Schema for GAF RNAi MNase - GAF RNAi MNase-Seq for Drosophila S2 Cells
  Database: dm6    Primary Table: GSE58956_GAF_RNAi_danpos    Row Count: 666,096   Data last updated: 2022-10-20
fieldexampleSQL type
bin 585smallint(5) unsigned
chrom chr2Lvarchar(255)
chromStart 4990int(10) unsigned
chromEnd 5131int(10) unsigned
name GSE58956_GAF_RNAi_danpos_42...varchar(255)
score 32int(10) unsigned
strand +char(1)
signalValue 77.0743float
pValue -1float
qValue -1float
peak 70int(11)

Sample Rows
 
binchromchromStartchromEndnamescorestrandsignalValuepValueqValuepeak
585chr2L49905131GSE58956_GAF_RNAi_danpos_42701132+77.0743-1-170
585chr2L51005241GSE58956_GAF_RNAi_danpos_427012392+57.1067-1-170
585chr2L52405381GSE58956_GAF_RNAi_danpos_427013768+56.2772-1-170
585chr2L54405581GSE58956_GAF_RNAi_danpos_427014824+57.5005-1-170
585chr2L56005741GSE58956_GAF_RNAi_danpos_427015264+65.6577-1-170
585chr2L58205961GSE58956_GAF_RNAi_danpos_427016464+58.9285-1-170
585chr2L59906131GSE58956_GAF_RNAi_danpos_427017652+52.6249-1-170
585chr2L62106351GSE58956_GAF_RNAi_danpos_427018328+57.6029-1-170
585chr2L63706511GSE58956_GAF_RNAi_danpos_427019624+52.0349-1-170
585chr2L65306671GSE58956_GAF_RNAi_danpos_427020984+50.0448-1-170

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.