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

Database: dm6 Primary Table: CSE99014_dH1_RNH1_treated_idr Row Count: 51 Data last updated: 2021-09-01

field	example	SQL type	info
`bin`	680	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	12493435	`int(10) unsigned`	range
`chromEnd`	12493800	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	697	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.64329	`float`	range
`pValue`	12.9814	`float`	range
`qValue`	8.99452	`float`	range
`peak`	238	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
680	chr2L	12493435	12493800	.	697	.	2.64329	12.9814	8.99452	238
600	chr2R	2016560	2017053	.	994	.	1.25252	1.03325	0.04721	374
600	chr2R	2016560	2017053	.	994	.	2.75366	15.3483	11.2664	143
615	chr2R	4014090	4015289	.	1000	.	8.68533	142.466	137.641	429
615	chr2R	4014090	4015289	.	1000	.	9.44043	156.67	151.258	665
615	chr2R	4014090	4015289	.	1000	.	9.53919	146.524	141.603	975
687	chr2R	13485649	13486405	.	1000	.	2.82192	15.0815	11.0038	642
687	chr2R	13485649	13486405	.	1000	.	2.98873	18.6926	14.5781	158
687	chr2R	13485649	13486405	.	1000	.	3.32976	22.16	18.0167	400
722	chr2R	18025278	18025831	.	585	.	1.3279	1.28176	0.13231	119

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