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Sample GSM1048180 Query DataSets for GSM1048180
Status Public on Mar 06, 2013
Title Buccal cell 18m twin 2, B1126
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: 12
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 B1126.2_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 0.889548441237872
cg00001349 0.823781301069756
cg00001583 0.0268310345028532
cg00002028 0.0633215211899111
cg00003202 0.0208641204897842
cg00003287 0.0859027129279406
cg00004121 0.57614551232118
cg00007036 0.961058664744064
cg00007898 0.0480759626731056
cg00008004 0.0606256990002483
cg00008647 0.0638849121074919
cg00009292 0.307584767086723
cg00009916 0.0381676596261592
cg00011717 0.915101339810645
cg00014168 0.743367874313663
cg00015286 0.75226843154299
cg00015930 0.986610195943571
cg00016238 0.804808542559774
cg00017221 0.046267793891269
cg00017437 0.0256644501506228

Total number of rows: 330168

Table truncated, full table size 9433 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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