Pfeiffer 14, Genome-wide identification of PIF1-binding sites

Description

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.

Source

Data available at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43283

Input file formats : SRA

Samples

From Arabidopsis at10 (TAIR10/araTha1) Assembly

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

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.

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