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Sample GSM1215398 Query DataSets for GSM1215398
Status Public on Feb 26, 2014
Title Bladder_BM419/4
Sample type genomic
Source name Autopsy
Organism Homo sapiens
Characteristics tissue: Bladder
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 0.250329787
cg00000108 0.939471387
cg00000109 0.696408178
cg00000165 0.132125656
cg00000236 0.736136541
cg00000289 0.714980233
cg00000292 0.594732894
cg00000321 0.349650217
cg00000363 0.18991535
cg00000622 0.004864737
cg00000658 0.810043331
cg00000714 0.096597384
cg00000721 0.885104478
cg00000734 0.072661644
cg00000769 0.054864154
cg00000807 0.792579064
cg00000884 0.886528233
cg00000905 0.10105205
cg00000924 0.574349904
cg00000948 0.888060582

Total number of rows: 485577

Table truncated, full table size 10699 Kbytes.

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

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