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

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Description

These tracks show changes in nucleosome positions based on the analysis of Micrococcal Nuclease sequencing (MNase-seq) of mock treated and NELF-RNAi treated Drosophila S2 cells.

The datasets were retrieved from the Gene Expression Omnibus database at NCBI under the accession number GSE22119. 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.

Credits

Gilchrist DA, Dos Santos G, Fargo DC, Xie B, Gao Y, Li L, Adelman K. Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation. Cell. 2010 Nov 12;143(4):540-51.

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.