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Sample GSM1048140 Query DataSets for GSM1048140
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 2, 2034
Sample type genomic
Source name Buccal cheek swab, MZ, birth
Organism Homo sapiens
Characteristics gender: female
age: birth
cell type: normal buccal cells
monozygotic: 1
dizygotic: 0
monochorionic: 0
sibship: 13
twin: 2
Extracted molecule genomic DNA
Extraction protocol gDNA was purified from buccal swabs using phenol chloroform extraction.
Label Cy5 and Cy3
Label protocol Bisulphite conversion was carried out using the Methyl Xceed bisulphite kit as per the manufacturer's instructions.
Hybridization protocol Bisulphite-converted DNA was amplified, fragmented and hybridised to the Illumina Infinium Human Methylation27 BeadChip using the standard llumina protocol.
Scan protocol Arrays were imaged using the BeadArray Reader using the standard recommended Illumina scanner setting.
Description 2034.2_B
Data processing Data were preprocessed using the Bioconductor Minfi package in R by the 'illumina' method and normalized to control probes. Subset quantile normalization was performed on type 1 and type 2 probes. Probes failing P detection cutoff of <0.01 were removed. Probes on the X and Y chromosomes have been removed from the processed data. Outlier samples were removed. Between-array quantile normalization was performed to arrive at the final data set of 330168 probes and 53 samples.
Submission date Dec 03, 2012
Last update date Mar 06, 2013
Contact name David Martino
Phone 0863191635
Organization name Telethon Kids Institute
Street address Perth Childrens Hospital, 15 Hospital Avenue
State/province Western Australia
ZIP/Postal code 6009
Country Australia
Platform ID GPL13534
Series (1)
GSE42700 Epigenome analysis of buccal cells from monozygotic and dizygotic twins

Data table header descriptions
VALUE Quantile-normalized average Beta

Data table
cg00000957 0.844176824068802
cg00001349 0.744893278192863
cg00001583 0.0273721837115241
cg00002028 0.0357194427966417
cg00003202 0.0166453340900674
cg00003287 0.0878055972660942
cg00004121 0.521280718939685
cg00007036 0.955802606338566
cg00007898 0.0296128918740264
cg00008004 0.117433605459332
cg00008647 0.0462791162180804
cg00009292 0.136680206660837
cg00009916 0.0224536308615935
cg00011717 0.958839609367463
cg00014168 0.757521572183006
cg00015286 0.796673082863317
cg00015930 0.971560258951673
cg00016238 0.913361461881944
cg00017221 0.023556607806599
cg00017437 0.0411637748877384

Total number of rows: 330168

Table truncated, full table size 9437 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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