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Sample GSM1024253 Query DataSets for GSM1024253
Status Public on Jun 01, 2013
Title Pongo abelii A949
Sample type genomic
 
Source name blood
Organism Pongo abelii
Characteristics gender: female
organism: Pongo abelii
tissue: blood
Extracted molecule genomic DNA
Extraction protocol unknown
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 A949
Data processing The methylation value was set to null for probes with a detection p-value < 0.01. A strict filtering step was performed to remove divergent probes based on the number and location of mismatches with their target site in each species genome assembly tested. We only retained those probes that had either a perfect match, or had 1 or 2 mismatches in the first 45bp but no mismatches in the 3' 5bp closest to the CpG site being assayed. Beta values from the autosomal probes and chromosome X probes were quantile normalized separately; additionally, chromosome X probes for male and female were quantile normalized separately.
 
Submission date Oct 23, 2012
Last update date Jun 01, 2013
Contact name Irene Hernando
E-mail(s) irene.hernando@upf.edu
Organization name UPF/CSIC
Street address Dr Aiguader 88
City Barcelona
ZIP/Postal code 08003
Country Spain
 
Platform ID GPL13534
Series (1)
GSE41782 A genome-wide comparative study of DNA methylation in great apes

Data table header descriptions
ID_REF IlmnID
VALUE Quantile normalized Beta (detection p-value < 0.01)
Detection Pval generated by GenomeStudio

Data table
ID_REF VALUE Detection Pval
cg00000029 0.323757852285695 0
cg00000165 0.190166402997916 0
cg00000289 0.791037720966675 0
cg00000292 0.729553566380984 0
cg00000363 0.323350770440815 0
cg00001261 0.723662054820322 0
cg00001364 0.849399062110499 0
cg00001446 0.846835780538831 0
cg00001583 0.0375287958472474 0
cg00001747 0.0535786410227493 0
cg00001793 0.71517041610707 0
cg00001874 0.449593347389495 0
cg00001930 0.887433960537726 0
cg00002033 0.522006389734588 0
cg00002190 0.81753437535055 0
cg00002406 0.0670712463521605 0
cg00002426 0.623577967472966 0
cg00002464 0.102933065126163 0
cg00002660 0.086941378988774 0
cg00002808 0.847015390127209 0

Total number of rows: 137797

Table truncated, full table size 4195 Kbytes.




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

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