GEI-11 Combined (GFP ChIP) recalled peaks

Identification of transcription factor binding regions (Snyder project, Snyder group)

General Description

We used the program Peakseq to define binding peaks of each factor, and used PeakRanger to identify the multiple summits inside each broad region found by PeakSeq. PeakRanger takes the broad regions and uses second-derivative information to find local summits. We extended each of these summits with a 100 bp flanking each side (if the initial region was smaller than 200 bp we just kept the small region size). The narrow binding regions (maximum 200 bp) around the summit found by PeakRanger were defined as narrow summit peaks.We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.


  1. Other Protocols: ChIP-seq_Peak_reanalysis

Sample Details


Related modENCODE submissions:

Release Date: 2011-02-25