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SRX1719980: GSM2130876: AT2G46270_GBF3_EtOH_ChIP_rep3; Arabidopsis thaliana; ChIP-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 28.3M spots, 2.8G bases, 1.9Gb downloads

Submitted by: NCBI (GEO)
Study: ChIP-seq of abscisic acid-reponsive transcription factors
show Abstracthide Abstract
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.
Sample: AT2G46270_GBF3_EtOH_ChIP_rep3
SAMN04884780 • SRS1407843 • All experiments • All runs
Instrument: Illumina HiSeq 2500
Strategy: ChIP-Seq
Selection: ChIP
Layout: SINGLE
Construction protocol: After formaldehyde crosslink and nuclei isolation, chromatin was sonicated to 100-500 bp fragments. YPet-tagged TF of interest was immunoprecipitated by a rabbit polyclonal GFP antibody (cat #A11122, Thermo Fisher USA). Mock ChIP was carried out by immunoprecipitating Col-0 with the same GFP antibody. Detailed ChIP protocol is described in Song et al. Curr. Protoc. plant Biol. 2016. Libraries were prepared according to Illumina's instructions accompanying TruSeq DNA sample prep kit and sequenced by Illumina HiSeq 2500 according to the manufacturer's instructions.
Experiment attributes:
GEO Accession: GSM2130876
Runs: 1 run, 28.3M spots, 2.8G bases, 1.9Gb
Run# of Spots# of BasesSizePublished


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