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Comparison of Epigenetic States in MYCN Amplified and ATRX Mutated Neuroblastomas

St. Jude Children's Research Hospital

48 4

Feb 14, 2020

PMID 32060267

2.6K

RNA Sequencing

ChIP Sequencing

Here we compare the epigenetic states of ARTX mutated NBL samples to MYCN amplified cases. This is a summary view of HMM states for patient derived xenografts of pediatric solid tumors. Hovering over each colored bars reveals the HMM state. The FPKM expression value of the first gene in the viewing window is displayed as a bar plot on the right.

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runproteinpaint({
  "host": "//proteinpaint.stjude.org",
  "holder": visualizationContainer[0],
  "noheader": true,
  "studyview": {
    "genome": "hg19",
    "name": "NBL Human",
    "assays": [
      "RNAPolII",
      "BRD4",
      "H3K27Ac",
      "H3K9-14Ac",
      "H3K4me1",
      "H3K4me2",
      "H3K4me3",
      "H3K36me3",
      "H3K27me3",
      "H3K9me3",
      "CTCF",
      "INPUT",
      "WGBS",
      "SuperEnhancer(SE)",
      "SE.Exclude.H3K4me3",
      "MYCN_NOD",
      "MYCN_DOX",
      "MYCN_ENDO",
"H3.3"
    ],
    "trackfacets": [
      {
        "name": "CHIPSEQ",
        "samples": [
          "SJNBL030014.ATRX_Mut",
          "CHLA90-ATRX_Mut",
          "SKNMM-ATRX_Mut",
          "SKNMM-DOX",
          "SKNMM-NOD",
          "SJNBL047443.ATRX_Mut-NF1Del",
          "FAM",
          "SJNBL046.MYCN_Amp",
          "SJNBL012407.MYCN_Amp",
          "SJNBL013762.MYCN_Amp",
          "SJNBL013763.MYCN_Amp",
          "IMR32-MYCN_Amp",
          "SKNBE2-MYCN_Amp",
          "NBLS-MYCN_AmpLow",
          "NB5-MYCN_Amp-NF1Del",
          "SKNFI-NF1Del",
          "LAN6-CDKN2ADel",
          "SJNBL108.CDKN2ADel",
          "SJNBL013761.WT",
"SJNBL015724.WT"
        ],
        "nosortassay": 1,
        "nosortsample": 1,
        "assays": [
          "SuperEnhancer(SE)",
          "SE.Exclude.H3K4me3",
          "WGBS",
          "RNAPolII",
          "BRD4",
          "H3K27Ac",
          "H3K9-14Ac",
          "H3K4me1",
          "H3K4me2",
          "H3K4me3",
          "H3K36me3",
          "H3K27me3",
          "H3K9me3",
          "CTCF",
"INPUT"
        ]
      },
      {
        "name": "CHIPSEQ-NMYC",
        "samples": [
          "SJNBL046.MYCN_Amp",
          "SJNBL012407.MYCN_Amp",
          "SJNBL013762.MYCN_Amp",
          "SKNFI-NF1Del",
          "SKNBE2-MYCN_Amp",
"SKNMM-ATRX_Mut"
        ],
        "nosortassay": 1,
        "nosortsample": 1,
        "assays": [
          "MYCN_NOD",
          "MYCN_DOX",
"MYCN_ENDO"
        ]
      },
      {
        "name": "Cut-and-Run",
        "samples": [
          "IMR32-MYCN_Amp",
          "SKNBE2-MYCN_Amp",
          "SKNFI-NF1Del",
          "LAN6-CDKN2ADel",
          "CHLA90-ATRX_Mut",
"SKNMM-ATRX_Mut"
        ],
        "nosortassay": 1,
        "nosortsample": 1,
        "assays": [
"H3.3"
        ]
      }
    ],
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        "type": "bigwig",
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      },
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          "height": 15
        }
      },
      "IMR32-MYCN_Amp": {
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          "height": 15
        }
      },
      "LAN6-CDKN2ADel": {
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          },
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          "height": 15
        }
      },
      "SKNBE2-MYCN_Amp": {
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        }
      },
      "SKNFI-NF1Del": {
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          "height": 15
        }
      },
      "SKNMM-ATRX_Mut": {
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          },
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          "height": 15
        },
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        }
      }
    },
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        }
      },
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          },
          "file": "files/mycn/CHIPSEQ/NMYC-AB1-SJNBL054859_X1-MAST3.bw",
          "height": 15
        }
      },
      "SJNBL012407.MYCN_Amp": {
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          },
          "file": "files/mycn/CHIPSEQ/NMYC-AB1-SJNBL054860_X1-MAST97.bw",
          "height": 15
        }
      },
      "SJNBL013762.MYCN_Amp": {
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          "pcolor2": "rgb(0,0,255)",
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            "min": 1
          },
          "file": "files/mycn/CHIPSEQ/NMYC-AB1-SJNBL054861_X1-MAST109.bw",
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        }
      }
    },
    "MYCN_NOD": {
      "config": {
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      },
      "SKNMM-ATRX_Mut": {
        "SKNMM-ATRX_Mut": {
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          "scale": {
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          },
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          "height": 15
        }
      }
    },
    "MYCN_DOX": {
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        "height": 10
      },
      "SKNMM-ATRX_Mut": {
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          "pcolor2": "rgb(0,0,255)",
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            "min": 1
          },
          "file": "files/mycn/CHIPSEQ/NMYC-AB1-SJNBL050758_C1-SKNMM-DOX.bw",
