Subtracks⇓  Description⇓  Henriques 2018 ChIP-Seq Track Settings
 
ChIP-Seq Data from Henriques 2018 for S2 cells   (All ChIP Seq Tracks)

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 H3K27ac IDR  H3K27ac IDR Peaks for S2 Cells   Schema 
 
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 H3K27ac MACS2  H3K27ac MACS2 Peaks for S2 Cells   Schema 
 
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 H3K27ac logLR  H3K27ac Log Likelihood Enrichment for S2 Cells   Schema 
 
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 H3K4me1 IDR  H3K4me1 IDR Peaks for S2 Cells   Schema 
 
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 H3K4me1 MACS2  H3K4me1 MACS2 Peaks for S2 Cells   Schema 
 
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 H3K4me1 logLR  H3K4me1 Log Likelihood Enrichment for S2 Cells   Schema 
 
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 H3K4me3 IDR  H3K4me3 IDR Peaks for S2 Cells   Schema 
 
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 H3K4me3 MACS2  H3K4me3 MACS2 Peaks for S2 Cells   Schema 
 
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 H3K4me3 logLR  H3K4me3 Log Likelihood Enrichment for S2 Cells   Schema 
 
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 Cohesin IDR  Cohesin IDR Peaks for S2 Cells   Schema 
 
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 Cohesin MACS2  Cohesin MACS2 Peaks for S2 Cells   Schema 
 
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 Cohesin logLR  Cohesin Log Likelihood Enrichment for S2 Cells   Schema 
 
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 RNA PolII IDR  RNA PolII IDR Peaks for S2 Cells   Schema 
 
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 RNA PolII MACS2  RNA PolII MACS2 Peaks for S2 Cells   Schema 
 
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 RNA PolII logLR  RNA PolII Log Likelihood Enrichment for S2 Cells   Schema 
 
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 RNA PolII Spt5-depleted IDR  RNA PolII Spt5-depleted IDR Peaks for S2 Cells   Schema 
 
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 RNA PolII Spt5-depleted MACS2  RNA PolII Spt5-depleted MACS2 Peaks for S2 Cells   Schema 
 
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 RNA PolII Spt5-depleted logLR  RNA PolII Spt5-depleted Log Likelihood Enrichment for S2 Cells   Schema 
    18 of 18 selected

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.

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