Pfeiffer 14a, Genome-wide identification of PIF4-binding sites

Description

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.

Source

Data available at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43284

Input file formats : SRA

Samples

From Arabidopsis at10 (TAIR10/araTha1) Assembly

Filename Description Feature GEO-ID
1 PIF4.sga Seedlings|PIF4|Dark|all reps PIF4 -
2 GSM1059963.sga Seedlings|PIF4|Dark|rep 1 PIF4 GSM1059963
3 GSM1059964.sga Seedlings|PIF4|Dark|rep 2 PIF4 GSM1059964
4 GSM1059965.sga Seedlings|PIF4|Dark|rep 3 PIF4 GSM1059965
5 WT.sga Seedlings|Control|Dark|all reps WT -
6 GSM1059966.sga Seedlings|Control|Dark|rep 1A WT GSM1059966
7 GSM1059967.sga Seedlings|Control|Dark|rep 2A WT GSM1059967
8 GSM1059968.sga Seedlings|Control|Dark|rep 3A WT GSM1059968

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. The 3 replica for each genetic background were merged to generate combine files.

References

  1. Pfeiffer A, Shi H, Tepperman JM, Zhang Y et al. Combinatorial complexity in a transcriptionally centered signaling hub in Arabidopsis. Mol Plant 2014 Nov;7(11):1598-618. PMID: 25122696