hkCP dCP STARR-Seq Track Settings
 
Housekeeping and Developmental Enhancers Identified by STARR-Seq   (All Expression and Regulation tracks)

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 hkCP (S2) MACS2  RpS12 (hkCP) Enhancers (S2) MACS2 Peaks   Schema 
 
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 hkCP (S2) logLR  RpS12 (hkCP) Enhancers (S2) Log Likelihood Enrichment   Schema 
 
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 hkCP (OSC) MACS2  RpS12 (hkCP) Enhancers (OSC) MACS2 Peaks   Schema 
 
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 hkCP (OSC) logLR  RpS12 (hkCP) Enhancers (OSC) Log Likelihood Enrichment   Schema 
 
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 eEF1delta (S2) MACS2  eEF1delta Enhancers (S2) MACS2 Peaks   Schema 
 
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 eEF1delta (S2) logLR  eEF1delta Enhancers (S2) Log Likelihood Enrichment   Schema 
 
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 NipB (S2) MACS2  NipB Enhancers (S2) MACS2 Peaks   Schema 
 
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 NipB (S2) logLR  NipB Enhancers (S2) Log Likelihood Enrichment   Schema 
 
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 X16 (S2) MACS2  X16 Enhancers (S2) MACS2 Peaks   Schema 
 
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 X16 (S2) logLR  X16 Enhancers (S2) Log Likelihood Enrichment   Schema 
 
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 dCP (S2) MACS2  DSCP (dCP) Enhancers (S2) MACS2 Peaks   Schema 
 
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 dCP (S2) logLR  DSCP (dCP) Enhancers (S2) Log Likelihood Enrichment   Schema 
 
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 dCP (OSC) MACS2  DSCP (dCP) Enhancers (OSC) MACS2 Peaks   Schema 
 
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 dCP (OSC) logLR  DSCP (dCP) Enhancers (OSC) Log Likelihood Enrichment   Schema 
 
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 pnr (S2) MACS2  pnr Enhancers (S2) MACS2 Peaks   Schema 
 
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 pnr (S2) logLR  pnr Enhancers (S2) Log Likelihood Enrichment   Schema 
    

Description

These tracks show the putative housekeeping (hkCP) and developmental (dCP) enhancers identified by STARR-Seq in S2 and OSC cells. The regions that are enriched in STARR-Seq reads were identified by MACS2. The log likelihood ratio evidence tracks were also produced by MACS2.

The STARR-Seq reporters used in this study are as follows:

ReporterDescriptionReporter Type
RpS12 (hkCP)Ribosomal protein gene 12Housekeeping
eEF1deltaEukaryotic translation elongation factor 1 deltaHousekeeping
NipBCohesin loader Nipped-BHousekeeping
X16Putative splicing factor x16Housekeeping
DSCP (dCP)Derived from the even-skipped transcription factorDevelopmental
pnrDerived from the pannier transcription factorDevelopmental

References

Zabidi MA, Arnold CD, Schernhuber K, Pagani M, Rath M, Frank O, Stark A. Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation. Nature. 2015 Feb 26;518(7540):556-9.

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.