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
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.