Zhang13, 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.


Data available at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39215

Input file formats : SRA


From Arabidopsis at10 (TAIR10/araTha1) Assembly

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

Technical Notes

Reads files were mapped to TAIR10 genome using bowtie. The resulting SAM filee were converted into SGA using samTools, BedTools and ChIP-Seq tools.


  1. Zhang Y, Mayba O, Pfeiffer A, Shi H et al. 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. PMID: 23382695