          "height": 15
        }
      },
      "SKNBE2-MYCN_Amp": {
        "SKNBE2-MYCN_Amp": {
          "pcolor": "rgb(0,0,255)",
          "pcolor2": "rgb(0,0,255)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/mycn/CHIPSEQ/NMYC-AB1-SJNBL054857_C1-BE-NMYC-DOX.bw",
          "height": 15
        }
      },
      "SKNFI-NF1Del": {
        "SKNFI-NF1Del": {
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          "pcolor2": "rgb(0,0,255)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/mycn/CHIPSEQ/NMYC-AB1-SJNBL054858_C1-FI-NMYC-DOX.bw",
          "height": 15
        }
      }
    },
    "SuperEnhancer(SE)": {
      "config": {
        "pcolor": "0,0,255",
        "type": "bedj",
        "height": 10
      },
      "SJNBL030014.ATRX_Mut": {
        "SJNBL030014.ATRX_Mut": {
          "stackspace": 1,
          "sampleID": "SJNBL030014.ATRX_Mut",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.MAST126-ATRX_Mut.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "MAST126-ATRX_Mut SE"
        }
      },
      "CHLA90-ATRX_Mut": {
        "CHLA90-ATRX_Mut": {
          "stackspace": 1,
          "sampleID": "CHLA90-ATRX_Mut",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.CHLA90-ATRX_Mut.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "CHLA90-ATRX_Mut SE"
        }
      },
      "SKNMM-ATRX_Mut": {
        "SKNMM-ATRX_Mut": {
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          "sampleID": "SKNMM-ATRX_Mut",
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          "file": "files/mycn/SE/SE.SKNMM-ATRX_Mut.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "SKNMM-ATRX_Mut SE"
        }
      },
      "SJNBL047443.ATRX_Mut-NF1Del": {
        "SJNBL047443.ATRX_Mut-NF1Del": {
          "stackspace": 1,
          "sampleID": "SJNBL047443.ATRX_Mut-NF1Del",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.MAST268-ATRX_Mut-NF1Del-ATRX_Mut-NF1Del.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "MAST268-ATRX_Mut-NF1Del SE"
        }
      },
      "FAM": {
        "FAM": {
          "stackspace": 1,
          "sampleID": "FAM",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.FAM.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "FAM SE"
        }
      },
      "SJNBL046.MYCN_Amp": {
        "SJNBL046.MYCN_Amp": {
          "stackspace": 1,
          "sampleID": "SJNBL046.MYCN_Amp",
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          "bottompad": 1,
          "file": "files/mycn/SE/SE.MAST3-MYCN_Amp.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "MAST3-MYCN_Amp SE"
        }
      },
      "SJNBL012407.MYCN_Amp": {
        "SJNBL012407.MYCN_Amp": {
          "stackspace": 1,
          "sampleID": "SJNBL012407.MYCN_Amp",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.MAST97-MYCN_Amp.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "MAST97-MYCN_Amp SE"
        }
      },
      "SJNBL013762.MYCN_Amp": {
        "SJNBL013762.MYCN_Amp": {
          "stackspace": 1,
          "sampleID": "SJNBL013762.MYCN_Amp",
          "toppad": 1,
          "bottompad": 1,
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          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "MAST109-MYCN_Amp SE"
        }
      },
      "SJNBL013763.MYCN_Amp": {
        "SJNBL013763.MYCN_Amp": {
          "stackspace": 1,
          "sampleID": "SJNBL013763.MYCN_Amp",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.MAST121-MYCN_Amp.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "MAST121-MYCN_Amp SE"
        }
      },
      "IMR32-MYCN_Amp": {
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          "sampleID": "IMR32-MYCN_Amp",
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          "file": "files/mycn/SE/SE.IMR32-MYCN_Amp.withK4me3.gz",
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          "type": "bedj",
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          "name": "IMR32-MYCN_Amp SE"
        }
      },
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          "sampleID": "SKNBE2-MYCN_Amp",
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          "type": "bedj",
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          "name": "SKNBE2-MYCN_Amp SE"
        }
      },
      "NBLS-MYCN_AmpLow": {
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          "stackspace": 1,
          "sampleID": "NBLS-MYCN_AmpLow",
          "toppad": 1,
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      },
      "NB5-MYCN_Amp-NF1Del": {
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      },
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        }
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    },
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        "height": 10
      },
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          "sampleID": "SJNBL030014.ATRX_Mut",
          "toppad": 1,
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          "stackheight": 15,
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          "name": "MAST126-ATRX_Mut SE noK4me3"
        }
      },
      "CHLA90-ATRX_Mut": {
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          "sampleID": "CHLA90-ATRX_Mut",
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          "onerow": 1,
          "name": "CHLA90-ATRX_Mut SE noK4me3"
        }
      },
      "SKNMM-ATRX_Mut": {
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          "sampleID": "SKNMM-ATRX_Mut",
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          "onerow": 1,
