GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1048163 Query DataSets for GSM1048163
Status Public on Mar 06, 2013
Title Buccal cell Birth twin 2, B1046
Sample type genomic
Source name Buccal cheek swab, MZ, birth
Organism Homo sapiens
Characteristics gender: male
age: birth
cell type: normal buccal cells
monozygotic: 1
dizygotic: 0
monochorionic: 0
sibship: 7
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 B1046.2_B
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 0.847515484312496
cg00001349 0.781682138480643
cg00001583 0.0301762922267116
cg00002028 0.0715253979030617
cg00003202 0.0160930105417917
cg00003287 0.0619815364228898
cg00004121 0.60121216187764
cg00007036 0.983010720825389
cg00007898 0.0508851334156256
cg00008004 0.0399488508354753
cg00008647 0.0926985650037054
cg00009292 0.142996181801084
cg00009916 0.0350331595739828
cg00011717 0.927755497484463
cg00014168 0.791236764059055
cg00015286 0.878035191201815
cg00015930 0.973746565559751
cg00016238 0.837731874451081
cg00017221 0.0420165353717298
cg00017437 0.0146738244371464

Total number of rows: 330168

Table truncated, full table size 9440 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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