Pfeiffer 2014, Genome-wide identification of PIF1-binding sites.


3-day-old dark-grown whole seedlings of wild type plants (Control) and 35S::PIL5-myc transgenic plants (PIF1) were studied to indentify the genome-wide PIF1 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 PIF1_allReplica.sga Seedlings|PIF1|Dark|All replica PIF1 -
2 GSM1059957.sga Seedlings|PIF1|Dark|rep 1 PIF1 GSM1059957
3 GSM1059958.sga Seedlings|PIF1|Dark|rep 2 PIF1 GSM1059958
4 GSM1059959.sga Seedlings|PIF1|Dark|rep 3 PIF1 GSM1059959
5 WT_allReplica.sga Seedlings|Control|Dark|All replica WT -
6 GSM1059960.sga Seedlings|Control|Dark|rep 1 WT GSM1059960
7 GSM1059961.sga Seedlings|Control|Dark|rep 2 WT GSM1059961
8 GSM1059962.sga Seedlings|Control|Dark|rep 3 WT GSM1059962

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