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Series GSE80566 Query DataSets for GSE80566
Status Public on Feb 03, 2017
Title ChIP-seq of abscisic acid-reponsive transcription factors [DIG]
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Abscisic acid (ABA) is an essential hormone that allows plants to respond to environmental stresses such as high salinity, drought and cold. It also plays a pivotal role in seed maturation and germination. Because of its importance, transcriptome changes in response to ABA have been profiled extensively by the plant community. Very few ChIP-chip/seq of ABA-related TFs have been reported to date. To fill the knowledge gap about how ABA works at the transcriptional level, we carried out ChIP-seq on 21 TFs from 11 different families using both mock- and ABA-treated conditions. Analyses of the resulting 122 ChIP-seq datasets identified 326,698 TF binding events using a stringent statistical cutoff. Based on our data, a comprehensive regulatory network in Arabidopsis thaliana was constructed. We uncovered determinants of dynamic TF binding and defined a hierarchy among TFs to explain differential gene expression and pathway feedback regulation. By extrapolating regulatory characteristics observed for the canonical ABA pathway components, we identified a new family of transcriptional regulators modulating ABA and salt responsiveness, and demonstrate their utility to modulate plant resilience to osmotic stress.
 
Overall design Identification of binding sites for 21 transcription factors using both mock- and ABA-treated conditions with mock IP of wild-type Col-0 ChIPped by anti-GFP antibody as control. Each experiment was carried out with at least two replicates.
 
Contributor(s) Song L, Huang SC, Castanon R, Ecker JR
Citation(s) 27811239
Submission date Apr 22, 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 (1)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
Samples (3)
GSM2131011 GFP_Dex_6h_ChIP
GSM2131012 AT3G45810_DIG1_Dex_6h_ChIP
GSM2131013 AT5G50360_DIG2_Dex_6h_ChIP
This SubSeries is part of SuperSeries:
GSE80568 ChIP-Seq and RNA-Seq of abscisic acid-reponsive transcription factors
Relations
BioProject PRJNA319317
SRA SRP073708

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
GSE80566_RAW.tar 800.0 Kb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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