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Series GSE33730 Query DataSets for GSE33730
Status Public on Dec 16, 2011
Title Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm
Organism Zea mays
Experiment type Methylation profiling by genome tiling array
Summary Imprinting describes the differential expression of alleles based upon their parent of origin. Deep sequencing of RNAs from maize endosperm and embryo tissue 14 days after pollination was used to identify imprinted genes among a set of ~12,000 genes that were expressed and contained sequence polymorphisms between the B73 and Mo17 genotypes. The analysis of parent-of-origin patterns of expression resulted in the identification of 100 putative imprinted genes in maize endosperm including 54 maternally expressed genes (MEGs) and 46 paternally expressed genes (PEGs). Three of these genes have been previously identified as imprinted while the remaining 97 genes represent novel imprinted maize genes. A genome-wide analysis of DNA methylation identified regions with reduced endosperm DNA methylation in, or near, 19 of the 100 imprinted genes. The reduced levels of DNA methylation in endosperm are caused by hypomethylation of the maternal allele for both MEGs and PEGs in all cases tested. Many of the imprinted genes with reduced DNA methylation levels also show endosperm-specific expression patterns. The imprinted maize genes were compared with imprinted genes identified in genome-wide screens of rice and Arabidopsis and at least 10 examples of conserved imprinting between maize and each of the other species were identified.
 
Overall design Methylation profiles across endosperm tissue in B73 and Mo17 were assayed for three biological replications using a custom 2.1M gene-focused NimbleGen array.
 
Contributor(s) Waters AJ, Swanson-Wagner RA, Eichten SR, Vaughn MW, Springer NM
Citation(s) 22198147
Submission date Nov 16, 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 (6)
GSM833496 B73 endosperm rep1
GSM833497 B73 endosperm rep2
GSM833498 B73 endosperm rep3
Relations
BioProject PRJNA148441

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
GSE33730_RAW.tar 604.9 Mb (http)(custom) TAR (of PAIR)
GSE33730_fit.B73_endo.05-12-11.txt.gz 141.6 Mb (ftp)(http) TXT
GSE33730_fit.Mo17_endo_c.05-12-11.txt.gz 141.4 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data are available on Series record

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