Schema for MBT Embryos MNase - MNase-Seq of Drosophila Embryos Under Midblastula Transition
  Database: dm6    Primary Table: GSE41686_MBT_danpos    Row Count: 661,812   Data last updated: 2022-10-20
fieldexampleSQL type
bin 585smallint(5) unsigned
chrom chr2Lvarchar(255)
chromStart 5090int(10) unsigned
chromEnd 5231int(10) unsigned
name GSE41686_MBT_danpos_410938varchar(255)
score 280int(10) unsigned
strand +char(1)
signalValue 52.5364float
pValue -1float
qValue -1float
peak 70int(11)

Sample Rows
 
binchromchromStartchromEndnamescorestrandsignalValuepValueqValuepeak
585chr2L50905231GSE41686_MBT_danpos_410938280+52.5364-1-170
585chr2L52305371GSE41686_MBT_danpos_410939272+54.6954-1-170
585chr2L54605601GSE41686_MBT_danpos_410940272+55.4712-1-170
585chr2L55605701GSE41686_MBT_danpos_410941288+58.6924-1-170
585chr2L57455886GSE41686_MBT_danpos_410942152+64.148-1-170
585chr2L59006041GSE41686_MBT_danpos_410943264+57.643-1-170
585chr2L60006141GSE41686_MBT_danpos_410944176+57.541-1-170
585chr2L61106251GSE41686_MBT_danpos_41094532+72.4204-1-170
585chr2L62506391GSE41686_MBT_danpos_410946112+62.7549-1-170
585chr2L63606501GSE41686_MBT_danpos_410947216+50.8906-1-170

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.