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Sample GSM1048176 Query DataSets for GSM1048176
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 1, B1107
Sample type genomic
Source name Buccal cheek swab, MZ, birth
Organism Homo sapiens
Characteristics gender: female
age: birth
cell type: normal buccal cells
monozygotic: 1
dizygotic: 0
monochorionic: 1
sibship: 11
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 B1107.1_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 0.839985515415761
cg00001349 0.767153124254543
cg00001583 0.0156727703651823
cg00002028 0.0603502800498523
cg00003202 0.0204539949064638
cg00003287 0.039798234056773
cg00004121 0.56114806500371
cg00007036 0.873702060017377
cg00007898 0.0359712029079776
cg00008004 0.0975741249903535
cg00008647 0.0671819564928764
cg00009292 0.164357319764398
cg00009916 0.015971244396311
cg00011717 0.911281475852947
cg00014168 0.700877748420511
cg00015286 0.836081361674812
cg00015930 0.975249042174184
cg00016238 0.933508737809384
cg00017221 0.0356427332565787
cg00017437 0.0149245648648636

Total number of rows: 330168

Table truncated, full table size 9439 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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