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Sample GSM1048137 Query DataSets for GSM1048137
Status Public on Mar 06, 2013
Title Buccal cell 18m twin 1, 2034
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: 0
sibship: 13
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 2034.1_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 0.853518213231666
cg00001349 0.685205327700434
cg00001583 0.0348547849890879
cg00002028 0.0682870231065488
cg00003202 0.0142829728034512
cg00003287 0.148399079615559
cg00004121 0.513814880467884
cg00007036 0.962297033940978
cg00007898 0.0281021140690119
cg00008004 0.108154689945004
cg00008647 0.0505635839525497
cg00009292 0.148620209860859
cg00009916 0.0186659961174631
cg00011717 0.930543797437581
cg00014168 0.803225430689879
cg00015286 0.727007555086323
cg00015930 0.970213426380266
cg00016238 0.944472158747342
cg00017221 0.0355088508400803
cg00017437 0.0380015063467459

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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