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

Database: dm6 Primary Table: CSE99014_wt_RNH1_treated_peakzilla Row Count: 9,306 Data last updated: 2021-09-01

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	123395	`int(10) unsigned`	range
`chromEnd`	123649	`int(10) unsigned`	range
`name`	peakzilla_13403	`varchar(255)`	values
`score`	1	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.05	`float`	range
`pValue`	-1	`float`	range
`qValue`	1.11014	`float`	range
`peak`	127	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	123395	123649	peakzilla_13403	1	.	2.05	-1	1.11014	127
586	chr2L	143879	144133	peakzilla_4227	2	.	2.5	-1	1.4437	127
586	chr2L	166389	166643	peakzilla_5919	2	.	3.05	-1	1.36957	127
586	chr2L	189950	190204	peakzilla_2447	2	.	3.03	-1	1.52143	127
586	chr2L	190238	190492	peakzilla_12234	1	.	2.3	-1	1.14935	127
586	chr2L	221921	222175	peakzilla_14464	1	.	2.1	-1	1.07727	127
586	chr2L	248249	248503	peakzilla_5759	2	.	2.94	-1	1.36957	127
587	chr2L	273342	273596	peakzilla_7649	1	.	2.64	-1	1.29414	127
587	chr2L	282258	282512	peakzilla_3824	2	.	3.22	-1	1.4698	127
587	chr2L	290412	290666	peakzilla_6557	2	.	2.65	-1	1.34104	127

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