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Sample GSM1048155 Query DataSets for GSM1048155
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 2, 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: 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 B1032.2_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 0.860501953343868
cg00001349 0.851316528100701
cg00001583 0.021133249357773
cg00002028 0.0754170845804629
cg00003202 0.0310326386388108
cg00003287 0.065618705651765
cg00004121 0.510866676549879
cg00007036 0.957382271811175
cg00007898 0.0429177620450642
cg00008004 0.0972330063267627
cg00008647 0.065986341428245
cg00009292 0.16525061159266
cg00009916 0.018813442892206
cg00011717 0.917946435126184
cg00014168 0.678040462166407
cg00015286 0.769157025798828
cg00015930 0.962466488855583
cg00016238 0.84420907512209
cg00017221 0.0454898711931542
cg00017437 0.023441487957214

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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