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Sample GSM1048178 Query DataSets for GSM1048178
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 2, 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: 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 B1107.2_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 0.854385319362967
cg00001349 0.761605674171979
cg00001583 0.0226602703266069
cg00002028 0.0446109186029134
cg00003202 0.00860086280814178
cg00003287 0.0547720172773867
cg00004121 0.506076723861182
cg00007036 0.943514584983683
cg00007898 0.0235199595702608
cg00008004 0.0781334621216905
cg00008647 0.0577398702114167
cg00009292 0.156602909211919
cg00009916 0.0175968302784206
cg00011717 0.949433390489622
cg00014168 0.794659394669205
cg00015286 0.809419108600983
cg00015930 0.970211590639258
cg00016238 0.933834476295278
cg00017221 0.0342316435375477
cg00017437 0.022099456167114

Total number of rows: 330168

Table truncated, full table size 9451 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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