Investigation Title Comparison of murine colonic mucosal DNA from postnatal day 90 (P90) to postnatal day 30 (P30) by MSAM
Comment[Submitted Name] Comparison of murine colonic mucosal DNA from postnatal day 90 (P90) to postnatal day 30 (P30) by MSAM
Experimental Design methylation profiling by array
Experimental Design Term Source REF EFO
Comment[SecondaryAccession] GSE18031
Comment[ArrayExpressReleaseDate] 2010-05-22
Comment[AEMIAMESCORE] 3
Comment[Publication DOI] 10.1093/hmg/ddq095
Comment[ArrayExpressAccession] E-GEOD-18031
Comment[MAGETAB TimeStamp_Version] 2010-08-03 13:24:50 Last Changed Rev: 13058
Experimental Factor Name AGE
Experimental Factor Type age
Experimental Factor Term Source REF
Person Last Name Kellermayer Shen
Person First Name Richard Lanlan
Person Mid Initials
Person Email
Person Phone
Person Fax
Person Address Baylor College of Medicine, One Baylor Plaza, Houston, U.S.A.
Person Affiliation Baylor College of Medicine
Person Roles submitter
Person Roles Term Source REF The MGED Ontology
Quality Control Type
Quality Control Term Source REF
Replicate Type
Replicate Term Source REF
Normalization Type
Normalization Term Source REF
Date of Experiment
Public Release Date 2010-05-22
PubMed ID 20197410
Publication DOI 20197410
Publication Author List Kellermayer R, Balasa A, Zhang W, Lee S, Mirza S, Chakravarty A, Szigeti R, Laritsky E, Tatevian N, Smith CW, Shen L, Waterland RA
Publication Title Epigenetic maturation in colonic mucosa continues beyond infancy in mice.
Publication Status journal_article
Publication Status Term Source REF The MGED Ontology
Experiment Description DNA methylation profiling of colonic mucosal DNA between P90 and P30 mice. 0.5ug of DNA was serially digested with SmaI and XmaI followed by an adaptor ligation and adaptor mediated PCR amplification Two independent P90 to P30 comparisons were performed as follows. Samples were labelled with Cy3 (P30) and Cy5 (P90) and two independent P90 to P30 comparisons were done on a 2x105k methylation specific amplification microarray (MSAM) containing 90,535 probes, covering 77% of the 31,019 SmaI intervals between 200 bp and 2 kb in the mouse genome (average 3.8 probes per interval)
Protocol Name P-GSE18031-4 P-GSE18031-3 P-GSE18031-5 P-GSE18031-6 P-GSE18031-7 P-GSE18031-9 P-GSE18031-2 P-GSE18031-1
Protocol Type nucleic_acid_extraction nucleic_acid_extraction labeling hybridization image_aquisition feature_extraction bioassay_data_transformation bioassay_data_transformation
Protocol Description Total DNA was extracted by standard phenol-chloroform isolation tissue isolation: Colonic mucosa was sheared by microscope slide and flash frozen on dry ice 4ug of the digested and amplified DNA was labelled from each sample with either Cy3 or Cy5 according to the Agilent Chip-on-chip mammalian protocol (version 9.1, 2006) Hybridization of the arrays was carried out according to the Agilent Chip-on-chipmammalian protocol (version 9.1, 2006) Scanned on an Agilent G2565AA scanner. Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Probe ratios within one SmaI interval were averaged and the mean of the P value log ratios of the probes within one interval was calculated. ID_REF =
VALUE = ratio (Cy5/Cy3) representing test/reference
30e = gProcessedSignal
90e = rProcessedSignal
90e/30e ratio = ID_REF =
VALUE = ratio (Cy5/Cy3) representing test/reference
30b = gProcessedSignal
90b = rProcessedSignal
90b/30b ratio =
Protocol Parameters
Protocol Hardware
Protocol Software
Protocol Contact
Protocol Term Source REF The MGED Ontology The MGED Ontology The MGED Ontology
SDRF File E-GEOD-18031.sdrf.txt
Term Source Name NCBI Taxonomy ArrayExpress EFO The MGED Ontology
Term Source File http://www.ncbi.nlm.nih.gov/Taxonomy/ http://www.ebi.ac.uk/arrayexpress http://www.ebi.ac.uk/efo/ http://mged.sourceforge.net/ontologies/MGEDontology.php
Term Source Version