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

Database: dm6 Primary Table: CSE99014_dH1_RNH1_treated_macs Row Count: 142 Data last updated: 2021-09-01

field	example	SQL type	info
`bin`	589	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	626860	`int(10) unsigned`	range
`chromEnd`	627148	`int(10) unsigned`	range
`name`	CSE99014_dH1_RNH1_treated_m...	`varchar(255)`	values
`score`	47	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.36114	`float`	range
`pValue`	8.41826	`float`	range
`qValue`	4.79052	`float`	range
`peak`	217	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
589	chr2L	626860	627148	CSE99014_dH1_RNH1_treated_macs_peak_1b	47	.	2.36114	8.41826	4.79052	217
589	chr2L	626860	627148	CSE99014_dH1_RNH1_treated_macs_peak_1a	32	.	2.1786	6.81039	3.28546	64
680	chr2L	12493604	12493749	CSE99014_dH1_RNH1_treated_macs_peak_2	89	.	2.64329	12.9814	8.99452	69
763	chr2L	23370926	23371135	CSE99014_dH1_RNH1_treated_macs_peak_3	31	.	1.52311	6.69506	3.18265	89
591	chr2R	870255	870560	CSE99014_dH1_RNH1_treated_macs_peak_4	63	.	1.6983	9.9845	6.30015	171
600	chr2R	2016613	2016778	CSE99014_dH1_RNH1_treated_macs_peak_5	112	.	2.75366	15.3483	11.2664	90
615	chr2R	4014110	4015271	CSE99014_dH1_RNH1_treated_macs_peak_6b	1512	.	9.44043	156.67	151.258	645
615	chr2R	4014110	4015271	CSE99014_dH1_RNH1_treated_macs_peak_6a	1376	.	8.68533	142.466	137.641	409
615	chr2R	4014110	4015271	CSE99014_dH1_RNH1_treated_macs_peak_6c	1416	.	9.53919	146.524	141.603	955
661	chr2R	10057757	10057915	CSE99014_dH1_RNH1_treated_macs_peak_7	76	.	2.37515	11.4283	7.61744	73

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