Schema for MBT Embryos MNase - MNase-Seq of Drosophila Embryos Under Midblastula Transition
  Database: dm6    Primary Table: GSE41686_MBT_danpos_smoothed    Row Count: 1   Data last updated: 2022-10-20
fieldexampleSQL type info
fileName /gbdb/dm6/bbi/MACC/GSE41686...varchar(255) values

Sample Rows
 
fileName
/gbdb/dm6/bbi/MACC/GSE41686_MBT_danpos.bw

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

MBT Embryos MNase (GSE41686_MNase) Track Description
 

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.