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Sample GSM1215447 Query DataSets for GSM1215447
Status Public on Feb 26, 2014
Title Gastric_mucosa_SJ600-5
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 0.467240268
cg00000108 0.963357961
cg00000109 0.842100792
cg00000165 0.31303896
cg00000236 0.859897544
cg00000289 0.673901264
cg00000292 0.753979683
cg00000321 0.395862343
cg00000363 0.364033862
cg00000622 0.003995169
cg00000658 0.841702276
cg00000714 0.19410975
cg00000721 0.866607138
cg00000734 0.067184462
cg00000769 0.05800119
cg00000807 0.734294634
cg00000884 0.881372113
cg00000905 0.070663474
cg00000924 0.55384446
cg00000948 0.879868581

Total number of rows: 485577

Table truncated, full table size 10752 Kbytes.

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

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