          "name": "SKNMM-ATRX_Mut SE noK4me3"
        }
      },
      "SJNBL047443.ATRX_Mut-NF1Del": {
        "SJNBL047443.ATRX_Mut-NF1Del": {
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          "sampleID": "SJNBL047443.ATRX_Mut-NF1Del",
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          "name": "MAST268-ATRX_Mut-NF1Del SE noK4me3"
        }
      },
      "FAM": {
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        }
      },
      "SJNBL046.MYCN_Amp": {
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          "sampleID": "SJNBL046.MYCN_Amp",
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      },
      "SJNBL012407.MYCN_Amp": {
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          "sampleID": "SJNBL012407.MYCN_Amp",
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          "name": "MAST97-MYCN_Amp SE noK4me3"
        }
      },
      "SJNBL013762.MYCN_Amp": {
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          "sampleID": "SJNBL013762.MYCN_Amp",
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              "file": "files/mycn/HMM/MAST3-MYCN_Amp.gz",
              "stackheight": 15,
              "type": "bedj",
              "onerow": 1,
              "name": "SJNBL046.MYCN_Amp"
            },
            {
              "stackspace": 1,
              "sampleID": "SJNBL012407.MYCN_Amp",
              "toppad": 1,
              "bottompad": 1,
              "file": "files/mycn/HMM/MAST97-MYCN_Amp.gz",
              "stackheight": 15,
              "type": "bedj",
              "onerow": 1,
              "name": "SJNBL012407.MYCN_Amp"
            },
            {
              "stackspace": 1,
              "sampleID": "SJNBL013762.MYCN_Amp",
              "toppad": 1,
              "bottompad": 1,
              "file": "files/mycn/HMM/MAST109-MYCN_Amp.gz",
              "stackheight": 15,
              "type": "bedj",
              "onerow": 1,
              "name": "SJNBL013762.MYCN_Amp"
            },
            {
              "stackspace": 1,
              "sampleID": "SJNBL013763.MYCN_Amp",
              "toppad": 1,
              "bottompad": 1,
              "file": "files/mycn/HMM/MAST121-MYCN_Amp.gz",
              "stackheight": 15,
              "type": "bedj",
              "onerow": 1,
              "name": "SJNBL013763.MYCN_Amp"
            },
            {
              "stackspace": 1,
              "sampleID": "IMR32.MYCN_Amp",
              "toppad": 1,
              "bottompad": 1,
              "file": "files/mycn/HMM/IMR32-MYCN_Amp.gz",
              "stackheight": 15,
              "type": "bedj",
              "onerow": 1,
              "name": "IMR32.MYCN_Amp"
            },
            {
              "stackspace": 1,
              "sampleID": "SKNBE2.MYCN_Amp",
              "toppad": 1,
              "bottompad": 1,
              "file": "files/mycn/HMM/SKNBE2-MYCN_Amp.gz",
              "stackheight": 15,
              "type": "bedj",
              "onerow": 1,
              "name": "SKNBE2.MYCN_Amp"
            },
            {
              "stackspace": 1,
              "sampleID": "NBLS.MYCN_AmpLow",
              "toppad": 1,
              "bottompad": 1,
              "file": "files/mycn/HMM/NBLS-MYCN_AmpLow.gz",
              "stackheight": 15,
              "type": "bedj",
              "onerow": 1,
              "name": "NBLS.MYCN_AmpLow"
            },
            {
              "stackspace": 1,
              "sampleID": "NB5.MYCN_Amp.NF1Del",
              "toppad": 1,
              "bottompad": 1,
              "file": "files/mycn/HMM/NB5-MYCN_Amp-NF1Del.gz",
              "stackheight": 15,
              "type": "bedj",
              "onerow": 1,
              "name": "NB5.MYCN_Amp.NF1Del"
            },
            {
              "stackspace": 1,
              "sampleID": "SKNFI.NF1Del",
              "toppad": 1,
              "bottompad": 1,
              "file": "files/mycn/HMM/SKNFI-NF1Del.gz",
              "stackheight": 15,
              "type": "bedj",
              "onerow": 1,
              "name": "SKNFI.NF1Del"
            },
            {
              "stackspace": 1,
              "sampleID": "LAN6.CDKN2ADel",
              "toppad": 1,
              "bottompad": 1,
              "file": "files/mycn/HMM/LAN6-CDKN2ADel.gz",
              "stackheight": 15,
              "type": "bedj",
              "onerow": 1,
              "name": "LAN6.CDKN2ADel"
            },
            {
              "stackspace": 1,
              "sampleID": "SJNBL108.CDKN2ADel",
              "toppad": 1,
              "bottompad": 1,
              "file": "files/mycn/HMM/MAST11-CDKN2ADel.gz",
              "stackheight": 15,
              "type": "bedj",
              "onerow": 1,
              "name": "SJNBL108.CDKN2ADel"
            },
            {
              "stackspace": 1,
              "sampleID": "SJNBL013761.WT",
              "toppad": 1,
              "bottompad": 1,
              "file": "files/mycn/HMM/MAST78-AmpC.gz",
              "stackheight": 15,
              "type": "bedj",
              "onerow": 1,
              "name": "SJNBL013761.WT"
            },
            {
              "stackspace": 1,
              "sampleID": "SJNBL015724.WT",
              "toppad": 1,
              "bottompad": 1,
              "file": "files/mycn/HMM/MAST127-TUBB2B_Amp.gz",
              "stackheight": 15,
              "type": "bedj",
              "onerow": 1,
              "name": "SJNBL015724.WT"
            }
          ]
        }
      ]
    }
  }
});

