Oh 2012, 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 from: GEO
• Input file format: SRA
• Download date: n/a

From A. thaliana (Feb 2011 TAIR10/araTha1).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM865710_Col0.sga	Seedlings|control|dark	control	GSM865709
2	GSM865709_PIF4.sga	Seedlings|PIF4|dark	PIF4	GSM865710

FASTQ files were extracted from SRA files using fastq-dump (SRA 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 (bedtools). SGA 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. 22820378
• GEO series GSE35315: Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses [ChIP-seq]