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SRX1005831: GSM1665428: ChIPSeq-PIF4_FLAG_Rep2; Arabidopsis thaliana; ChIP-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 18.4M spots, 1.8G bases, 883.4Mb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: Cryptochromes interact directly with PIFs to control plant growth in limiting blue light
show Abstracthide Abstract
Sun-loving plants have the ability to detect and avoid shading through sensing of both blue and red light wavelengths. Higher plant cryptochromes (CRYs) control how plants modulate growth in response to changes in blue light. For growth under a canopy, where blue light is diminished, CRY1 and CRY2 perceive this change and respond by directly contacting two bHLH transcription factors, PIF4 and PIF5. These factors are also known to be controlled by phytochromes, the red/far-red photoreceptors; however, transcriptome analyses indicate that the gene regulatory programs induced by the different light wavelengths are distinct. Our results indicate that CRYs signal by modulating PIF activity genome-wide, and that these factors integrate binding of different plant photoreceptors to facilitate growth changes under different light conditions. Overall design: We performed whole-genome chromatin immunoprecipitation with sequencing (ChIP-Seq) analysis on 5 day old Flash-CRY2, PIF4-Flash and PIF5-Flash treated in low blue-light for 16h.
Sample: ChIPSeq-PIF4_FLAG_Rep2
SAMN03565851 • SRS921447 • All experiments • All runs
Instrument: Illumina HiSeq 2500
Strategy: ChIP-Seq
Selection: ChIP
Layout: SINGLE
Construction protocol: Please see accompanying publication for detailed protocol. Briefly, ChIP-seq experiments for PIF4 and CRY2 were performed as described (Kaufmann et al., 2010) using 5 day-old seedlings harboring either a PIF4-Flash (Thines et al., 2014) or UBQ10pro::Flash-CRY2 transgene. A monoclonal anti-FLAG antibody (Sigma) was used in all experiments. The CRY2 ChIP experiment was performed with two modifications. Instead of 2g starting material that we used to precipitate PIF4, 18g starting material was used for CRY2. Moreover, we conducted a dual cross-linking procedure for CRY2 using the additional cross-linker ethylene glycol bis-succinimidylsuccinate. ChIP DNA was used to generate sequencing libraries as per Illumina protocol (Illumina, CA). 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: GSM1665428
External link:
Runs: 1 run, 18.4M spots, 1.8G bases, 883.4Mb
Run# of Spots# of BasesSizePublished


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