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Series GSE63384 Query DataSets for GSE63384
Status Public on Apr 30, 2015
Title Multi-platform Characterization of Stage I Lung Adenocarcinoma (Genome-wide DNA Methylation)
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Genome wide DNA methylation profiling of Stage I Lung Adenocarcinoma and non-tumor adjacent tissues. The Illumina Infinium 27k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Samples included tumor and adjacent non-tumor tissues excised from a cohort of 35 patients with Stage I Lung Adenocarcinoma. Candidate prognostic biomarkers were validated by pyrosequencing in independent cohorts.
 
Overall design Total genomic DNA was bisulfite converted and hybridized to Infinium Human Methylation27Beadchips. Fluorescent signals were collated via Bead Studio software and converted into β-values. Illumina Bead Studio software output data were normalized using SSN (simple scaling normalization), to correct for dye bias and transformed into M-values (M = log2 intensity of methylated probe/ intensity of unmethylated probe), using the R package lumi.
 
Contributor(s) Robles AI, Harris CC
Citation(s) 26134223
Submission date Nov 17, 2014
Last update date Jun 08, 2016
Contact name Ana I Robles
E-mail(s) Ana_Robles@nih.gov
Phone 301-496-1729
Organization name National Cancer Institute/NIH
Lab Laboratory of Human Carcinogenesis
Street address 37 Convent Dr 37/3060D
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platforms (1)
GPL8490 Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2)
Samples (70)
GSM1547818 lung, nontumor adjacent_12839
GSM1547819 lung, adenocarcinoma_12839
GSM1547820 lung, nontumor adjacent_12860
Relations
BioProject PRJNA267607

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE63384_RAW.tar 5.8 Mb (http)(custom) TAR
GSE63384_Unmethylated_and_methylated_signal_intensities.txt.gz 10.7 Mb (ftp)(http) TXT
GSE63384_accession_sampleID_correspondences.txt.gz 595 b (ftp)(http) TXT
Processed data included within Sample table

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