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Series GSE80744 Query DataSets for GSE80744
Status Public on Jul 14, 2016
Title Epigenomic and genome structural diversity in a worldwide collection of Arabidopsis thaliana
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary Epigenetic variation can impact gene transcription and may play roles in phenotypic diversity and adaptation. Here we report 1,107 high quality single-base resolution methylomes, and 1,210 transcriptomes from the 1001 Arabidopsis Genomes population. Analyses reveal strong effects of geographic origin on average DNA methylation levels, alterations of gene expression by epialleles and a highly complex genetic basis for DNA methylation. Physical genome maps for nine of the most diverse accessions revealed how transposable elements and other structural variations shaped the epigenome to allow rapid adaptation to environmental changes, with strong emphasis on disease resistance. Analysis of the cistromes and epicistromes in these accessions revealed a significant association between both methylation and nucleotide variation and the conservation of transcription factor binding sites. The Arabidopsis thaliana 1001 Epigenomes Project now provides a comprehensive resource to help further understand how epigenetic variation contributes to both molecular and phenotypes in natural populations of the most widely studied reference plant.
 
Overall design RNA-seq profiling of 728 Arabidopsis thaliana accessions
Please note that the sample 'Cod-0 (9836)' is missing from the data columns in the normalized expression matrix ('ath1001_tx_norm_2016-04-21-UQ_gNorm_normCounts_k4.tsv') since the read count distribution from this sample was incompatible with the upper-quartile normalization method applied to all the samples, therefore excluded from the expression matrix.
Web link http://1001epigenomes.org
 
Contributor(s) Huang SC, Kawakatsu T, Jupe F, Schmitz RJ, Urich M, Castanon R, Nery JR, Chen H, Ecker JR
Citation(s) 27419873
Submission date Apr 28, 2016
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 (2)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
GPL21785 Illumina HiSeq 4000 (Arabidopsis thaliana)
Samples (728)
GSM2135714 Tuescha-9 (10000)
GSM2135715 TueV-13 (10001)
GSM2135716 TueWal-2 (10002)
Relations
BioProject PRJNA319904
SRA SRP074107

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
GSE80744_RAW.tar 92.3 Mb (http)(custom) TAR (of TXT)
GSE80744_ath1001_tx_norm_2016-04-21-UQ_gNorm_normCounts_k4.tsv.gz 25.6 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data is available on Series record

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