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_position Row Count: 422 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	14121	`int(10) unsigned`	range
`chromEnd`	14322	`int(10) unsigned`	range
`name`	diff_GAF_position_107	`varchar(255)`	values
`score`	469	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`signalValue`	-0.85042	`float`	range
`pValue`	69.9183	`float`	range
`qValue`	2.34968	`float`	range
`peak`	100	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	14121	14322	diff_GAF_position_107	469	+	-0.85042	69.9183	2.34968	100
586	chr2L	222211	222412	diff_GAF_position_108	547	+	1.20642	92.7748	2.73503	100
589	chr2L	626736	626937	diff_GAF_position_109	535	+	-1.67288	89.9916	2.67704	100
591	chr2L	835786	835987	diff_GAF_position_110	491	+	-0.76967	80.1355	2.45791	100
592	chr2L	970536	970737	diff_GAF_position_111	489	+	0.92611	78.7802	2.44979	100
593	chr2L	1178666	1178867	diff_GAF_position_112	532	+	-0.75368	89.7884	2.66367	100
602	chr2L	2303556	2303757	diff_GAF_position_113	407	+	-1.00303	58.3461	2.03606	100
602	chr2L	2350761	2350962	diff_GAF_position_114	480	+	0.90706	74.4429	2.40404	100
606	chr2L	2753126	2753327	diff_GAF_position_115	567	+	1.37216	98.7897	2.83976	100
609	chr2L	3184131	3184332	diff_GAF_position_116	473	+	-1.50599	71.5777	2.36927	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