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

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 Configure 		 Nucelosomes LacZ-RNAi  LacZ-RNAi S2 Cells Nucleosome Positions   Schema 
 
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 Configure 		 LacZ-RNAi Smoothed Coverage  MNase-Seq Smoothed Coverage for LacZ-RNAi S2 Cells   Schema 
 
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 Configure 		 LacZ-RNAi RPGC Coverage  MNase-Seq RPGC Coverage for LacZ-RNAi S2 Cells   Schema 
 
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 Configure 		 Nucelosomes GAF-RNAi  GAF-RNAi S2 Cells Nucleosome Positions   Schema 
 
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 Configure 		 GAF-RNAi Smoothed Coverage  MNase-Seq Smoothed Coverage for GAF-RNAi S2 Cells   Schema 
 
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 Configure 		 GAF-RNAi RPGC Coverage  MNase-Seq RPGC Coverage for GAF-RNAi S2 Cells   Schema 
    

Description

These tracks show the read coverage from Micrococcal Nuclease sequencing (MNase-seq) of LacZ-RNAi and GAF-RNAi 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 BAM alignment files for the different replicates were merged. The nucleosome positions and the smoothed coverage track were created using DANPOS2 with default parameters and --paired 1. The Reads Per Genomic Content (RPGC) coverage track was created using deepTools with the following parameters: --MNase --binSize 1 --normalizeTo1x 142000000.

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.

Ramírez F, Dündar F, Diehl S, Grüning BA, Manke T. deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W187-91.

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.