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Sample GSM893476 Query DataSets for GSM893476
Status Public on May 17, 2012
Title tumor 54 [MSNP]
Sample type genomic
 
Source name lung adenocarcinoma
Organism Homo sapiens
Characteristics tissue: lung
disease state: adenocarcinoma
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using Qiagen’s QIAamp DNA minikit and Affymetrix DNA prep instructions using the StyI restriction enzyme digestion. These samples were then additionally digested by HpaII, a methylation sensitive restriction enzyme, following the MSNP protocol (Yuan et al, PMID: 16585166).
Label biotin
Label protocol Followed Affymetrix instructions.
 
Hybridization protocol Followed Affymetrix instructions.
Scan protocol Arrays were scanned using the Affmetrix Gene Chip Scanner.
Data processing The DNA specimens in this dataset were additionally digested by HpaII restriction enzyme, which is methylation sensitive. These samples were concurrently analyzed with their StyI-only digested counterpart, which are contained in GSE36363 identified with the same Sample Name [see 'Affiliated with' link below]. All CEL files were processed by CRMAv2 (Bengtsson, et al. PMID: 19535535) and sample-wise median centered using control probes (those in a fragment without a HpaII binding site). For probes in fragments having a HpaII binding site, methylation values were calculated using the StyI-only digestion and the StyI+HpaII digestion arrays for each sample. The methylation normalized values were calculated as (StyI - StyI+HpaII)/StyI to give a relative estimate of methylation percentage. These values are given in the data table below.
Note that methylation values are given only for 'methylation sensitive' probesets that measure DNA fragments with a HpaII binding site - those that are methylation sensitive. Methylation sensitive probesets were identified by searching for the HpaII binding site in the StyI digested DNA. For more information on probeset classification, see Yuan et al. (PMID: 16585166). Control site probes have null values in the data table below.
 
Submission date Mar 12, 2012
Last update date May 17, 2012
Contact name Matthew D Wilkerson
E-mail(s) [email protected]
Phone 919-966-3864
Fax 919-966-8212
URL http://cancer.unc.edu/nhayes
Organization name University of North Carolina at Chapel Hill
Department Lineberger Comprehensive Cancer Center
Lab D. Neil Hayes
Street address 450 West Drive
City Chapel Hill
State/province NC
ZIP/Postal code 27599-7295
Country USA
 
Platform ID GPL3720
Series (2)
GSE36438 Human lung adenocarcinoma DNA methylation profiling by MSNP
GSE36471 Human lung adenocarcinoma
Relations
Affiliated with GSM889666

Data table header descriptions
ID_REF
VALUE normalized methylation of each probe.

Data table
ID_REF VALUE
SNP_A-2236359 0.234970678939773
SNP_A-2116190 0.5940861634969
SNP_A-2109914 -0.0718118104912429
SNP_A-2291997 0.337678133237742
SNP_A-4277872 -0.0282553502649759
SNP_A-2118217 0.551223541037804
SNP_A-1866065 0.0394180245729297
SNP_A-2288244 0.0163083415486903
SNP_A-1783407 0.817311381234943
SNP_A-4271011 0.221366151389085
SNP_A-2082515 -0.0964522565088156
SNP_A-1910751 -0.0400863072606307
SNP_A-2081399 0.205614463249007
SNP_A-2223642 0.16797078564489
SNP_A-1856955 -0.102695769125445
SNP_A-1799863 0.273198589606346
SNP_A-1908463 -0.0260161938953089
SNP_A-1955996 0.227041937731673
SNP_A-2203009 0.225138341517388
SNP_A-2098546 0.388399777004956

Total number of rows: 238378

Table truncated, full table size 5172 Kbytes.




Supplementary file Size Download File type/resource
GSM893476_EXPID7179.CEL.gz 24.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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