Pfeiffer 2014a, Genome-wide identification of PIF4-binding sites.


2-day-old dark-grown whole seedlings of wild type plants (Control) and pif4 plants transgormed with a 35S::PIF4-myc (PIF4) were studied to indentify the genome-wide PIF4 binding sites. The chip-antibody used was anti-Myc.



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

ChIP-seq data:

Filename Description Feature GEO-ID
1 PIF4.sga Seedlings|PIF4|Dark|all reps PIF4 -
2 GSM1059963.sga Seedlings|PIF4|Dark|rep1 PIF4 GSM1059963
3 GSM1059964.sga Seedlings|PIF4|Dark|rep2 PIF4 GSM1059964
4 GSM1059965.sga Seedlings|PIF4|Dark|rep3 PIF4 GSM1059965
5 WT.sga Seedlings|Control|Dark|all reps WT -
6 GSM1059966.sga Seedlings|Control|Dark|rep1A WT GSM1059966
7 GSM1059967.sga Seedlings|Control|Dark|rep2A WT GSM1059967
8 GSM1059968.sga Seedlings|Control|Dark|rep3A WT GSM1059968

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 (ChIP-Seq v. 1.5.3).


Last update: 1 Oct 2018