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_fuzziness Row Count: 1,684 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	13496	`int(10) unsigned`	range
`chromEnd`	13697	`int(10) unsigned`	range
`name`	diff_NELF_fuzziness_1105	`varchar(255)`	values
`score`	529	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`signalValue`	0.49857	`float`	range
`pValue`	51.8572	`float`	range
`qValue`	2.64534	`float`	range
`peak`	100	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	13496	13697	diff_NELF_fuzziness_1105	529	+	0.49857	51.8572	2.64534	100
585	chr2L	19831	20032	diff_NELF_fuzziness_1106	627	+	1.14914	70.539	3.13542	100
585	chr2L	103461	103662	diff_NELF_fuzziness_1107	714	+	-0.29211	81.8082	3.57475	100
585	chr2L	104796	104997	diff_NELF_fuzziness_1108	594	+	0.36299	60.6922	2.97269	100
586	chr2L	169801	170002	diff_NELF_fuzziness_1109	406	+	0.46188	35.0458	2.0338	100
586	chr2L	176841	177042	diff_NELF_fuzziness_1110	432	+	0.62893	38.7632	2.16398	100
586	chr2L	225711	225912	diff_NELF_fuzziness_1111	416	+	0.62359	35.8184	2.08339	100
587	chr2L	271851	272052	diff_NELF_fuzziness_1112	428	+	0.65581	38.1779	2.14339	100
587	chr2L	284691	284892	diff_NELF_fuzziness_1113	695	+	-0.3142	79.8988	3.47784	100
588	chr2L	495091	495292	diff_NELF_fuzziness_1114	529	+	0.52064	51.9405	2.64534	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