These tracks show changes in nucleosome positions based on the analysis of Micrococcal Nuclease sequencing (MNase-seq) of LacZ-RNAi and GAF-RNAi treated Drosophila S2 cells.
The datasets were retrieved from the Gene Expression Omnibus database at NCBI under the
accession number GSE58956. The MNase-seq reads were mapped against the D. melanogaster genome using bowtie with the following parameters:
-m 1 -v 2 --fr.
The differential nucleosome positions and the smoothed coverage track were created using DANPOS2 with default parameters and
Fuda NJ, Guertin MJ, Sharma S, Danko CG, Martins AL, Siepel A, Lis JT.
GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters. PLoS Genet. 2015 Mar 27;11(3):e1005108.
Chen K, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S, He X, Li W. DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Res. 2013 Feb;23(2):341-51.