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Series GSE39215 Query DataSets for GSE39215
Status Public on Feb 01, 2013
Title Genome-wide identification of PIF3-binding sites and direct-target genes of PIF3 transcriptional regulation in skotomorphogenesis [ChIP-Seq]
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting bHLH Factors (PIF1, 3, 4 and 5) are critically necessary to maintaining this developmental state, and that light activation of phy induces a switch to photomorphogenic development by inducing rapid degradation of the PIFs. Here, using combined ChIP-seq and RNA-seq analyses, we have identified genes that are direct targets of PIF3 transcriptional regulation, and we provide evidence that the quartet collectively regulate these genes by shared, direct binding to the target promoters in promoting skotomorphogenesis.
 
Overall design Four biological replicates data of PIF3-binding sites were collected by comparing the parallel ChIP samples from transgenic seedlings overexpressing Myc-epitope-tagged PIF3 (35S:PIF3-5xMyc, P3M) in pif3-3 null mutant background and the wild-type (WT) control.
 
Contributor(s) Zhang Y, Mayba O, Quail PH
Citation(s) 23382695, 35251080
Submission date Jul 10, 2012
Last update date Mar 09, 2022
Contact name Yu Zhang
E-mail(s) yuzhang@berkeley.edu
Phone 1-510-559-5889
Organization name UC Berkeley
Department Plant and Microbial Biology
Lab Peter H. Quail
Street address 800 Buchanan Street
City Albany
State/province California
ZIP/Postal code 94710
Country USA
 
Platforms (1)
GPL11221 Illumina Genome Analyzer IIx (Arabidopsis thaliana)
Samples (8)
GSM958269 P3M-ChIP-1
GSM958270 P3M-ChIP-2
GSM958271 P3M-ChIP-3
This SubSeries is part of SuperSeries:
GSE39217 Genome-wide identification of PIF3-binding sites and direct-target genes of PIF3 transcriptional regulation in skotomorphogenesis
Relations
BioProject PRJNA170238
SRA SRP014179

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
GSE39215_PIF3-peaks-1.xlsx.gz 52.0 Kb (ftp)(http) XLSX
GSE39215_PIF3-peaks-2.xlsx.gz 178.7 Kb (ftp)(http) XLSX
GSE39215_PIF3-peaks-3.xlsx.gz 40.5 Kb (ftp)(http) XLSX
GSE39215_PIF3-peaks-4.xlsx.gz 207.2 Kb (ftp)(http) XLSX
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Processed data are available on Series record
Raw data are available in SRA

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