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.

• 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	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

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 GSE43283: Genome-wide identification of PIF1-binding sites and direct-target genes of PIF1 transcriptional regulation in skotomorphogenesis