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Sample GSM1048174 Query DataSets for GSM1048174
Status Public on Mar 06, 2013
Title Buccal cell 18m twin 2, B1072
Sample type genomic
Source name Buccal cheek swab, DZ, 18 months
Organism Homo sapiens
Characteristics gender: female
age: 18 months
cell type: normal buccal cells
monozygotic: 0
dizygotic: 1
monochorionic: 0
sibship: 10
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 B1072.2_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 0.821591236404281
cg00001349 0.827737659741858
cg00001583 0.0300244774169065
cg00002028 0.0648701020647218
cg00003202 0.020960743268406
cg00003287 0.0300939363821804
cg00004121 0.458271542324889
cg00007036 0.959284096081978
cg00007898 0.0317471873698055
cg00008004 0.190308672307519
cg00008647 0.0674152881144894
cg00009292 0.188320334290075
cg00009916 0.0355259871862536
cg00011717 0.925047529892239
cg00014168 0.706920330696102
cg00015286 0.742823136292672
cg00015930 0.965282976712642
cg00016238 0.718779804411429
cg00017221 0.046195781185266
cg00017437 0.0205879172324847

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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