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Sample GSM1048179 Query DataSets for GSM1048179
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 1, B1126
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: 12
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 B1126.1_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 0.824888618109508
cg00001349 0.759310820656451
cg00001583 0.0245011576905867
cg00002028 0.0793229517484598
cg00003202 0.0199429644503928
cg00003287 0.0602241293627001
cg00004121 0.505943423718954
cg00007036 0.925558939814055
cg00007898 0.0129292213252041
cg00008004 0.0958326662610232
cg00008647 0.0728648303958929
cg00009292 0.145278949922728
cg00009916 0.027857594161192
cg00011717 0.895565758523192
cg00014168 0.736182456016214
cg00015286 0.742265890198273
cg00015930 0.970009468518824
cg00016238 0.898137492387509
cg00017221 0.0217830549904119
cg00017437 0.0169385344512014

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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