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Sample GSM1215411 Query DataSets for GSM1215411
Status Public on Feb 26, 2014
Title Gastric_mucosa_KA522
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 0.429118426
cg00000108 0.946747577
cg00000109 0.801765258
cg00000165 0.253764554
cg00000236 0.862117585
cg00000289 0.691013546
cg00000292 0.656037244
cg00000321 0.403601643
cg00000363 0.30570875
cg00000622 0.010242973
cg00000658 0.807265418
cg00000714 0.158083467
cg00000721 0.875840186
cg00000734 0.078488678
cg00000769 0.054322655
cg00000807 0.741984667
cg00000884 0.875635808
cg00000905 0.074168178
cg00000924 0.561880985
cg00000948 0.878779846

Total number of rows: 485577

Table truncated, full table size 10712 Kbytes.

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

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