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Series GSE43858 Query DataSets for GSE43858
Status Public on Mar 05, 2013
Title Patterns of Population Epigenomic Diversity in Arabidopsis thaliana (RNA-Seq)
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to phenotypic diversity, its interaction with genetic variation requires further investigation. Here, we report population-wide DNA sequencing of genomes, transcriptomes, and methylomes of wild Arabidopsis thaliana accessions. Single cytosine methylation polymorphisms are unlinked to genotype. However, the rate of linkage disequilibrium decay amongst differentially methylated regions targeted by RNA-directed DNA methylation is similar to the rate for single nucleotide polymorphisms. Association analyses of these RNA-directed DNA methylation regions with genetic variants identified 2,372 methylQTL, which revealed the first population estimate of genetically dependent methylation variation. Analysis of invariably methylated transposons and genes across this population indicates that loci targeted by RNA-directed DNA methylation are epigenetically reactivated during male gametogenesis, which facilitates their silencing across generations.
 
Overall design RNA-seq from naturally-occurring Arabidopsis accessions
 
Contributor(s) Schmitz RJ, Schultz MD, Ecker JR
Citation(s) 23467092
Submission date Jan 29, 2013
Last update date May 15, 2019
Contact name Joseph R Ecker
E-mail(s) ecker@salk.edu
Phone 8584534100
Organization name HHMI-Salk-Institute
Department Genomic Analysis Laboratory
Lab Ecker lab
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platforms (1)
GPL14599 AB SOLiD 4 System (Arabidopsis thaliana)
Samples (144)
GSM1086809 Aa_0
GSM1086810 Abd_0
GSM1086811 Ak_1
Relations
BioProject PRJNA187928
SRA SRP018264

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE43858_RAW.tar 65.7 Mb (http)(custom) TAR (of TSV)
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Raw data are available in SRA
Processed data is available on Series record
Processed data provided as supplementary file

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