Zhang 2013, Genome-wide identification of PIF3-binding sites.


2-day-old dark-grown whole seedlings of wild type Col-0 plants (Control) and pif3-3/35:PIF3-5xMyc transgenic plants (PIF3) were studied to indentify the genome-wide PIF3 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 PIF3.sga Seedlings|PIF3|Dark|all reps P3M -
2 GSM958269.sga Seedlings|PIF3|Dark|rep1 P3M GSM958269
3 GSM958270.sga Seedlings|PIF3|Dark|rep2 P3M GSM958270
4 GSM958271.sga Seedlings|PIF3|Dark|rep3 P3M GSM958271
5 GSM958272.sga Seedlings|PIF3|Dark|rep4 P3M GSM958272
6 WT.sga Seedlings|Control|Dark|all reps WT -
7 GSM958273.sga Seedlings|Control|Dark|rep1 WT GSM958273
8 GSM958274.sga Seedlings|Control|Dark|rep2 WT GSM958274
9 GSM958275.sga Seedlings|Control|Dark|rep3 WT GSM958275
10 GSM958276.sga Seedlings|Control|Dark|rep4 WT GSM958276

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