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.



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

Technical Notes

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).


Last update: 1 Oct 2018