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Sample GSM1215396 Query DataSets for GSM1215396
Status Public on Feb 26, 2014
Title Tonsils_BM419/4_1
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 0.560612144
cg00000108 0.954372244
cg00000109 0.854198822
cg00000165 0.305356406
cg00000236 0.905233867
cg00000289 0.646914356
cg00000292 0.756215423
cg00000321 0.433160709
cg00000363 0.409763445
cg00000622 0.007851535
cg00000658 0.837573541
cg00000714 0.179083256
cg00000721 0.898726722
cg00000734 0.069301252
cg00000769 0.040025355
cg00000807 0.760791827
cg00000884 0.918291127
cg00000905 0.063052754
cg00000924 0.530161607
cg00000948 0.88973303

Total number of rows: 485577

Table truncated, full table size 10757 Kbytes.

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

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