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Sample GSM1048177 Query DataSets for GSM1048177
Status Public on Mar 06, 2013
Title Buccal cell 18m twin 2, B1107
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: 11
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 B1107.2_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 0.764875392730544
cg00001349 0.780314088418539
cg00001583 0.0517504187165601
cg00002028 0.0793479494508812
cg00003202 0.0182524018218844
cg00003287 0.105906671735963
cg00004121 0.51724927015753
cg00007036 0.937628040560331
cg00007898 0.0221273777155458
cg00008004 0.100169175827821
cg00008647 0.0525451846207478
cg00009292 0.11817211980287
cg00009916 0.0104228070997571
cg00011717 0.914152333357496
cg00014168 0.760019394931374
cg00015286 0.714771439609269
cg00015930 0.974402270739548
cg00016238 0.900032169238344
cg00017221 0.0427918546868997
cg00017437 0.011757766259329

Total number of rows: 330168

Table truncated, full table size 9437 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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