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Series GSE97258 Query DataSets for GSE97258
Status Public on Jun 01, 2017
Title Auxin regulates functional gene groups in a fold-specific manner in Arabidopsis root
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary Auxin plays a pivotal role in virtually every aspect of plant morphogenesis. It simultaneously orchestrates a wide variety of processes, including cell wall biogenesis, transition through the cell cycle, and metabolism of a wide range of chemical substances, among others. The coordination principles for such complex regulation in a cell at a system level are poorly understood.
Here, we apply a whole-genome approach to estimate the coherence of the auxin-regulated transcriptional response in gene groups, united by a certain biological process, molecular function or cell component, based on the fold change of the expression level.
The corresponding analysis of RNA-Seq data for Arabidopsis roots treated with auxin for 6 h revealed that the intervals for the fold change of gene expression levels are quite narrow for many functional gene groups. The fold-specific manner of auxin response in most of these groups was confirmed using independent microarray data. To predict the mechanisms underlying such a coordinated expression, we performed motif enrichment analysis, which revealed TBX1-3, SBX, REG and TCP/site 2 as the candidates associated with fold-specific responses to auxin.
Overall design mRNA profiles of 3 dag wild type (WT) and 6h IAA treated Arabidopsis roots were generated by RNA sequencing, in triplicate, using AB SOLiD technology
Contributor(s) Omelyanchuk NA, Mironova VV, Vasiliev GV
Citation(s) 28559568
Submission date Mar 31, 2017
Last update date May 15, 2019
Contact name Daniil Wiebe
Organization name ICG SBRAS
Street address Lavrentyeva 10
City Novosibirsk
ZIP/Postal code 630090
Country Russia
Platforms (2)
GPL13396 AB SOLiD System (Arabidopsis thaliana)
GPL16033 AB 5500xl Genetic Analyzer (Arabidopsis thaliana)
Samples (6)
GSM2560250 Control rep1
GSM2560251 Control rep2
GSM2560252 Control rep3
BioProject PRJNA381131
SRA SRP102803

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Supplementary file Size Download File type/resource
GSE97258_differential_expression.xls.gz 908.5 Kb (ftp)(http) XLS
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