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Sample GSM1566951 Query DataSets for GSM1566951
Status Public on Jun 01, 2016
Title OT_sample2
Sample type genomic
Source name Ovarian Teratoma
Organism Homo sapiens
Characteristics disease status: Ovarian Teratoma
tissue: Peripheral Blood
gender: Female
Extracted molecule genomic DNA
Extraction protocol All samples were identified and obtained from collaborating clinical genetics laboratories. As these samples were provided by many different contributors, it is likely that the DNA extraction protocols varies among samples.
Label Cy3, Cy5
Label protocol Standard Illumina labelling protocol
Hybridization protocol bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
Scan protocol Arrays were imaged using standard recommended Illumina scanner protocol
Description none
Data processing The methylation value was set to null for probes with a detection p-value >0.01. Probe sequences (50-mer oligonucleotides) were uniquely mapped to the reference human genome hg18 (NCBI36) using BLAT, allowing up to 2 mismatches and 1 gap. Beta values from the autosomal probes were quantile normalized using lumi package in R.
Submission date Dec 16, 2014
Last update date Jun 01, 2016
Contact name Ricky Shantilal Joshi
Organization name Mount Sinai School of Medicine
Department Genetics and Genomic Sciences
Street address 1470 Madison Avenue
City New York City
State/province NY
ZIP/Postal code 10128
Country USA
Platform ID GPL13534
Series (1)
GSE64244 DNA Methylation Profiling of Uniparental Disomy Subjects Provides a Map of Parental Epigenetic Bias in the Human Genome.

Data table header descriptions
VALUE Quantile normalized Beta
Detection Pval generated by GenomeStudio

Data table
ID_REF VALUE Detection Pval
cg13869341 0.83119 0.00000
cg14008030 0.67089 0.00000
cg12045430 0.05124 0.00000
cg20826792 0.17423 0.00000
cg00381604 0.01687 0.00000
cg20253340 0.48159 0.00000
cg21870274 0.83014 0.00000
cg03130891 0.38392 0.00667
cg16162899 0.88083 0.00000
cg17149495 0.84428 0.00000
cg22802167 0.92392 0.00000
cg17308840 0.14129 0.00000
cg17866181 0.86983 0.00000
cg08477687 0.13666 0.00000
cg00645010 0.02364 0.00000
cg15394630 0.12469 0.00000
cg23917638 0.28593 0.00000
cg18761878 0.37901 0.00000
cg27534567 0.02469 0.00000
cg21996134 0.96988 0.00000

Total number of rows: 461272

Table truncated, full table size 12111 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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