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Series GSE42408 Query DataSets for GSE42408
Status Public on Mar 02, 2013
Organism Arabidopsis thaliana
Experiment type Expression profiling by genome tiling array
Summary Understanding the patterns and processes driving natural genetic variation in gene expression is of fundamental importance to biology. In this study, we examined genetic variation in gene transcription through expression QTL (eQTL) analysis in the Tsu-1 x Kas-1 recombinant inbred line (RIL) mapping population of Arabidopsis thaliana. To understand how natural variation in transcription responds to abiotic stress, we conducted eQTL in both well watered and soil drying conditions. Further, we evaluated whether elements of genome structure were associated with eQTL occurance and genes responding to treatment conditions. Overall, we identified thousands of genes that responded to soil moisture availability and hundreds of eQTLs. However, we identified very few interactions between eQTLs and environmental conditions, and both treatment conditions were enriched for similar gene ontology (GO) categories. We did find strong evidence for associations between genome structure and natural variation in transcription. In general, genes with eQTLs were positively associated with local recombination rates and levels of polymorphism while genes responding to the treatment were negatively correlated with these factors. Our study provides further insight into the origin and maintenance of natural variation in transcription and how that variation responds to environmental conditions.
Expression analysis by hybridization to atSNPTILE array (Affymetrix).
Overall design Seed of the 104 RILs from reciprocal crosses between A. thaliana (L.) Heynh. accessions Kas-1 (CS903) and Tsu-1 (CS1640) were sown on fritted clay (Profile Products LLC, Buffalo Grove, IL) in 2.5-inch pots. Plants were arranged in a randomized complete block design consisting of 4 blocks, and then the pots were refrigerated at 4°C in darkness for 6 d to cold-stratify the seeds prior to commencement of a 12 h photoperiod in Conviron ATC60 growth chambers (Controlled Environments, Winnipeg, MB), at 23°C and 40% humidity during the day and 20°C and 50% humidity during the dark period. Light intensity was approximately 330 µmol m-2 s-1. After four weeks of growth, half of the plants were given a drought treatment, while the others remained fully watered. The drought treatment was randomly assigned to 2 of the 4 blocks and consisted of a slow decrease in soil moisture content over the course of one week. Each day, all pots assigned to the drought treatment were weighed, and water was added to individual pots to bring them to the target gravimetric water content. The target water content decreased each day, in the following series: 100%, 90%, 80%, 70%, 60%, 45%, and 40% of field capacity. At the end of the treatment, leaf tissue was collected from both treatments for RNA extraction.
Contributor(s) Lowry DB, Logan T, Santuari L, Hardtke CS, Richards JH, McKay JK, Sen S, Juenger TE, DeRose-Wilson LJ
Citation(s) 24045022
Submission date Nov 20, 2012
Last update date Apr 21, 2014
Contact name David Bryant Lowry
Organization name University of Texas at Austin
Department Integrative Biology
Lab Thomas Juenger
Street address 1 University Station #C0930
City Austin
State/province TX
ZIP/Postal code 78712
Country USA
Platforms (1)
GPL16303 [atSNPtilx520433] Arabidopsis Tiling array [TAIR9-based custom CDF, ORF version]
Samples (208)
GSM1039267 RIL KT117, wet treatment
GSM1039268 RIL KT117, dry treatment
GSM1039269 RIL KT120, wet treatment
BioProject PRJNA181341

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
GSE42408_RAW.tar 1.7 Gb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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