tissue of origin: Non-Small Cell Lung age: 62 gender: male prior treatment: None epithelial: yes ploidy: 4n+/-, Near-tetraploid 92+/- (81-103) p53 mutation: MT doubling time (hrs): 79.5 contributing institute: Johns Hopkins University contributing person: M.Liu
Treatment protocol
Untreated
Growth protocol
Cells grown in RPMI 1640 with 5% FBS (Bio Whittaker, not heat inactivated) and 1% L-glutamine. Cells not grown past 80% confluencey for attached cells, or 0.5 x 10^6 cells for suspended. Trypsinize (for attached cells) cells with 5 ml trypsin-EDTA per T162, for 15 min., at 37C. Spin down suspended cells, and resuspend in ~3ml growth media. Count cells. Pass 1x10^6 cells into new T162's w 30 ml media. Repeat growth cycle until desired amount of cells are available. Cells are not grown past passage 20.
Extracted molecule
genomic DNA
Extraction protocol
Genomic DNA was purified from cells using either the QIAamp DNA Blood Maxi Kit, or the Blood & Cell Culture DNA Maxi Kit (Qiagen Inc., Valencia, CA) according to manufacturer's instructions. Quality was assessed by optical density 260/280 ratio using a spectrophotometer (Beckman-Coulter, Fullerton, CA) and by 0.8% agarose (SeaKem GTG, FMC BioProducts, Rockland, ME) gel electrophoresis in 1x TAE (Roche, Indianapolis, IN).
Label
biotin, dinitrophenyl
Label protocol
Done according to array manufacturer's specifications. The labels are C-Bio and A-DNP. C and G nucleotides are biotin labeled and A and T nucleotides were dinitrophenyl labeled
Hybridization protocol
Done according to array manufacturer's specifications
Scan protocol
Done according to array manufacturer's specifications
Description
S1975150457 Large cell-undifferentiated
Data processing
Probe intensities were normalized using the crlmmCopynumber method from Bioconductor's crlmm package (http://www.bioconductor.org/packages/release/bioc/html/crlmm.html). Log probe intensities were mean centered to have a mean of zero for each sample. Normalized data consists of mean centered probe intensities (mean of each sample subtracted from the log probe intensities for the sample, to give a mean of zero for the sample). Non-normalized data is the copy number data from crlmmCopynumber method from Bioconductor's crlmm package (http://www.bioconductor.org/packages/release/bioc/html/crlmm.html).
