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

Database: dm6 Primary Table: GSE22119_Untreated_danpos Row Count: 635,912 Data last updated: 2022-10-20

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5130	5271	GSE22119_Untreated_danpos_406491	248	+	52.3381	-1	-1	70
585	chr2L	5320	5461	GSE22119_Untreated_danpos_406492	96	+	64.9844	-1	-1	70
585	chr2L	5550	5691	GSE22119_Untreated_danpos_406493	128	+	56.3311	-1	-1	70
585	chr2L	5780	5921	GSE22119_Untreated_danpos_406494	160	+	54.8744	-1	-1	70
585	chr2L	5990	6131	GSE22119_Untreated_danpos_406495	120	+	50.1371	-1	-1	70
585	chr2L	6180	6321	GSE22119_Untreated_danpos_406496	16	+	57.7857	-1	-1	70
585	chr2L	6350	6491	GSE22119_Untreated_danpos_406497	128	+	52.4299	-1	-1	70
585	chr2L	6480	6621	GSE22119_Untreated_danpos_406498	144	+	56.2579	-1	-1	70
585	chr2L	6700	6841	GSE22119_Untreated_danpos_406499	216	+	55.426	-1	-1	70
585	chr2L	7100	7241	GSE22119_Untreated_danpos_406500	112	+	53.7134	-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