GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1048182 Query DataSets for GSM1048182
Status Public on Mar 06, 2013
Title Buccal cell 18m twin 1, 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: 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 B3006.1_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 0.860408421356649
cg00001349 0.801008249538718
cg00001583 0.0416904374994969
cg00002028 0.072439551136665
cg00003202 0.0254949490463289
cg00003287 0.107351281338493
cg00004121 0.617983303859667
cg00007036 0.946746999685058
cg00007898 0.0403976549508394
cg00008004 0.0511555347598458
cg00008647 0.080019270271127
cg00009292 0.14178013116053
cg00009916 0.0119154901314542
cg00011717 0.89746749639509
cg00014168 0.750693418740142
cg00015286 0.72513641571555
cg00015930 0.972873357069416
cg00016238 0.883542197739063
cg00017221 0.0345767175344872
cg00017437 0.0260521533309777

Total number of rows: 330168

Table truncated, full table size 9429 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap