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Series GSE29099 Query DataSets for GSE29099
Status Public on Nov 21, 2011
Title Heritable epigenetic variation among maize inbreds
Organism Zea mays
Experiment type Methylation profiling by genome tiling array
Summary Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence. Methylation of cytosine residues provides a mechanism for the inheritance of epigenetic information. We have profiled the distribution of DNA methylation in the large, complex genome of Zea mays (ssp. mays). DNA methylation levels are higher near the centromeres and are generally inversely correlated with recombination and gene expression levels. However, genes that are located in non-syntenic genomic positions relative to species related closely to maize exhibit higher levels of DNA methylation independent of expression state. A comparison of the DNA methylation levels in two different inbred genotypes, B73 and Mo17, allowed for the identification of approximately 700 differentially methylated regions. The regions of differential methylation in B73 and Mo17 often occur in intergenic regions but some of these regions are located within or near genes. There is evidence that variation in DNA methylation levels can occur in genomic regions that are identical-by-descent, illustrating the potential for epigenetic variation that is not tightly linked to genetic changes. A comparison of the genotype and epigenotype in a panel of near-isogenic lines reveals evidence for epigenetic variation that is conditioned by linked regions as well as examples of epigenetic variation that is conditioned by unlinked genomic regions. Our many examples of epigenetic variation, including some without tightly linked genetic variation, have implications for plant breeding and for natural selection.
 
Overall design Methylation profiles in seedling tissue of the maize inbred lines B73 and Mo17. Each genotype was compared for three biological replications using a gene-focused custom 2.1M NimbleGen array.
 
Contributor(s) Swanson-Wagner RA, Eichten SR, Vaughn MW, Springer NM
Citation(s) 22125494
Submission date May 05, 2011
Last update date Jul 29, 2013
Contact name Steve R Eichten
E-mail(s) eicht021@umn.edu
Organization name University of Minnesota
Department Plant Biology
Lab Springer Lab
Street address 1445 Gortner Ave
City St. Paul
State/province MN
ZIP/Postal code 55108
Country USA
 
Platforms (1)
GPL13499 NimbleGen 2.1M Maize Methylation Array
Samples (3)
GSM721082 B73
GSM721083 Mo17
GSM721084 B73 Control
Relations
BioProject PRJNA140355

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE29099_CGH_differential_methylation.txt.gz 20.5 Mb (ftp)(http) TXT
GSE29099_RAW.tar 685.7 Mb (http)(custom) TAR (of PAIR)
GSE29099_full_proccessed_methylation.txt.gz 44.1 Mb (ftp)(http) TXT
GSE29099_proccessed_linked_contrasts.txt.gz 43.6 Mb (ftp)(http) TXT
GSE29099_processed_methylation_values.txt.gz 20.8 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data are available on Series record

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