Schema for GAF RNAi MNase - GAF RNAi MNase-Seq for Drosophila S2 Cells
  Database: dm6    Primary Table: GSE58956_LacZ_RNAi_danpos    Row Count: 667,452   Data last updated: 2022-10-20
fieldexampleSQL type
bin 585smallint(5) unsigned
chrom chr2Lvarchar(255)
chromStart 4970int(10) unsigned
chromEnd 5111int(10) unsigned
name GSE58956_LacZ_RNAi_danpos_4...varchar(255)
score 32int(10) unsigned
strand +char(1)
signalValue 79.7572float
pValue -1float
qValue -1float
peak 70int(11)

Sample Rows
 
binchromchromStartchromEndnamescorestrandsignalValuepValueqValuepeak
585chr2L49705111GSE58956_LacZ_RNAi_danpos_42738232+79.7572-1-170
585chr2L51205261GSE58956_LacZ_RNAi_danpos_427383616+58.3087-1-170
585chr2L52405381GSE58956_LacZ_RNAi_danpos_427384880+54.8493-1-170
585chr2L54405581GSE58956_LacZ_RNAi_danpos_427385884+55.5886-1-170
585chr2L55905731GSE58956_LacZ_RNAi_danpos_427386272+68.8985-1-170
585chr2L57505891GSE58956_LacZ_RNAi_danpos_427387876+53.467-1-170
585chr2L60006141GSE58956_LacZ_RNAi_danpos_427388696+49.6404-1-170
585chr2L61906331GSE58956_LacZ_RNAi_danpos_427389472+49.7861-1-170
585chr2L63706511GSE58956_LacZ_RNAi_danpos_427390848+51.4343-1-170
585chr2L65206661GSE58956_LacZ_RNAi_danpos_4273911000+52.9811-1-170

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

GAF RNAi MNase (GSE58956_MNase) Track Description
 

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.