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Sample GSM1215394 Query DataSets for GSM1215394
Status Public on Feb 26, 2014
Title Gastric_mucosa_BM419/4
Sample type genomic
Source name Autopsy
Organism Homo sapiens
Characteristics tissue: Gastric_mucosa
gender: female
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 0.34760848
cg00000108 0.942200916
cg00000109 0.78663702
cg00000165 0.14162495
cg00000236 0.746281158
cg00000289 0.643188686
cg00000292 0.609993535
cg00000321 0.371444789
cg00000363 0.2101523
cg00000622 0.012127337
cg00000658 0.786729851
cg00000714 0.097471294
cg00000721 0.910831986
cg00000734 0.060532367
cg00000769 0.060869565
cg00000807 0.771668265
cg00000884 0.889238186
cg00000905 0.077892279
cg00000924 0.545176275
cg00000948 0.886036195

Total number of rows: 485577

Table truncated, full table size 10757 Kbytes.

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

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