Oh 12, PIF4 ChIP-seq .
Study of the phytochrome-interacting factor 4 (PIF4)
transcription factor in Arabidopsis thaliana using
ChIP-seq. The authors used two plant strains, both of Col-0
ecotype, to study PIF4. 'PIF4' labelled sample below is made
from plants expressing PIF4-myc from a PIF4 native promoter in
a pifq background (pifq are K/O for PIF1, PIF3,
PIF4 and PIF5). The negative control used - labelled 'control'
below - comes from non-transgenic wild-type plants. PIF4 was
isolated using a mouse anti-myc antibody.
- Raw data was downloaded
- Input file format: SRA
- Download date: n/a
From A. thaliana (Feb 2011 TAIR10/araTha1).
FASTQ files were extracted from SRA files using fastq-dump
toolkit v2.5.0) and mapped to the genome
using Bowtie v0.12.8. SAM
files were then converted into bam
using samtools v0.1.14
and to bed using bamToBed v2.12.0
conversion was carried out using bed2sga.pl
(ChIP-Seq v. 1.5.3).
Oh E, Zhu JY, Wang ZY
Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses.
Nat Cell Biol. 2012 Aug;14(8):802-9. doi: 10.1038/ncb2545. Epub 2012 Jul 22.
Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses [ChIP-seq]