GAF vs. LacZ RNAi MNase Track Settings
GAF vs. LacZ RNAi MNase-Seq for Drosophila S2 Cells   (All MNase Tracks)

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 Position Shift  GAF RNAi Position Shift Nucleosomes   Schema 
 Fuzziness Change  GAF RNAi Fuzziness Change Nucleosomes   Schema 
 Occupancy Change  GAF RNAi Occupancy Change Nucleosomes   Schema 
 Differential Smoothed Coverage  GAF RNAi Differential Smoothed Coverage   Schema 


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 --paired 1.


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.