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.

• Raw data was downloaded from: GEO
• Input file format: SRA
• Download date: n/a

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

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).

• Oh E, Zhu JY, Bai MY, Arenhart RA, Sun Y, Wang ZY
  Cell elongation is regulated through a central circuit of interacting transcription factors in the Arabidopsis hypocotyl. Elife. 2014 May 27;3. doi: 10.7554/eLife.03031. 24867218
• GEO series GSE51770: Interactions of ARF6 with PIF4, BZR1, and RGA integrate auxin signaling with environmental and other hormonal signals in Arabidopsis [ChIP-Seq]