Subtracks⇓  Description⇓  MACS2 DHS Track Settings
 
DNaseI Hypersensitive Sites Identified by MACS2   (All Expression and Regulation tracks)

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SRP010823 
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SRP112733 
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 S2 (modENCODE)  DHS Positions for S2 Cells (modENCODE)   Schema 
 
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 S2 (modENCODE) DHS logLR  DHS logLR for S2 Cells (modENCODE)   Schema 
 
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 Kc167 (modENCODE)  DHS Positions for Kc167 Cells (modENCODE)   Schema 
 
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 Kc167 (modENCODE) DHS logLR  DHS logLR for Kc167 Cells (modENCODE)   Schema 
 
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 Stage 5 (modENCODE)  DHS Positions for Stage 5 Embryos (DS9481 and DS9482)   Schema 
 
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 Stage 5 (modENCODE) DHS logLR  DHS logLR for Stage 5 Embryos (DS9481 and DS9482)   Schema 
 
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 Stage 9 (modENCODE)  DHS Positions for Stage 9 Embryos (DS9127 and DS9128)   Schema 
 
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 Stage 9 (modENCODE) DHS logLR  DHS logLR for Stage 9 Embryos (DS9127 and DS9128)   Schema 
 
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 Stage 10 (modENCODE)  DHS Positions for Stage 10 Embryos (DS8816 and DS8820)   Schema 
 
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 Stage 10 (modENCODE) DHS logLR  DHS logLR for Stage 10 Embryos (DS8816 and DS8820)   Schema 
 
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 Stage 11 (modENCODE)  DHS Positions for Stage 11 Embryos (DS9485 and DS9486)   Schema 
 
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 Stage 11 (modENCODE) DHS logLR  DHS logLR for Stage 11 Embryos (DS9485 and DS9486)   Schema 
 
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 Stage 14 (modENCODE)  DHS Positions for Stage 14 Embryos (DS9477 and DS9478)   Schema 
 
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 Stage 14 (modENCODE) DHS logLR  DHS logLR for Stage 14 Embryos (DS9477 and DS9478)   Schema 
 
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 S2 (Arnold 2013)  DHS Positions for S2 Cells (Arnold 2013)   Schema 
 
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 S2 (Arnold 2013) DHS logLR  DHS logLR for S2 Cells (Arnold 2013)   Schema 
 
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 OSC (Arnold 2013)  DHS Positions for OSC Cells (Arnold 2013)   Schema 
 
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 OSC (Arnold 2013) DHS logLR  DHS logLR for OSC Cells (Arnold 2013)   Schema 
 
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 Whole Embryos  DHS Positions for 6-8hr Whole Embryos (Cusanovich 2018)   Schema 
 
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 Whole Embryos DHS logLR  DHS logLR for 6-8hr Whole Embryos (Cusanovich 2018)   Schema 
 
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 Elav Embryos  DHS Positions for 6-8hr Elav Embryos (Cusanovich 2018)   Schema 
 
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 Elav Embryos DHS logLR  DHS logLR for 6-8hr Elav Embryos (Cusanovich 2018)   Schema 
 
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 Mef2 Embryos  DHS Positions for 6-8hr Mef2 Embryos (Cusanovich 2018)   Schema 
 
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 Mef2 Embryos DHS logLR  DHS logLR for 6-8hr Mef2 Embryos (Cusanovich 2018)   Schema 
    24 of 24 selected

Description

These tracks show the positions of DNase I Hypersensitive Sites (DHS). The peak calls and the log likelihood ratio evidence tracks were produced by MACS2.

The DHS datasets were obtained from the Sequence Read Archive at NCBI under the following accession numbers:

AccessionDevelopmental Stages / Cell LinesReference
SRP010823 S2 Kharchenko PV et al., 2011
SRP005657 Kc167 Kharchenko PV et al., 2011
SRP002474 Embryonic Stages 5, 9, 10, 11, 14 Thomas S et al., 2011
SRP015758 S2, OSC Arnold CD et al., 2013
SRP112733 Wild-type, Elav+, Mef2+ 6-8hr Embryonic Nuclei Cusanovich DA et al., 2018

References

Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SC, Kuroda MI, Pirrotta V, Karpen GH, Park PJ. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature. 2011 Mar 24;471(7339):480-5.

Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A, Celniker SE, Biggin MD, Stamatoyannopoulos JA. Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome Biol. 2011;12(5):R43.

Arnold CD, Gerlach D, Stelzer C, Boryń ŁM, Rath M, Stark A. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science. 2013 Mar 1;339(6123):1074-7.

Cusanovich DA, Reddington JP, Garfield DA, Daza RM, Aghamirzaie D, Marco-Ferreres R, Pliner HA, Christiansen L, Qiu X, Steemers FJ, Trapnell C, Shendure J, Furlong EEM. The cis-regulatory dynamics of embryonic development at single-cell resolution. Nature. 2018 Mar 22;555(7697):538-542.

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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