MBT Embryos MNase Track Settings

MNase-Seq of Drosophila Embryos Under Midblastula Transition (All MNase Tracks)

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	hide	Nucleosomes MBT Embryos	MBT Embryos Nucleosome Positions	Schema
	hide	MBT Smoothed Coverage	MNase-Seq Smoothed Coverage for MBT Embryos	Schema
	hide	MBT RPGC Coverage	MNase-Seq RPGC Coverage for MBT Embryos	Schema

Description

These tracks show the results from Micrococcal Nuclease sequencing (MNase-seq) of Drosophila embryos during the midblastula transition (MBT).

The datasets were retrieved from the Gene Expression Omnibus database at NCBI under the accession number GSE41686. 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

Chen K, Johnston J, Shao W, Meier S, Staber C, Zeitlinger J. A global change in RNA polymerase II pausing during the Drosophila midblastula transition. Elife. 2013 Aug 13;2:e00861.

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.