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Sample GSM1215431 Query DataSets for GSM1215431
Status Public on Feb 26, 2014
Title Joint_cartilage_KT538
Sample type genomic
Source name Autopsy
Organism Homo sapiens
Characteristics tissue: Joint_cartilage
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 0.363122963
cg00000108 0.935411593
cg00000109 0.728622957
cg00000165 0.16447904
cg00000236 0.814620509
cg00000289 0.635060069
cg00000292 0.567122974
cg00000321 0.248339318
cg00000363 0.237806402
cg00000622 0
cg00000658 0.831905587
cg00000714 0.14661337
cg00000721 0.955883903
cg00000734 0.064700468
cg00000769 0.05701094
cg00000807 0.792776015
cg00000884 0.907871366
cg00000905 0.080249724
cg00000924 0.52221647
cg00000948 0.881560613

Total number of rows: 485577

Table truncated, full table size 10629 Kbytes.

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

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