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_occupancy Row Count: 5,585 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	15131	`int(10) unsigned`	range
`chromEnd`	15332	`int(10) unsigned`	range
`name`	diff_GAF_occupancy_1148	`varchar(255)`	values
`score`	437	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`signalValue`	-0.7088	`float`	range
`pValue`	64.2478	`float`	range
`qValue`	2.18655	`float`	range
`peak`	100	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	15131	15332	diff_GAF_occupancy_1148	437	+	-0.7088	64.2478	2.18655	100
585	chr2L	67721	67922	diff_GAF_occupancy_1149	409	+	-1.02699	58.7603	2.04865	100
585	chr2L	80431	80632	diff_GAF_occupancy_1150	571	+	-1.28543	100.709	2.85997	100
585	chr2L	87176	87377	diff_GAF_occupancy_1151	480	+	-0.78753	74.8729	2.40404	100
585	chr2L	102911	103112	diff_GAF_occupancy_1152	439	+	0.62192	64.8319	2.19992	100
585	chr2L	105451	105652	diff_GAF_occupancy_1153	486	+	-0.67902	76.2407	2.434	100
585	chr2L	119381	119582	diff_GAF_occupancy_1154	443	+	0.69134	65.5387	2.2184	100
585	chr2L	121001	121202	diff_GAF_occupancy_1155	467	+	1.35686	69.1026	2.33709	100
586	chr2L	161676	161877	diff_GAF_occupancy_1156	483	+	1.0319	76.1184	2.41876	100
586	chr2L	189401	189602	diff_GAF_occupancy_1157	442	+	-0.81595	65.2048	2.2137	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