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Sample GSM1048158 Query DataSets for GSM1048158
Status Public on Mar 06, 2013
Title Buccal cell 18m twin 2, B1042
Sample type genomic
Source name Buccal cheek swab, DZ, 18 months
Organism Homo sapiens
Characteristics gender: male
age: 18 months
cell type: normal buccal cells
monozygotic: 0
dizygotic: 1
monochorionic: 0
sibship: 6
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 B1042.2_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 0.883075795802399
cg00001349 0.763379682549761
cg00001583 0.0343028728439322
cg00002028 0.0615832319541523
cg00003202 0.0214627571584098
cg00003287 0.0715777951843738
cg00004121 0.400744129615858
cg00007036 0.959456241590665
cg00007898 0.0531033915190637
cg00008004 0.126846337543213
cg00008647 0.0642792602326901
cg00009292 0.162923065791705
cg00009916 0.0325037126041608
cg00011717 0.921646056519798
cg00014168 0.890379896830517
cg00015286 0.781801839047982
cg00015930 0.959605870479132
cg00016238 0.760904695751171
cg00017221 0.037968918751921
cg00017437 0.0260490109654428

Total number of rows: 330168

Table truncated, full table size 9434 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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