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Sample GSM1215450 Query DataSets for GSM1215450
Status Public on Feb 26, 2014
Title Tonsils_SJ600-5_1
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 0.216518339
cg00000108 0.95100445
cg00000109 0.784590256
cg00000165 0.144398736
cg00000236 0.85272842
cg00000289 0.701479086
cg00000292 0.61591616
cg00000321 0.402167518
cg00000363 0.234874446
cg00000622 0.011402157
cg00000658 0.792996344
cg00000714 0.122475691
cg00000721 0.927716265
cg00000734 0.074647588
cg00000769 0.08217078
cg00000807 0.796164747
cg00000884 0.904884526
cg00000905 0.082695816
cg00000924 0.554380816
cg00000948 0.879146038

Total number of rows: 485577

Table truncated, full table size 10779 Kbytes.

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

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