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Sample GSM1048184 Query DataSets for GSM1048184
Status Public on Mar 06, 2013
Title Buccal cell 18m twin 2, B3006
Sample type genomic
Source name Buccal cheek swab, DZ, 18 months
Organism Homo sapiens
Characteristics gender: male
age: 18 months
cell type: normal buccal cells
monozygotic: 0
dizygotic: 1
monochorionic: 0
sibship: 14
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 B3006.2_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 0.848740654984935
cg00001349 0.756307744986531
cg00001583 0.0406311541538372
cg00002028 0.059217894980673
cg00003202 0.0189319891800999
cg00003287 0.089228382601674
cg00004121 0.606563682411295
cg00007036 0.917128562682812
cg00007898 0.0291347757435245
cg00008004 0.0697186610571343
cg00008647 0.069204214487019
cg00009292 0.137325500211645
cg00009916 0.0241628074567276
cg00011717 0.900754363937038
cg00014168 0.740678627466319
cg00015286 0.678891209919926
cg00015930 0.953843772295482
cg00016238 0.873561838510716
cg00017221 0.039443257862139
cg00017437 0.0125375019067307

Total number of rows: 330168

Table truncated, full table size 9431 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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