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_position Row Count: 296 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	591	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	833901	`int(10) unsigned`	range
`chromEnd`	834102	`int(10) unsigned`	range
`name`	diff_NELF_position_187	`varchar(255)`	values
`score`	406	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`signalValue`	-2.89372	`float`	range
`pValue`	91.9091	`float`	range
`qValue`	2.0338	`float`	range
`peak`	100	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
591	chr2L	833901	834102	diff_NELF_position_187	406	+	-2.89372	91.9091	2.0338	100
602	chr2L	2356106	2356307	diff_NELF_position_188	413	+	-2.71001	97.0022	2.0696	100
608	chr2L	3098406	3098607	diff_NELF_position_189	835	+	-7.43717	316.24	4.17681	100
608	chr2L	3144286	3144487	diff_NELF_position_190	552	+	-3.76248	163.114	2.76184	100
609	chr2L	3251136	3251337	diff_NELF_position_191	430	+	-3.34744	103.955	2.15151	100
609	chr2L	3262986	3263187	diff_NELF_position_192	635	+	3.95177	192.792	3.17681	100
614	chr2L	3809676	3809877	diff_NELF_position_193	482	+	-3.54009	128.93	2.41339	100
615	chr2L	4044686	4044887	diff_NELF_position_194	403	+	-5.97774	89.531	2.01545	100
620	chr2L	4594386	4594587	diff_NELF_position_195	428	+	-2.76248	103.609	2.14339	100
625	chr2L	5330986	5331187	diff_NELF_position_196	458	+	2.16035	117.538	2.29032	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