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

Database: dm6 Primary Table: CSE99014_wt_RNH1_untreated_peakzilla Row Count: 26,608 Data last updated: 2021-09-01

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5751	`int(10) unsigned`	range
`chromEnd`	6003	`int(10) unsigned`	range
`name`	peakzilla_21967	`varchar(255)`	values
`score`	2	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	3	`float`	range
`pValue`	-1	`float`	range
`qValue`	1.51286	`float`	range
`peak`	126	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5751	6003	peakzilla_21967	2	.	3	-1	1.51286	126
585	chr2L	16894	17146	peakzilla_9902	3	.	4.68	-1	1.8729	126
585	chr2L	19675	19927	peakzilla_12836	2	.	3.74	-1	1.80688	126
585	chr2L	52504	52756	peakzilla_30300	1	.	2.28	-1	0.63227	126
585	chr2L	123363	123615	peakzilla_11085	3	.	3.46	-1	1.83565	126
586	chr2L	171613	171865	peakzilla_22903	2	.	2.69	-1	1.46471	126
586	chr2L	174246	174498	peakzilla_13724	2	.	3.55	-1	1.78781	126
586	chr2L	188033	188285	peakzilla_13216	2	.	3.82	-1	1.79317	126
586	chr2L	189157	189409	peakzilla_23411	2	.	2.7	-1	1.43533	126
586	chr2L	190042	190294	peakzilla_583	6	.	7.46	-1	1.92445	126

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