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Sample GSM1048153 Query DataSets for GSM1048153
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 1, B1032
Sample type genomic
Source name Buccal cheek swab, DZ, birth
Organism Homo sapiens
Characteristics gender: female
age: birth
cell type: normal buccal cells
monozygotic: 0
dizygotic: 1
monochorionic: 0
sibship: 4
twin: 1
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 B1032.1_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 0.794567246917263
cg00001349 0.821816726569764
cg00001583 0.0318386649556772
cg00002028 0.101776724462523
cg00003202 0.0234959900220272
cg00003287 0.059485891182015
cg00004121 0.511867729735476
cg00007036 0.940791882639564
cg00007898 0.0357102304969664
cg00008004 0.088878984425803
cg00008647 0.0850103669626179
cg00009292 0.159487692964112
cg00009916 0.0112248468675418
cg00011717 0.864830891026774
cg00014168 0.631783464321403
cg00015286 0.746328826118425
cg00015930 0.972549740056298
cg00016238 0.896741554455847
cg00017221 0.0171542905350414
cg00017437 0.0297527607200816

Total number of rows: 330168

Table truncated, full table size 9441 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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