Visualization Code

runproteinpaint({
  "host": "//proteinpaint.stjude.org",
  "holder": visualizationContainer[0],
  "noheader": true,
  "studyview": {
    "genome": "hg19",
    "name": "NBL Human",
    "assays": [
      "RNAPolII",
      "BRD4",
      "H3K27Ac",
      "H3K9-14Ac",
      "H3K4me1",
      "H3K4me2",
      "H3K4me3",
      "H3K36me3",
      "H3K27me3",
      "H3K9me3",
      "CTCF",
      "INPUT",
      "WGBS",
      "SuperEnhancer(SE)",
      "SE.Exclude.H3K4me3",
      "MYCN_NOD",
      "MYCN_DOX",
      "MYCN_ENDO",
"H3.3"
    ],
    "trackfacets": [
      {
        "name": "CHIPSEQ",
        "samples": [
          "SJNBL030014.ATRX_Mut",
          "CHLA90-ATRX_Mut",
          "SKNMM-ATRX_Mut",
          "SKNMM-DOX",
          "SKNMM-NOD",
          "SJNBL047443.ATRX_Mut-NF1Del",
          "FAM",
          "SJNBL046.MYCN_Amp",
          "SJNBL012407.MYCN_Amp",
          "SJNBL013762.MYCN_Amp",
          "SJNBL013763.MYCN_Amp",
          "IMR32-MYCN_Amp",
          "SKNBE2-MYCN_Amp",
          "NBLS-MYCN_AmpLow",
          "NB5-MYCN_Amp-NF1Del",
          "SKNFI-NF1Del",
          "LAN6-CDKN2ADel",
          "SJNBL108.CDKN2ADel",
          "SJNBL013761.WT",
"SJNBL015724.WT"
        ],
        "nosortassay": 1,
        "nosortsample": 1,
        "assays": [
          "SuperEnhancer(SE)",
          "SE.Exclude.H3K4me3",
          "WGBS",
          "RNAPolII",
          "BRD4",
          "H3K27Ac",
          "H3K9-14Ac",
          "H3K4me1",
          "H3K4me2",
          "H3K4me3",
          "H3K36me3",
          "H3K27me3",
          "H3K9me3",
          "CTCF",
"INPUT"
        ]
      },
      {
        "name": "CHIPSEQ-NMYC",
        "samples": [
          "SJNBL046.MYCN_Amp",
          "SJNBL012407.MYCN_Amp",
          "SJNBL013762.MYCN_Amp",
          "SKNFI-NF1Del",
          "SKNBE2-MYCN_Amp",
"SKNMM-ATRX_Mut"
        ],
        "nosortassay": 1,
        "nosortsample": 1,
        "assays": [
          "MYCN_NOD",
          "MYCN_DOX",
"MYCN_ENDO"
        ]
      },
      {
        "name": "Cut-and-Run",
        "samples": [
          "IMR32-MYCN_Amp",
          "SKNBE2-MYCN_Amp",
          "SKNFI-NF1Del",
          "LAN6-CDKN2ADel",
          "CHLA90-ATRX_Mut",
"SKNMM-ATRX_Mut"
        ],
        "nosortassay": 1,
        "nosortsample": 1,
        "assays": [
"H3.3"
        ]
      }
    ],
    "H3.3": {
      "config": {
        "pcolor": "rgb(204,0,41)",
        "type": "bigwig",
        "height": 10
      },
      "CHLA90-ATRX_Mut": {
        "CHLA90-ATRX_Mut": {
          "pcolor": "rgb(204,0,41)",
          "pcolor2": "rgb(204,0,41)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/mycn/CutRun/CutRun-H3.3-CHLA90-ATRX_Mut-Rep1.CRall.bw",
          "height": 15
