 |
 |
GEO help: Mouse over screen elements for information. |
|
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 |
E-mail(s) |
daniil.wiebe@gmail.com
|
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)
|
|
Relations |
BioProject |
PRJNA381131 |
SRA |
SRP102803 |
Supplementary file |
Size |
Download |
File type/resource |
GSE97258_differential_expression.xls.gz |
908.5 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
 |