GAF vs. LacZ RNAi MNase Track Settings

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

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

Description

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.

Credits

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.