NELF RNAi vs. Mock MNase Track Settings

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

Maximum display mode: Reset to defaults

Select views (Help):

Peaks ▾

Smoothed ▾

List subtracks: only selected/visible all
	hide Configure	Position Shift	NELF RNAi Position Shift Nucleosomes	Schema
	hide Configure	Fuzziness Change	NELF RNAi Fuzziness Change Nucleosomes	Schema
	hide Configure	Occupancy Change	NELF RNAi Occupancy Change Nucleosomes	Schema
	hide	Differential Smoothed Coverage	NELF RNAi Differential Smoothed Coverage	Schema

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.