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Sample GSM471095 Query DataSets for GSM471095
Status Public on Feb 25, 2014
Title lung_adenocarcinoma_DNA (85050022): MP
Sample type genomic
 
Source name lung, adenocarcinoma
Organism Homo sapiens
Characteristics disease state: adenocarcinoma
sample number: 85050022
Growth protocol Tissues were excised during surgical ressection for tumor removal.
Extracted molecule genomic DNA
Extraction protocol Tumour and normal samples were obtained during surgical ressection. After pathology review, tumors were microdissected to ensure tumor cells comprised 80% of cells extracted. DNA was extracted using proteinase K digestion, followed by phenol:chloroform extraction and ethanol precipitation.
Label Cy3 and Cy5
Label protocol Bisulfite conversion and labelling was carried out according to Illumina directions by the Illumina Cspro service center at Oxford University.
Bisulfite conversion leads to the deamination of non-methylated cytosines to uracils, while methylated cytosines are refractory to the effects of bisulfite and remain cytosine.
Methylated alleles labeled with Cy3, unmethylated labeled with Cy5
 
Hybridization protocol Hybridization was carried out according to Illumina directions by the Illumina Cspro service center at Oxford University.
Scan protocol Scanning was carried out according to Illumina directions by the Illumina Cspro service center at Oxford University.
Description For each normal/tumor pair, the sample numbers are paired but offset by one with the tumor being the lower of the two numbers. For example, 85040001 is the adenocarcinoma tumor profile that pairs with 85040002.
Data processing Data processing was performed according to Illumina directions by the Illumina Cspro service center at Oxford University. Data were normalized using the average setting. Software was BSGX version 3.2.3.
Beta values (Intensity Ratio Values) represent methylation level of the CpG locus. ß-values were calculated using the ratio of intensities between methylated and unmethylated alleles, i.e., (Intensity of methylated bead type)/(Intensity of methylated bead type + Intensity of unmethylated bead type).
 
Submission date Nov 16, 2009
Last update date Feb 25, 2014
Contact name Ian Michael Wilson
E-mail(s) iwilson@bccrc.ca
Phone 6046758000x7703
URL http://www.bccrc.ca/cg/people_iwilson.html
Organization name British Columbia Cancer Research Centre
Department Cancer Genetics
Lab Wan Lam Lab
Street address 675 West 10th Avenue
City Vancouver
State/province BC
ZIP/Postal code V5Z1L3
Country Canada
 
Platform ID GPL8490
Series (1)
GSE19034 EYA4 is a non-small cell lung cancer tumor suppressor located in the susceptibility locus on chromosome 6q

Data table header descriptions
ID_REF
VALUE Illumina Average Beta
DETECTION P-VALUE

Data table
ID_REF VALUE DETECTION P-VALUE
cg00000292 0.5778615 3.68E-38
cg00002426 0.4436393 3.68E-38
cg00003994 0.1012658 3.68E-38
cg00005847 0.2890744 3.99E-16
cg00006414 0.03173458 3.68E-38
cg00007981 0.04109723 3.68E-38
cg00008493 0.9824446 3.68E-38
cg00008713 0.0215694 3.68E-38
cg00009407 0.04364872 3.68E-38
cg00010193 0.6693084 3.68E-38
cg00011459 0.6893939 7.01E-07
cg00012199 0.01139535 3.68E-38
cg00012386 0.02763485 3.68E-38
cg00012792 0.07537805 3.68E-38
cg00013618 0.5698976 3.68E-38
cg00014085 0.02395378 3.68E-38
cg00014837 0.8701082 3.68E-38
cg00015770 0.1385487 3.68E-38
cg00016968 0.6642095 3.68E-38
cg00019495 0.1188223 3.68E-38

Total number of rows: 27578

Table truncated, full table size 822 Kbytes.




Supplementary file Size Download File type/resource
GSM471095_4493586005_E_Grn.idat.gz 365.8 Kb (ftp)(http) IDAT
GSM471095_4493586005_E_Red.idat.gz 365.5 Kb (ftp)(http) IDAT
Processed data included within Sample table

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