Schema for R-Loop DRIP-Seq (S2) - R-Loop DRIP-Seq in S2 Cells

Database: dm6 Primary Table: CSE99014_wt_RNH1_treated_idr Row Count: 543 Data last updated: 2021-09-01

field	example	SQL type	info
`bin`	589	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	626435	`int(10) unsigned`	range
`chromEnd`	628076	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	7.80301	`float`	range
`pValue`	55.2878	`float`	range
`qValue`	51.0166	`float`	range
`peak`	652	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
589	chr2L	626435	628076	.	1000	.	7.80301	55.2878	51.0166	652
589	chr2L	626435	628076	.	1000	.	6.12773	36.6758	32.9254	382
589	chr2L	626435	628076	.	1000	.	4.28707	18.523	14.9147	1403
589	chr2L	626435	628076	.	1000	.	3.54594	12.7352	9.20888	1153
593	chr2L	1077365	1077620	.	575	.	2.4936	6.45394	3.35599	122
593	chr2L	1120508	1120756	.	549	.	2.61208	7.25588	4.03062	153
595	chr2L	1411789	1412001	.	695	.	2.78362	12.7411	9.21463	123
601	chr2L	2175619	2175839	.	627	.	2.69574	7.13365	3.92221	89
601	chr2L	2203414	2203600	.	604	.	2.30277	4.54812	1.97868	89
603	chr2L	2378421	2378877	.	1000	.	3.09989	8.9034	5.51466	136

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

R-Loop DRIP-Seq (S2) (rloopDRIPSeq) Track Description


	Description These tracks show the putative locations of R-loops based on DRIP-Seq data from Drosophila melanogaster S2 Cells. The samples that were treated with RNase H served as additional controls for identifying R-loops. The regions that are enriched in the DRIP-Seq reads were identified by MACS2 and Peakzilla. The log likelihood ratio evidence tracks were produced by MACS2. The Irreproducible Discovery Rate (IDR) peak calls were produced by the idr program using a global IDR threshold of 0.05. The DRIP-Seq datasets were obtained from the Gene Expression Omnibus database at NCBI under the accession number GSE99014. References Bayona-Feliu A, Casas-Lamesa A, Reina O, Bernués J, Azorin F. Linker histone H1 prevents R-loop accumulation and genome instability in heterochromatin. Nat Commun. 2017 Aug 18;8(1):283. Bardet AF, Steinmann J, Bafna S, Knoblich JA, Zeitlinger J, Stark A. Identification of transcription factor binding sites from ChIP-seq data at high resolution. Bioinformatics. 2013 Nov 1;29(21):2705-13. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.

Description