GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1048141 Query DataSets for GSM1048141
Status Public on Mar 06, 2013
Title Buccal cell 18m twin 1, 3014
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: 1
sibship: 15
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 3014.1_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 0.806937748477958
cg00001349 0.88571374991458
cg00001583 0.0322477346298405
cg00002028 0.0442756019647995
cg00003202 0.020658909879965
cg00003287 0.103484360807699
cg00004121 0.657882193084963
cg00007036 0.967906211482732
cg00007898 0.0287971088846948
cg00008004 0.160760651407725
cg00008647 0.0504788757884399
cg00009292 0.177136146617117
cg00009916 0.0518053825676086
cg00011717 0.95489153378728
cg00014168 0.779744740743633
cg00015286 0.77100784798267
cg00015930 0.962706656129364
cg00016238 0.714525235975395
cg00017221 0.0286959111511769
cg00017437 0.039362008952053

Total number of rows: 330168

Table truncated, full table size 9431 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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