Schema for NELF RNAi vs. Mock MNase - NELF RNAi vs. Mock MNase-Seq for Drosophila S2 Cells

Database: dm6 Primary Table: GSE22119_NELF_vs_Mock_occupancy Row Count: 7,300 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	9761	`int(10) unsigned`	range
`chromEnd`	9962	`int(10) unsigned`	range
`name`	diff_NELF_occupancy_4871	`varchar(255)`	values
`score`	495	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`signalValue`	-6.43717	`float`	range
`pValue`	132.753	`float`	range
`qValue`	2.47784	`float`	range
`peak`	100	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	9761	9962	diff_NELF_occupancy_4871	495	+	-6.43717	132.753	2.47784	100
585	chr2L	11551	11752	diff_NELF_occupancy_4872	403	+	-5.97774	89.531	2.01545	100
585	chr2L	24641	24842	diff_NELF_occupancy_4873	695	+	-7.0652	228.731	3.47784	100
585	chr2L	32711	32912	diff_NELF_occupancy_4874	500	+	-2.19613	133.573	2.50472	100
585	chr2L	62196	62397	diff_NELF_occupancy_4875	695	+	-7.0652	228.731	3.47784	100
585	chr2L	65021	65222	diff_NELF_occupancy_4876	524	+	-6.5627	148.444	2.62051	100
585	chr2L	65781	65982	diff_NELF_occupancy_4877	654	+	6.9295	203.425	3.27372	100
585	chr2L	82521	82722	diff_NELF_occupancy_4878	403	+	-5.97774	89.531	2.01545	100
585	chr2L	104001	104202	diff_NELF_occupancy_4879	447	+	-6.29966	117.38	2.2373	100
585	chr2L	106831	107032	diff_NELF_occupancy_4880	428	+	-2.76248	103.609	2.14339	100

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

NELF RNAi vs. Mock MNase (GSE22119_diff_MNase) Track Description


	Description These tracks show changes in nucleosome positions based on the analysis of Micrococcal Nuclease sequencing (MNase-seq) of 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 differential nucleosome positions and the smoothed coverage track were created using DANPOS2 with default parameters and `--paired 1`. 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. 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