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Sample GSM1048168 Query DataSets for GSM1048168
Status Public on Mar 06, 2013
Title Buccal cell 18m twin 1, B1058
Sample type genomic
Source name Buccal cheek swab, MZ, 18 months
Organism Homo sapiens
Characteristics gender: male
age: 18 months
cell type: normal buccal cells
monozygotic: 1
dizygotic: 0
monochorionic: 0
sibship: 9
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 B1058.1_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 0.844098483821855
cg00001349 0.783173480707583
cg00001583 0.0581721546111163
cg00002028 0.0480060808108528
cg00003202 0.0155498098721953
cg00003287 0.106707809847777
cg00004121 0.544582748869814
cg00007036 0.929148799661341
cg00007898 0.0186107616032946
cg00008004 0.146290830875842
cg00008647 0.0643324939119165
cg00009292 0.169980805096787
cg00009916 0.0254901996346041
cg00011717 0.917505621776926
cg00014168 0.709970560055435
cg00015286 0.761128587399551
cg00015930 0.970706467809489
cg00016238 0.918741700252711
cg00017221 0.0426860516196927
cg00017437 0.0312802972691057

Total number of rows: 330168

Table truncated, full table size 9435 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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