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Sample GSM554611 Query DataSets for GSM554611
Status Public on Jul 29, 2010
Title Tumor 179
Sample type genomic
 
Source name DNA
Organism Homo sapiens
Characteristics tissue: fresh frozen breast tumor
age: 78
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 sodium bisulfite modified using the EZ DNA Methylation Kit (Zymo Research, Orange, CA).
 
Hybridization protocol Illumina GoldenGateĀ® 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.
Scan protocol Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93.
Description DNA (bisulfite modified)
Data processing Illumina BeadStudio Methylation software was used for dataset assembly. Fluorescent signals for methylated (Cy5) and unmethylated (Cy3) alleles give methylation level: (max(Cy5 , 0))/(|Cy3| + |Cy5| + 100) with ~30 replicate bead measurements per locus. 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 10, 2010
Last update date Jul 28, 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 (1)
GSE22290 Breast tumor DNA methylation

Data table header descriptions
ID_REF
VALUE Average beta value

Data table
ID_REF VALUE
AATK_E63_R 0.94803
AATK_P519_R 0.93419
AATK_P709_R 0.79907
ABCA1_E120_R 0.01928
ABCA1_P45_F 0.02655
ABCB4_E429_F 0.96895
ABCB4_P51_F 0.95193
ABCB4_P892_F 0.17245
ABCC2_E16_R 0.95982
ABCC2_P88_F 0.96399
ABCC5_P444_F 0.01487
ABCG2_P178_R 0.0268
ABCG2_P310_R 0.04117
ABL1_P53_F 0.04042
ABL2_P459_R 0.02051
ABO_E110_F 0.02143
ABO_P312_F 0.05021
ACTG2_E98_R 0.91238
ACTG2_P346_F 0.88123
ACTG2_P455_R 0.96879

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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