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Sample GSM1215399 Query DataSets for GSM1215399
Status Public on Feb 26, 2014
Title Gallbladder_BM419/4
Sample type genomic
Source name Autopsy
Organism Homo sapiens
Characteristics tissue: Gallbladder
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 0.217582503
cg00000108 0.914052534
cg00000109 0.816111318
cg00000165 0.16846699
cg00000236 0.77589923
cg00000289 0.726715901
cg00000292 0.602681667
cg00000321 0.382169254
cg00000363 0.217974493
cg00000622 0.006531739
cg00000658 0.788025476
cg00000714 0.132974846
cg00000721 0.916770693
cg00000734 0.080029563
cg00000769 0.047751729
cg00000807 0.767550492
cg00000884 0.908156823
cg00000905 0.054150041
cg00000924 0.53868847
cg00000948 0.909911155

Total number of rows: 485577

Table truncated, full table size 10715 Kbytes.

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

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