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Series GSE54680 Query DataSets for GSE54680
Status Public on Jan 01, 2015
Title DNA methylation variation in Arabidopsis has a genetic basis and appears to be involved in local adaptation
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary We investigated DNA methylation variation in Swedish Arabidopsis thaliana accessions. We found that methylation of transposable elements is temperature sensitive and associated with genetic polymorphism in both cis and trans, whereas gene body methylation is associated with genetic polymorphism in trans. Additionally, complementary RNA-Seq data for the Arabidopsis accessions were used to correlate methylation changes with gene expression across environments.
 
Overall design mRNA-sequencing (mRNA-Seq) of 160 Arabidopsis thaliana accessions grown at 10 C and 163 grown at 16 C. The source tissue for RNA collection was whole rosette at the 9-leaf stage.
 
Contributor(s) Osborne EJ, Zhang P, Remigereau MS, Drewe P, Rätsch G, Nordborg M, Clark RM
Citation(s) 25939354
Submission date Feb 04, 2014
Last update date May 04, 2016
Contact name Richard M Clark
Organization name University of Utah
Department Department of Biology
Lab Clark Laboratory
Street address 257 So. 1400 East, RM 204 SB
City Salt Lake City
State/province Utah
ZIP/Postal code 84112
Country USA
 
Platforms (1)
GPL11221 Illumina Genome Analyzer IIx (Arabidopsis thaliana)
Samples (323)
GSM1321737 s991_10C
GSM1321738 s991_16C
GSM1321739 s992_10C
Relations
BioProject PRJNA237342
SRA SRP036643

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

Supplementary file Size Download File type/resource
GSE54680_RAW.tar 112.7 Mb (http)(custom) TAR (of TXT)
Raw data are available in SRA
Processed data provided as supplementary file

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