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Sample GSM1215430 Query DataSets for GSM1215430
Status Public on Feb 26, 2014
Title Gastric_mucosa_KT538
Sample type genomic
Source name Autopsy
Organism Homo sapiens
Characteristics tissue: Gastric_mucosa
gender: male
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from 25 mg samples of the tissue specimens using the NucleoSpin® Tissue kit (Macherey-Nagel GmbH, Düren, Germany)
Label Cy5 and Cy3
Label protocol According to Illumina protocol
Hybridization protocol According to Illumina protocol
Scan protocol According to Illumina protocol
Data processing The raw data were subject to quality control and normalization using the standard protocols suggested for the bioconductor R package minfi. All probes containing single nucleotide polymorphisms and CpG sites from the X and Y chromosomes were removed from the analysis.
matrix processed value definition: Average Beta
matrix signal intensities value definition: Matrix signal intensities (non-normalized) contains unmethylated (signal A) and methylated (Signal B) signal intensities
Submission date Aug 26, 2013
Last update date Feb 26, 2014
Contact name Kaie Lokk
Organization name University of Tartu
Street address Riia 23
City Tartu
ZIP/Postal code 501010
Country Estonia
Platform ID GPL13534
Series (1)
GSE50192 DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns

Data table header descriptions
VALUE minfi normalized signal intensity

Data table
cg00000029 0.349317605
cg00000108 1
cg00000109 0.920345992
cg00000165 0.212480362
cg00000236 0.897741633
cg00000289 0.677316882
cg00000292 0.694230739
cg00000321 0.386885161
cg00000363 0.254345684
cg00000622 0
cg00000658 0.87026677
cg00000714 0.148944768
cg00000721 0.956540102
cg00000734 0.097429174
cg00000769 0.037620205
cg00000807 0.801380868
cg00000884 0.994697866
cg00000905 0.066138228
cg00000924 0.580984187
cg00000948 0.900188497

Total number of rows: 485577

Table truncated, full table size 10305 Kbytes.

Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

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