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Series GSE80564 Query DataSets for GSE80564
Status Public on Feb 03, 2017
Title ChIP-seq of abscisic acid-reponsive transcription factors
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 (124)
GSM2130859 AT5G47640_NFYB2_ABA_ChIP_rep1
GSM2130860 AT5G47640_NFYB2_EtOH_ChIP_rep1
GSM2130861 AT5G47640_NFYB2_ABA_ChIP_rep2
This SubSeries is part of SuperSeries:
GSE80568 ChIP-Seq and RNA-Seq of abscisic acid-reponsive transcription factors
Relations
BioProject PRJNA319319
SRA SRP073709

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
GSE80564_AT1G22640_MYB3_ABA_optimal_narrowPeak_p16.bed.gz 121.2 Kb (ftp)(http) BED
GSE80564_AT1G22640_MYB3_EtOH_optimal_narrowPeak_p16.bed.gz 67.5 Kb (ftp)(http) BED
GSE80564_AT1G49720_ABF1_ABA_optimal_narrowPeak_p16.bed.gz 163.1 Kb (ftp)(http) BED
GSE80564_AT1G49720_ABF1_EtOH_optimal_narrowPeak_p16.bed.gz 49.0 Kb (ftp)(http) BED
GSE80564_AT1G51140_FBH3_ABA_optimal_narrowPeak_p16.bed.gz 4.3 Kb (ftp)(http) BED
GSE80564_AT1G51140_FBH3_EtOH_optimal_narrowPeak_p16.bed.gz 22.3 Kb (ftp)(http) BED
GSE80564_AT1G56170_NFYC2_ABA_optimal_narrowPeak_p16.bed.gz 162.8 Kb (ftp)(http) BED
GSE80564_AT1G56170_NFYC2_EtOH_optimal_narrowPeak_p16.bed.gz 113.6 Kb (ftp)(http) BED
GSE80564_AT1G77450_ANAC032_ABA_optimal_narrowPeak_p16.bed.gz 152.5 Kb (ftp)(http) BED
GSE80564_AT1G77450_ANAC032_EtOH_optimal_narrowPeak_p16.bed.gz 16.8 Kb (ftp)(http) BED
GSE80564_AT2G22430_HB6_ABA_optimal_narrowPeak_p16.bed.gz 222.3 Kb (ftp)(http) BED
GSE80564_AT2G22430_HB6_EtOH_optimal_narrowPeak_p16.bed.gz 190.0 Kb (ftp)(http) BED
GSE80564_AT2G46270_GBF3_ABA_optimal_narrowPeak_p16.bed.gz 309.0 Kb (ftp)(http) BED
GSE80564_AT2G46270_GBF3_EtOH_optimal_narrowPeak_p16.bed.gz 272.9 Kb (ftp)(http) BED
GSE80564_AT2G46680_HB7_ABA_optimal_narrowPeak_p16.bed.gz 261.6 Kb (ftp)(http) BED
GSE80564_AT2G46680_HB7_EtOH_optimal_narrowPeak_p16.bed.gz 72.9 Kb (ftp)(http) BED
GSE80564_AT3G19290_ABF4_ABA_optimal_narrowPeak_p16.bed.gz 171.6 Kb (ftp)(http) BED
GSE80564_AT3G19290_ABF4_EtOH_optimal_narrowPeak_p16.bed.gz 123.6 Kb (ftp)(http) BED
GSE80564_AT4G01120_GBF2_ABA_optimal_narrowPeak_p16.bed.gz 209.2 Kb (ftp)(http) BED
GSE80564_AT4G01120_GBF2_EtOH_optimal_narrowPeak_p16.bed.gz 201.4 Kb (ftp)(http) BED
GSE80564_AT4G27410_RD26_ABA_optimal_narrowPeak_p16.bed.gz 226.0 Kb (ftp)(http) BED
GSE80564_AT4G27410_RD26_EtOH_optimal_narrowPeak_p16.bed.gz 149.2 Kb (ftp)(http) BED
GSE80564_AT4G34000_ABF3_ABA_optimal_narrowPeak_p16.bed.gz 219.5 Kb (ftp)(http) BED
GSE80564_AT4G34000_ABF3_EtOH_optimal_narrowPeak_p16.bed.gz 180.7 Kb (ftp)(http) BED
GSE80564_AT4G37790_HAT22_ABA_optimal_narrowPeak_p16.bed.gz 184.6 Kb (ftp)(http) BED
GSE80564_AT4G37790_HAT22_EtOH_optimal_narrowPeak_p16.bed.gz 151.9 Kb (ftp)(http) BED
GSE80564_AT5G04340_ZAT6_ABA_optimal_narrowPeak_p16.bed.gz 223.5 Kb (ftp)(http) BED
GSE80564_AT5G04340_ZAT6_EtOH_optimal_narrowPeak_p16.bed.gz 101.7 Kb (ftp)(http) BED
GSE80564_AT5G04760_ABA_optimal_narrowPeak_p16.bed.gz 214.8 Kb (ftp)(http) BED
GSE80564_AT5G04760_EtOH_optimal_narrowPeak_p16.bed.gz 181.9 Kb (ftp)(http) BED
GSE80564_AT5G05410_DREB2A_ABA_optimal_narrowPeak_p16.bed.gz 31.8 Kb (ftp)(http) BED
GSE80564_AT5G05410_DREB2A_EtOH_optimal_narrowPeak_p16.bed.gz 480 b (ftp)(http) BED
GSE80564_AT5G43840_HSFA6A_ABA_optimal_narrowPeak_p16.bed.gz 38.3 Kb (ftp)(http) BED
GSE80564_AT5G43840_HSFA6A_EtOH_optimal_narrowPeak_p16.bed.gz 875 b (ftp)(http) BED
GSE80564_AT5G47640_NFYB2_ABA_optimal_narrowPeak_p16.bed.gz 343.0 Kb (ftp)(http) BED
GSE80564_AT5G47640_NFYB2_EtOH_optimal_narrowPeak_p16.bed.gz 281.1 Kb (ftp)(http) BED
GSE80564_AT5G63790_ANAC102_ABA_optimal_narrowPeak_p16.bed.gz 92.7 Kb (ftp)(http) BED
GSE80564_AT5G63790_ANAC102_EtOH_optimal_narrowPeak_p16.bed.gz 56.0 Kb (ftp)(http) BED
GSE80564_AT5G65310_HB5_ABA_optimal_narrowPeak_p16.bed.gz 185.7 Kb (ftp)(http) BED
GSE80564_AT5G65310_HB5_EtOH_optimal_narrowPeak_p16.bed.gz 194.8 Kb (ftp)(http) BED
GSE80564_AT5G67300_MYB44_ABA_optimal_narrowPeak_p16.bed.gz 222.6 Kb (ftp)(http) BED
GSE80564_AT5G67300_MYB44_EtOH_optimal_narrowPeak_p16.bed.gz 140.1 Kb (ftp)(http) BED
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Processed data are available on Series record
Raw data are available in SRA

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