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

Database: dm6 Primary Table: CSE99014_dH1_RNH1_untreated_macs Row Count: 43,470 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5101	`int(10) unsigned`	range
`chromEnd`	5347	`int(10) unsigned`	range
`name`	CSE99014_dH1_RNH1_untreated...	`varchar(255)`	values
`score`	36	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.17467	`float`	range
`pValue`	5.08059	`float`	range
`qValue`	3.67268	`float`	range
`peak`	219	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5101	5347	CSE99014_dH1_RNH1_untreated_macs_peak_1b	36	.	2.17467	5.08059	3.67268	219
585	chr2L	5101	5347	CSE99014_dH1_RNH1_untreated_macs_peak_1a	89	.	3.14331	10.9125	8.91533	72
585	chr2L	5497	5632	CSE99014_dH1_RNH1_untreated_macs_peak_2	73	.	2.81859	9.18275	7.33632	67
585	chr2L	5773	5994	CSE99014_dH1_RNH1_untreated_macs_peak_3	212	.	4.29946	24.0214	21.2029	101
585	chr2L	9894	10052	CSE99014_dH1_RNH1_untreated_macs_peak_4	118	.	3.6838	14.0916	11.8524	69
585	chr2L	16870	17121	CSE99014_dH1_RNH1_untreated_macs_peak_5	82	.	3.16391	10.1825	8.24555	89
585	chr2L	19728	19889	CSE99014_dH1_RNH1_untreated_macs_peak_6	119	.	3.71759	14.2449	11.989	77
585	chr2L	36227	36392	CSE99014_dH1_RNH1_untreated_macs_peak_7	51	.	2.49384	6.73662	5.13511	66
585	chr2L	47342	47484	CSE99014_dH1_RNH1_untreated_macs_peak_8	88	.	2.69811	10.8512	8.85906	61
585	chr2L	102536	102748	CSE99014_dH1_RNH1_untreated_macs_peak_9	101	.	3.21189	12.2852	10.1802	110

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