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Sample GSM1048139 Query DataSets for GSM1048139
Status Public on Mar 06, 2013
Title Buccal cell 18m twin 2, 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: 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 2034.2_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 0.848653183722462
cg00001349 0.776468950550907
cg00001583 0.0590969846953533
cg00002028 0.0501058288063029
cg00003202 0.00771402514223566
cg00003287 0.0897490402546673
cg00004121 0.538459801780496
cg00007036 0.951235176994568
cg00007898 0.0243838890440603
cg00008004 0.0884886116010045
cg00008647 0.0481039874398047
cg00009292 0.14516102975291
cg00009916 0.0213549920272629
cg00011717 0.937523000363202
cg00014168 0.790973983873136
cg00015286 0.709747137535092
cg00015930 0.983858500506036
cg00016238 0.927031735829407
cg00017221 0.0182823158236422
cg00017437 0.0350743588523312

Total number of rows: 330168

Table truncated, full table size 9436 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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