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Sample GSM416171 Query DataSets for GSM416171
Status Public on Jul 28, 2009
Title pleural mesothelioma_9177
Sample type genomic
 
Source name pleural mesothelioma
Organism Homo sapiens
Characteristics disease state: pleural mesothelioma
age: 56
gender: female
Extracted molecule genomic DNA
Extraction protocol DNA from fresh frozen tissue was isolated with QIAamp DNA mini kit (Qiagen, Valencia, CA)
Label Cy3,Cy5
Label protocol DNA was sodium bisulfite modified using the EZ DNA Methylation Kit (Zymo Research, Orange, CA).
 
Hybridization protocol Illumina GoldenGate® methylation bead arrays interrogated 1505 CpG loci associated with 803 cancer-related genes processed at the UCSF Institute for Human Genetics, Genomics Core Facility as described in Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93.
Bisulfite-converted DNAs are biotinylated and hybridized to query oligos, and washed. The hybridized oligos are then extended and ligated to create amplifiable templates with methylation-specific primers. The PCR that follows uses fluorescently labeled universal PCR primers.
Scan protocol Arrays were imaged using a BeadArray Reader scanner (Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93.)
Description no additional information
Data processing Illumina BeadStudio Methylation software (version 3.2.0) was used for dataset assembly. Fluorescent signals for methylated (Cy5) and unmethylated (Cy3) alleles give methylation level (β) = (max(Cy5 , 0))/(|Cy3| + |Cy5| + 100) with ~30 replicate bead measurements per locus. The β-value provides a continuous measure of levels of DNA methylation in samples, ranging from 0 in the case of completely unmethylated sites to 1 in completely methylated sites. Detection P-values determined poor performing samples (n=2) and CpG loci (n=8), which were removed from analysis. X chromosome loci were also removed, leaving 1413 CpG loci associated with 773 genes. Raw average beta values were used and not subjected to normalization as per manufacturer's recommendations.
 
Submission date Jun 11, 2009
Last update date Apr 13, 2010
Contact name Brock Clarke Christensen
E-mail(s) brock.clarke.christensen@dartmouth.edu
Organization name Dartmouth Medical School
Street address 7650 Remsen
City Hanover
State/province NH
ZIP/Postal code 03755
Country USA
 
Platform ID GPL9183
Series (3)
GSE16559 Lung adenocarcinoma and mesothelioma DNA methylation
GSE20989 Mesothelioma integrative genomics: DNA methylation
GSE21058 Integrated profiling reveals a global correlation between epigenetic and genetic alterations in mesothelioma

Data table header descriptions
ID_REF
VALUE raw average beta values (continuous and bounded by 0 & 1)

Data table
ID_REF VALUE
AATK_E63_R 0.94232
AATK_P519_R 0.90237
AATK_P709_R 0.82084
ABCA1_E120_R 0.02043
ABCA1_P45_F 0.02496
ABCB4_E429_F 0.95312
ABCB4_P51_F 0.94598
ABCB4_P892_F 0.36662
ABCC2_E16_R 0.9693
ABCC2_P88_F 0.9536
ABCC5_P444_F 0.03168
ABCG2_P178_R 0.06341
ABCG2_P310_R 0.72804
ABL1_P53_F 0.0917
ABL2_P459_R 0.07325
ABO_E110_F 0.04043
ABO_P312_F 0.04095
ACTG2_E98_R 0.89321
ACTG2_P346_F 0.91383
ACTG2_P455_R 0.96421

Total number of rows: 1413

Table truncated, full table size 28 Kbytes.




Supplementary data files not provided
Processed data not applicable for this record

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