Oh 2014, ARF6 ChIP-seq.


ChIP-seq analysis of the ARF6 transcription factor. ARFs are transcription factors that bind the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs). Transgenic plants expressiong ARF6-Myc driven by native ARF6 promoter (ARF6p::ARF6-Myc) are grown in the dark for 5 days. The etiolated seedlings are then used as input for chromatin extraction with an anti-myc antibody.



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

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM1252254.sga ARF6 ARF6 GSM1252254
2 GSM1252255.sga GFP GFP GSM1252255

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