R-Loop DRIP-Seq (S2) Track Settings

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R-Loop DRIP-Seq in S2 Cells (All ChIP Seq Tracks)

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All	*Condition*	Wild Type	dH1 RNAi
*Treatment*
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RNase H

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	hide Configure	Wild Type IDR	DRIP-Seq of Wild-Type Sample (without RNase H) IDR Peaks	Schema
	hide Configure	Wild Type MACS2	DRIP-Seq of Wild-Type Sample (without RNase H) MACS2 Peaks	Schema
	hide Configure	Wild Type Peakzilla	DRIP-Seq of Wild-Type Sample (without RNase H) Peakzilla Peaks	Schema
	hide Configure	Wild Type logLR	DRIP-Seq of Wild-Type Sample (without RNase H) Log Likelihood Enrichment	Schema
	hide Configure	Wild Type (RNaseH) IDR	DRIP-Seq of Wild-Type Sample (with RNase H) IDR Peaks	Schema
	hide Configure	Wild Type (RNaseH) MACS2	DRIP-Seq of Wild-Type Sample (with RNase H) MACS2 Peaks	Schema
	hide Configure	Wild Type (RNaseH) Peakzilla	DRIP-Seq of Wild-Type Sample (with RNase H) Peakzilla Peaks	Schema
	hide Configure	Wild Type (RNaseH) logLR	DRIP-Seq of Wild-Type Sample (with RNase H) Log Likelihood Enrichment	Schema
	hide Configure	dH1 RNAi IDR	DRIP-Seq of dH1 RNAi Sample (without RNase H) IDR Peaks	Schema
	hide Configure	dH1 RNAi MACS2	DRIP-Seq of dH1 RNAi Sample (without RNase H) MACS2 Peaks	Schema
	hide Configure	dH1 RNAi Peakzilla	DRIP-Seq of dH1 RNAi Sample (without RNase H) Peakzilla Peaks	Schema
	hide Configure	dH1 RNAi logLR	DRIP-Seq of dH1 RNAi Sample (without RNase H) Log Likelihood Enrichment	Schema
	hide Configure	dH1 RNAi (RNaseH) IDR	DRIP-Seq of dH1 RNAi Sample (with RNase H) IDR Peaks	Schema
	hide Configure	dH1 RNAi (RNaseH) MACS2	DRIP-Seq of dH1 RNAi Sample (with RNase H) MACS2 Peaks	Schema
	hide Configure	dH1 RNAi (RNaseH) Peakzilla	DRIP-Seq of dH1 RNAi Sample (with RNase H) Peakzilla Peaks	Schema
	hide Configure	dH1 RNAi (RNaseH) logLR	DRIP-Seq of dH1 RNAi Sample (with RNase H) Log Likelihood Enrichment	Schema

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.