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Sample GSM1048152 Query DataSets for GSM1048152
Status Public on Mar 06, 2013
Title Buccal cell 18m twin 2, B1024
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: 3
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 B1024.2_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 0.854143177537791
cg00001349 0.888143325784116
cg00001583 0.0448649433676694
cg00002028 0.0640317226119761
cg00003202 0.00996271831941967
cg00003287 0.0867236501466187
cg00004121 0.608433590363995
cg00007036 0.95265106046932
cg00007898 0.0565088451631099
cg00008004 0.125799138268764
cg00008647 0.0718043686256929
cg00009292 0.120670651684118
cg00009916 0.0362724502823559
cg00011717 0.912725386554951
cg00014168 0.74220089465553
cg00015286 0.797193461743639
cg00015930 0.972921465798886
cg00016238 0.896427342187271
cg00017221 0.0675078660831101
cg00017437 0.0404474771511411

Total number of rows: 330168

Table truncated, full table size 9432 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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