Toronto, ON, Canada, using standard Affymetrix procedures.
Scan protocol
Microarray slides were scanned using the GeneArray 2500 scanner (Agilent Technologies).
Description
U133Plus2_112307W_SKB06_HN07-354
# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).
Data processing
Data were processed using the BrainArray Entrez-gene centric alternative CDF, with GC-RMA background correction and normalization.
