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

Database: dm6 Primary Table: CSE99014_dH1_RNH1_untreated_idr Row Count: 1,184 Data last updated: 2021-09-01

field	example	SQL type	info
`bin`	586	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	192081	`int(10) unsigned`	range
`chromEnd`	193057	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	564	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	1.49569	`float`	range
`pValue`	1.51739	`float`	range
`qValue`	0.6627	`float`	range
`peak`	122	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
586	chr2L	192081	193057	.	564	.	1.49569	1.51739	0.6627	122
586	chr2L	192081	193057	.	564	.	2.03144	3.62066	2.40987	859
586	chr2L	192081	193057	.	564	.	2.80504	7.91222	6.1916	318
586	chr2L	192081	193057	.	564	.	2.87958	8.39823	6.62904	420
586	chr2L	192081	193057	.	564	.	4.82524	23.9852	21.1704	561
588	chr2L	521042	521444	.	1000	.	6.79106	67.6943	63.045	277
588	chr2L	521042	521444	.	1000	.	1.66069	2.80077	1.71056	78
589	chr2L	626381	628143	.	1000	.	3.51539	16.6468	14.2369	126
589	chr2L	626381	628143	.	1000	.	4.10905	19.4149	16.8432	1250
589	chr2L	626381	628143	.	1000	.	4.61035	28.7726	25.7292	1522

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