Henriques 2018 ChIP-Seq Track Settings

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ChIP-Seq Data from Henriques 2018 for S2 cells (All ChIP Seq Tracks)

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All	*MarkType*	Histones modifications	Chromosomal proteins
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H3K27ac
H3K4me1
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Cohesin
RNA PolII

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	hide Configure	H3K27ac IDR	H3K27ac IDR Peaks for S2 Cells	Schema
	hide Configure	H3K27ac MACS2	H3K27ac MACS2 Peaks for S2 Cells	Schema
	hide Configure	H3K27ac logLR	H3K27ac Log Likelihood Enrichment for S2 Cells	Schema
	hide Configure	H3K4me1 IDR	H3K4me1 IDR Peaks for S2 Cells	Schema
	hide Configure	H3K4me1 MACS2	H3K4me1 MACS2 Peaks for S2 Cells	Schema
	hide Configure	H3K4me1 logLR	H3K4me1 Log Likelihood Enrichment for S2 Cells	Schema
	hide Configure	H3K4me3 IDR	H3K4me3 IDR Peaks for S2 Cells	Schema
	hide Configure	H3K4me3 MACS2	H3K4me3 MACS2 Peaks for S2 Cells	Schema
	hide Configure	H3K4me3 logLR	H3K4me3 Log Likelihood Enrichment for S2 Cells	Schema
	hide Configure	Cohesin IDR	Cohesin IDR Peaks for S2 Cells	Schema
	hide Configure	Cohesin MACS2	Cohesin MACS2 Peaks for S2 Cells	Schema
	hide Configure	Cohesin logLR	Cohesin Log Likelihood Enrichment for S2 Cells	Schema
	hide Configure	RNA PolII IDR	RNA PolII IDR Peaks for S2 Cells	Schema
	hide Configure	RNA PolII MACS2	RNA PolII MACS2 Peaks for S2 Cells	Schema
	hide Configure	RNA PolII logLR	RNA PolII Log Likelihood Enrichment for S2 Cells	Schema
	hide Configure	RNA PolII Spt5-depleted IDR	RNA PolII Spt5-depleted IDR Peaks for S2 Cells	Schema
	hide Configure	RNA PolII Spt5-depleted MACS2	RNA PolII Spt5-depleted MACS2 Peaks for S2 Cells	Schema
	hide Configure	RNA PolII Spt5-depleted logLR	RNA PolII Spt5-depleted Log Likelihood Enrichment for S2 Cells	Schema

Description

These tracks show the analysis results for the ChIP-Seq data produced by Henriques and colleagues (PMID: 29378787). The regions that are enriched in the histone modifications and chromosomal proteins were identified by MACS2. 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 ChIP-Seq datasets were obtained from the NCBI Gene Expression Omnibus database under the accession number GSE85191.

References

Henriques T, Scruggs BS, Inouye MO, Muse GW, Williams LH, Burkholder AB, Lavender CA, Fargo DC, Adelman K. Widespread transcriptional pausing and elongation control at enhancers. Genes Dev. 2018 Jan 1;32(1):26-41.

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.