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Sample GSM1048149 Query DataSets for GSM1048149
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 2, B1022
Sample type genomic
Source name Buccal cheek swab, MZ, birth
Organism Homo sapiens
Characteristics gender: male
age: birth
cell type: normal buccal cells
monozygotic: 1
dizygotic: 0
monochorionic: 1
sibship: 2
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 B1022.2_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 0.883797563991267
cg00001349 0.808282684180733
cg00001583 0.0358706107648438
cg00002028 0.0506693404029497
cg00003202 0.0111639923711766
cg00003287 0.0774313115283009
cg00004121 0.554158070175347
cg00007036 0.963964925535373
cg00007898 0.0130627222919892
cg00008004 0.0770153425129106
cg00008647 0.0554972695208761
cg00009292 0.176194307624283
cg00009916 0.021164148214982
cg00011717 0.917502239881737
cg00014168 0.808198652540928
cg00015286 0.857633339348561
cg00015930 0.962739211036003
cg00016238 0.782346083320511
cg00017221 0.0500514011668516
cg00017437 0.0219596575969754

Total number of rows: 330168

Table truncated, full table size 9440 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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