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

Database: dm6 Primary Table: CSE99014_wt_RNH1_treated_macs Row Count: 626 Data last updated: 2021-09-01

field	example	SQL type	info
`bin`	588	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	477208	`int(10) unsigned`	range
`chromEnd`	477337	`int(10) unsigned`	range
`name`	CSE99014_wt_RNH1_treated_ma...	`varchar(255)`	values
`score`	36	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.11758	`float`	range
`pValue`	6.8365	`float`	range
`qValue`	3.66663	`float`	range
`peak`	117	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
588	chr2L	477208	477337	CSE99014_wt_RNH1_treated_macs_peak_1	36	.	2.11758	6.8365	3.66663	117
588	chr2L	502820	503052	CSE99014_wt_RNH1_treated_macs_peak_2	61	.	2.20819	9.61357	6.18277	192
589	chr2L	561081	561261	CSE99014_wt_RNH1_treated_macs_peak_3	40	.	2.60671	7.23252	4.00942	70
589	chr2L	626479	628019	CSE99014_wt_RNH1_treated_macs_peak_4a	329	.	6.12773	36.6758	32.9254	338
589	chr2L	626479	628019	CSE99014_wt_RNH1_treated_macs_peak_4b	510	.	7.80301	55.2878	51.0166	608
589	chr2L	626479	628019	CSE99014_wt_RNH1_treated_macs_peak_4c	92	.	3.54594	12.7352	9.20888	1109
589	chr2L	626479	628019	CSE99014_wt_RNH1_treated_macs_peak_4d	149	.	4.28707	18.523	14.9147	1359
593	chr2L	1158948	1159125	CSE99014_wt_RNH1_treated_macs_peak_5	60	.	2.48081	9.45626	6.03238	66
595	chr2L	1394590	1394715	CSE99014_wt_RNH1_treated_macs_peak_6	42	.	2.2735	7.50376	4.2409	75
595	chr2L	1411848	1411977	CSE99014_wt_RNH1_treated_macs_peak_7	92	.	2.78362	12.7411	9.21463	64

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