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Sample GSM1048133 Query DataSets for GSM1048133
Status Public on Mar 06, 2013
Title Buccal cell 18m twin 1, 1035
Sample type genomic
Source name Buccal cheek swab, MZ, 18 months
Organism Homo sapiens
Characteristics gender: female
age: 18 months
cell type: normal buccal cells
monozygotic: 1
dizygotic: 0
monochorionic: 1
sibship: 5
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 1035.1_18M
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 0.815277602170737
cg00001349 0.772310672532334
cg00001583 0.0383692405790187
cg00002028 0.0557817359521865
cg00003202 0.0116544811006245
cg00003287 0.0948748329507462
cg00004121 0.522748972644924
cg00007036 0.951191199172898
cg00007898 0.0270697940052695
cg00008004 0.089191709097374
cg00008647 0.0523323215503173
cg00009292 0.166923616180478
cg00009916 0.051664042102927
cg00011717 0.938484372836937
cg00014168 0.801051717624157
cg00015286 0.809532294705779
cg00015930 0.978642818061314
cg00016238 0.908843462027975
cg00017221 0.04591516067717
cg00017437 0.0514587348626

Total number of rows: 330168

Table truncated, full table size 9438 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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