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

Database: dm6 Primary Table: CSE99014_wt_RNH1_untreated_macs Row Count: 44,895 Data last updated: 2021-09-01

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5786	`int(10) unsigned`	range
`chromEnd`	5999	`int(10) unsigned`	range
`name`	CSE99014_wt_RNH1_untreated_...	`varchar(255)`	values
`score`	50	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.37719	`float`	range
`pValue`	6.60151	`float`	range
`qValue`	5.02341	`float`	range
`peak`	113	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5786	5999	CSE99014_wt_RNH1_untreated_macs_peak_1	50	.	2.37719	6.60151	5.02341	113
585	chr2L	8017	8213	CSE99014_wt_RNH1_untreated_macs_peak_2	35	.	2.19739	4.96078	3.58022	52
585	chr2L	16915	17143	CSE99014_wt_RNH1_untreated_macs_peak_3	104	.	3.2721	12.5899	10.4016	124
585	chr2L	19738	19945	CSE99014_wt_RNH1_untreated_macs_peak_4	112	.	3.37059	13.5324	11.2649	65
585	chr2L	38571	38704	CSE99014_wt_RNH1_untreated_macs_peak_5	75	.	2.87144	9.43622	7.54704	61
585	chr2L	38967	39228	CSE99014_wt_RNH1_untreated_macs_peak_6	39	.	2.27044	5.38095	3.9391	54
585	chr2L	42136	42269	CSE99014_wt_RNH1_untreated_macs_peak_7	35	.	2.15682	4.89704	3.52211	63
585	chr2L	52539	52673	CSE99014_wt_RNH1_untreated_macs_peak_8	72	.	2.7035	9.10891	7.25632	68
585	chr2L	73670	73794	CSE99014_wt_RNH1_untreated_macs_peak_9	23	.	1.84501	3.5476	2.34723	45
585	chr2L	99227	99447	CSE99014_wt_RNH1_untreated_macs_peak_10	23	.	1.93655	3.53748	2.33892	32

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