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Sample GSM1215397 Query DataSets for GSM1215397
Status Public on Feb 26, 2014
Title Tonsils_BM419/4_2
Sample type genomic
Source name Autopsy
Organism Homo sapiens
Characteristics tissue: Tonsils
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 0.513613518
cg00000108 0.952225251
cg00000109 0.831113461
cg00000165 0.332919307
cg00000236 0.883768178
cg00000289 0.493392314
cg00000292 0.760376051
cg00000321 0.445689388
cg00000363 0.460570878
cg00000622 0.009579871
cg00000658 0.820508542
cg00000714 0.176025292
cg00000721 0.961605921
cg00000734 0.072888544
cg00000769 0.028421689
cg00000807 0.741546247
cg00000884 0.917191521
cg00000905 0.055035268
cg00000924 0.546250348
cg00000948 0.855860556

Total number of rows: 485577

Table truncated, full table size 10689 Kbytes.

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

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