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Sample GSM1215451 Query DataSets for GSM1215451
Status Public on Feb 26, 2014
Title Tonsils_SJ600-5_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 0.211109442
cg00000108 0.968808567
cg00000109 0.809327052
cg00000165 0.171865977
cg00000236 0.867069433
cg00000289 0.717938947
cg00000292 0.637079291
cg00000321 0.467631345
cg00000363 0.221442986
cg00000622 0
cg00000658 0.84791207
cg00000714 0.126270261
cg00000721 0.927875667
cg00000734 0.09433298
cg00000769 0.052002027
cg00000807 0.818980834
cg00000884 0.903968108
cg00000905 0.08091512
cg00000924 0.567326518
cg00000948 0.905573723

Total number of rows: 485577

Table truncated, full table size 10510 Kbytes.

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

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