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Sample GSM1215416 Query DataSets for GSM1215416
Status Public on Feb 26, 2014
Title Tonsils_KA522_2
Sample type genomic
Source name Autopsy
Organism Homo sapiens
Characteristics tissue: Tonsils
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 0.596404315
cg00000108 0.945884176
cg00000109 0.859115711
cg00000165 0.344773612
cg00000236 0.892088528
cg00000289 0.723533017
cg00000292 0.75951079
cg00000321 0.461468388
cg00000363 0.405619744
cg00000622 0.002497191
cg00000658 0.84073861
cg00000714 0.197620074
cg00000721 0.896167987
cg00000734 0.074294614
cg00000769 0.04464927
cg00000807 0.7440262
cg00000884 0.88507501
cg00000905 0.077950148
cg00000924 0.57065522
cg00000948 0.866853879

Total number of rows: 485577

Table truncated, full table size 10756 Kbytes.

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

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