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.

• 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	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

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).

• Pfeiffer A, Shi H, Tepperman JM, Zhang Y, Quail PH
  Combinatorial complexity in a transcriptionally centered signaling hub in Arabidopsis. Mol Plant. 2014 Nov;7(11):1598-618. doi: 10.1093/mp/ssu087. Epub 2014 Aug 13. 25122696
• GEO series GSE43284: Genome-wide identification of PIF4-binding sites and direct-target genes of PIF4 transcriptional regulation in skotomorphogenesis