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

Database: dm6 Primary Table: CSE99014_dH1_RNH1_treated_peakzilla Row Count: 1,711 Data last updated: 2021-09-01

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	106116	`int(10) unsigned`	range
`chromEnd`	106342	`int(10) unsigned`	range
`name`	peakzilla_3306	`varchar(255)`	values
`score`	1	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.24	`float`	range
`pValue`	-1	`float`	range
`qValue`	0.73353	`float`	range
`peak`	113	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	106116	106342	peakzilla_3306	1	.	2.24	-1	0.73353	113
587	chr2L	324917	325143	peakzilla_362	2	.	4.03	-1	0.7607	113
588	chr2L	505053	505279	peakzilla_53	3	.	2.82	-1	0.6347	113
588	chr2L	505338	505564	peakzilla_159	2	.	2.57	-1	0.74376	113
588	chr2L	516614	516840	peakzilla_2079	1	.	2.21	-1	0.72033	113
589	chr2L	613215	613441	peakzilla_3668	1	.	2.23	-1	0.72262	113
589	chr2L	626819	627045	peakzilla_231	2	.	3.8	-1	0.77186	113
589	chr2L	626966	627192	peakzilla_764	1	.	2.32	-1	0.76145	113
590	chr2L	748891	749117	peakzilla_4313	1	.	2.14	-1	0.7176	113
591	chr2L	844323	844549	peakzilla_2475	1	.	2.22	-1	0.72769	113

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