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

Database: dm6 Primary Table: CSE99014_wt_RNH1_untreated_idr Row Count: 20,404 Data last updated: 2021-09-01

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	16906	`int(10) unsigned`	range
`chromEnd`	17155	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	757	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	3.2721	`float`	range
`pValue`	12.5899	`float`	range
`qValue`	10.4016	`float`	range
`peak`	133	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	16906	17155	.	757	.	3.2721	12.5899	10.4016	133
585	chr2L	19692	19979	.	1000	.	3.37059	13.5324	11.2649	111
585	chr2L	110224	110434	.	543	.	2.71493	8.51646	6.72359	90
586	chr2L	168269	168871	.	602	.	2.53755	7.07483	5.43549	487
586	chr2L	168269	168871	.	602	.	2.82017	9.36381	7.48915	319
586	chr2L	171577	172085	.	579	.	2.13688	4.60513	3.26076	319
586	chr2L	171577	172085	.	579	.	2.82017	9.36381	7.48915	163
586	chr2L	174279	174696	.	816	.	3.52521	15.2724	12.8524	126
586	chr2L	187998	188419	.	709	.	3.40566	13.712	11.4238	168
586	chr2L	189607	190518	.	1000	.	4.93922	37.1049	33.2029	541

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