Schema for NELF RNAi MNase - NELF RNAi MNase-Seq for Drosophila S2 Cells
  Database: dm6    Primary Table: GSE22119_NELF_depleted_danpos    Row Count: 646,505   Data last updated: 2022-10-20
fieldexampleSQL type
bin 585smallint(5) unsigned
chrom chr2Lvarchar(255)
chromStart 5140int(10) unsigned
chromEnd 5281int(10) unsigned
name GSE22119_NELF_depleted_danp...varchar(255)
score 112int(10) unsigned
strand +char(1)
signalValue 42.1148float
pValue -1float
qValue -1float
peak 70int(11)

Sample Rows
 
binchromchromStartchromEndnamescorestrandsignalValuepValueqValuepeak
585chr2L51405281GSE22119_NELF_depleted_danpos_411787112+42.1148-1-170
585chr2L53005441GSE22119_NELF_depleted_danpos_411788112+47.336-1-170
585chr2L55405681GSE22119_NELF_depleted_danpos_411789120+57.0326-1-170
585chr2L57055846GSE22119_NELF_depleted_danpos_411790104+57.356-1-170
585chr2L58706011GSE22119_NELF_depleted_danpos_411791184+48.0197-1-170
585chr2L59906131GSE22119_NELF_depleted_danpos_41179232+70.0546-1-170
585chr2L62306371GSE22119_NELF_depleted_danpos_41179316+70.4921-1-170
585chr2L63406481GSE22119_NELF_depleted_danpos_41179480+47.4033-1-170
585chr2L65506691GSE22119_NELF_depleted_danpos_411795200+47.6566-1-170
585chr2L67206861GSE22119_NELF_depleted_danpos_411796168+52.2363-1-170

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

NELF RNAi MNase (GSE22119_MNase) Track Description
 

Description

These tracks show the read coverage from Micrococcal Nuclease sequencing (MNase-seq) of untreated, mock treated, and NELF-RNAi treated Drosophila S2 cells.

The datasets were retrieved from the Gene Expression Omnibus database at NCBI under the accession number GSE22119. 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

Gilchrist DA, Dos Santos G, Fargo DC, Xie B, Gao Y, Li L, Adelman K. Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation. Cell. 2010 Nov 12;143(4):540-51.

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.