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Series GSE14570 Query DataSets for GSE14570
Status Public on Jun 12, 2009
Title Extensive demethylation of repetitive elements during seed development underlies gene imprinting
Organism Arabidopsis thaliana
Experiment type Methylation profiling by genome tiling array
Methylation profiling by high throughput sequencing
Summary DNA methylation is an epigenetic mark associated with transposable element silencing and gene imprinting in flowering plants and mammals. In plants, imprinting occurs in the endosperm, which nourishes the embryo during seed development. We have profiled Arabidopsis DNA methylation genome-wide in the embryo and endosperm. Large-scale methylation changes accompany endosperm development and endosperm-specific gene expression. Transposable element fragments are extensively demethylated in the endosperm. We discovered new imprinted genes by identifying candidate genes associated with the top differentially methylated regions. Our data suggest that imprinting in plants evolved from genome defense against transposable elements.

Keywords: Affinity-purification on microarray
Overall design All experiments were done using two channels per chip. Immunoprecipitated methylated DNA (IP) was compared to control genomic DNA (input). Both the IP and input represent Cy5 and Cy3 labeled Illumina GA libraries.
Contributor(s) Gehring M, Henikoff S
Citation(s) 19520961
Submission date Jan 26, 2009
Last update date May 15, 2019
Contact name Jorja Henikoff
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
Platforms (2)
GPL3371 FHCRC Arabidopsis Tiling Array
GPL9062 Illumina Genome Analyzer (Arabidopsis thaliana)
Samples (10)
GSM364540 Embryo DNA methylation IP/total DNA (MGE_220227)
GSM364541 Endosperm DNA methylation IP/total DNA (MGE_220242)
GSM364542 dme-2 endosperm DNA methylation IP/total DNA (MGd_220241)
SRA SRP000779
BioProject PRJNA111577

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
GSE14570_RAW.tar 875.1 Mb (http)(custom) TAR (of BEDGRAPH, GFF, PAIR, TXT)
GSE14570_README.txt 1.2 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data included within Sample table
Processed data provided as supplementary file

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