Oh12, phytochrome-interacting factor 4 (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.


Files downloaded from GEO series : GSE35315
Input file format : sra


From Arabidopsis thalianna at10 (araTha1) assembly

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

Reads were mapped agains the genome using bowtie with a seed lenght of 28bp. Surprisingly, only ~5 and ~13% of the reads could be mapped for GSM865710_Col0 and GSM865709_PIF4 respectively. Since read trimming could not substantially increase the mapping efficiency, the reads were kept as they were in the original files for mapping.


  1. Oh E, Zhu JY, Wang ZY. Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses. Nature Cell Biology 2012 14:802-809. PMID : 22820378

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