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

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 Configure 		 Nucleosomes Untreated  Untreated S2 Cells Nucleosome Positions   Schema 
 
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 Configure 		 Untreated S2 Smoothed Coverage  MNase-Seq Smoothed Coverage for Untreated S2 Cells   Schema 
 
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 Configure 		 Untreated S2 RPGC Coverage  MNase-Seq RPGC Coverage for Untreated S2 Cells   Schema 
 
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 Configure 		 Nucleosomes Mock Treated  Mock Treated S2 Cells Nucleosome Positions   Schema 
 
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 Configure 		 Mock Treated Smoothed Coverage  MNase-Seq Smoothed Coverage for Mock Treated S2 Cells   Schema 
 
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 Configure 		 Mock Treated RPGC Coverage  MNase-Seq RPGC Coverage for Mock Treated S2 Cells   Schema 
 
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 Configure 		 Nucleosomes NELF Depleted  NELF Depleted S2 Cells Nucleosome Positions   Schema 
 
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 Configure 		 NELF Depleted Smoothed Coverage  MNase-Seq Smoothed Coverage for NELF Depleted S2 Cells   Schema 
 
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 Configure 		 NELF Depleted RPGC Coverage  MNase-Seq RPGC Coverage for NELF Depleted S2 Cells   Schema 
    

Description

These tracks show the read coverage from Micrococcal Nuclease sequencing (MNase-seq) of untreated, 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 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

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.

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.