Schema for GAF vs. LacZ RNAi MNase - GAF vs. LacZ RNAi MNase-Seq for Drosophila S2 Cells

Database: dm6 Primary Table: GSE58956_GAF_vs_LacZ_fuzziness Row Count: 2,688 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	46781	`int(10) unsigned`	range
`chromEnd`	46982	`int(10) unsigned`	range
`name`	diff_GAF_fuzziness_464	`varchar(255)`	values
`score`	628	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`signalValue`	-0.13579	`float`	range
`pValue`	70.7077	`float`	range
`qValue`	3.14079	`float`	range
`peak`	100	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	46781	46982	diff_GAF_fuzziness_464	628	+	-0.13579	70.7077	3.14079	100
585	chr2L	72261	72462	diff_GAF_fuzziness_465	405	+	-0.15954	34.9284	2.0299	100
585	chr2L	107956	108157	diff_GAF_fuzziness_466	1000	+	-0.34375	167.454	307.653	100
586	chr2L	143531	143732	diff_GAF_fuzziness_467	491	+	-0.18475	45.4329	2.45791	100
586	chr2L	166926	167127	diff_GAF_fuzziness_468	435	+	-0.30051	40.0862	2.17786	100
586	chr2L	200726	200927	diff_GAF_fuzziness_469	601	+	-0.18167	65.0407	3.0061	100
586	chr2L	203976	204177	diff_GAF_fuzziness_470	430	+	0.1588	38.4971	2.1528	100
587	chr2L	268791	268992	diff_GAF_fuzziness_471	527	+	-0.1782	50.6976	2.63812	100
587	chr2L	307376	307577	diff_GAF_fuzziness_472	1000	+	-0.33295	120.179	307.653	100
587	chr2L	375921	376122	diff_GAF_fuzziness_473	543	+	0.17183	53.1641	2.71979	100

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

GAF vs. LacZ RNAi MNase (GSE58956_diff_MNase) Track Description


	Description These tracks show changes in nucleosome positions based on the analysis of Micrococcal Nuclease sequencing (MNase-seq) of LacZ-RNAi and GAF-RNAi treated Drosophila S2 cells. The datasets were retrieved from the Gene Expression Omnibus database at NCBI under the accession number GSE58956. 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 Fuda NJ, Guertin MJ, Sharma S, Danko CG, Martins AL, Siepel A, Lis JT. GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters. PLoS Genet. 2015 Mar 27;11(3):e1005108. 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