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.

• 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	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

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).

• Zhang Y, Mayba O, Pfeiffer A, Shi H, Tepperman JM, Speed TP, Quail PH
  A quartet of PIF bHLH factors provides a transcriptionally centered signaling hub that regulates seedling morphogenesis through differential expression-patterning of shared target genes in Arabidopsis. PLoS Genet. 2013;9(1):e1003244. doi: 10.1371/journal.pgen.1003244. Epub 2013 Jan 31. 23382695
• GEO series GSE39215: Genome-wide identification of PIF3-binding sites and direct-target genes of PIF3 transcriptional regulation in skotomorphogenesis [ChIP-Seq]