Schema for NELF RNAi MNase - NELF RNAi MNase-Seq for Drosophila S2 Cells

Database: dm6 Primary Table: GSE22119_Mock_treated_danpos Row Count: 664,579 Data last updated: 2022-10-20

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5020	5161	GSE22119_Mock_treated_danpos_877	32	+	66.154	-1	-1	70
585	chr2L	5140	5281	GSE22119_Mock_treated_danpos_878	144	+	57.3296	-1	-1	70
585	chr2L	5270	5411	GSE22119_Mock_treated_danpos_879	176	+	54.8399	-1	-1	70
585	chr2L	5490	5631	GSE22119_Mock_treated_danpos_880	96	+	62.7255	-1	-1	70
585	chr2L	5590	5731	GSE22119_Mock_treated_danpos_881	128	+	59.9637	-1	-1	70
585	chr2L	5730	5871	GSE22119_Mock_treated_danpos_882	184	+	52.8929	-1	-1	70
585	chr2L	5910	6051	GSE22119_Mock_treated_danpos_883	144	+	56.2987	-1	-1	70
585	chr2L	6215	6356	GSE22119_Mock_treated_danpos_884	24	+	64.7635	-1	-1	70
585	chr2L	6360	6501	GSE22119_Mock_treated_danpos_885	120	+	53.0723	-1	-1	70
585	chr2L	6520	6661	GSE22119_Mock_treated_danpos_886	120	+	61.0207	-1	-1	70

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.

Description