        }
      },
      "IMR32-MYCN_Amp": {
        "IMR32-MYCN_Amp": {
          "pcolor": "rgb(204,0,41)",
          "pcolor2": "rgb(204,0,41)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/mycn/CutRun/CutRun-H3.3-IMR32-MYCN_Amp-Rep1.CRall.bw",
          "height": 15
        }
      },
      "LAN6-CDKN2ADel": {
        "LAN6-CDKN2ADel": {
          "pcolor": "rgb(204,0,41)",
          "pcolor2": "rgb(204,0,41)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/mycn/CutRun/CutRun-H3.3-LAN6-CDKN2ADel-Rep1.CRall.bw",
          "height": 15
        }
      },
      "SKNBE2-MYCN_Amp": {
        "SKNBE2-MYCN_Amp": {
          "pcolor": "rgb(204,0,41)",
          "pcolor2": "rgb(204,0,41)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/mycn/CutRun/CutRun-H3.3-SKNBE2-MYCN_Amp-Rep1.CRall.bw",
          "height": 15
        }
      },
      "SKNFI-NF1Del": {
        "SKNFI-NF1Del": {
          "pcolor": "rgb(204,0,41)",
          "pcolor2": "rgb(204,0,41)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/mycn/CutRun/CutRun-H3.3-SKNFI-NF1Del-Rep1.Fresh.CRall.bw",
          "height": 15
        }
      },
      "SKNMM-ATRX_Mut": {
        "noDox": {
          "pcolor": "rgb(204,0,41)",
          "pcolor2": "rgb(204,0,41)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/mycn/CutRun/CutRun-H3.3-SKNMM-ATRX_Mut.WTandnoDOX.CRall.bw",
          "height": 15
        },
        "Dox": {
          "pcolor": "rgb(204,0,41)",
          "pcolor2": "rgb(204,0,41)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/mycn/CutRun/CutRun-H3.3-SKNMM-ATRX_Mut.withDox.CRall.bw",
          "height": 15
        }
      }
    },
    "MYCN_ENDO": {
      "config": {
        "pcolor": "0,51,255",
        "type": "bigwig",
        "height": 10
      },
      "SKNBE2-MYCN_Amp": {
        "SKNBE2-MYCN_Amp": {
          "pcolor": "rgb(0,0,255)",
          "pcolor2": "rgb(0,0,255)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/mycn/CHIPSEQ/NMYC-AB1-SJNBL054856_C1-SKNBE2.bw",
          "height": 15
        }
      },
      "SJNBL046.MYCN_Amp": {
        "SJNBL046.MYCN_Amp": {
          "pcolor": "rgb(0,0,255)",
          "pcolor2": "rgb(0,0,255)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/mycn/CHIPSEQ/NMYC-AB1-SJNBL054859_X1-MAST3.bw",
          "height": 15
        }
      },
      "SJNBL012407.MYCN_Amp": {
        "SJNBL012407.MYCN_Amp": {
          "pcolor": "rgb(0,0,255)",
          "pcolor2": "rgb(0,0,255)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/mycn/CHIPSEQ/NMYC-AB1-SJNBL054860_X1-MAST97.bw",
          "height": 15
        }
      },
      "SJNBL013762.MYCN_Amp": {
        "SJNBL013762.MYCN_Amp": {
          "pcolor": "rgb(0,0,255)",
          "pcolor2": "rgb(0,0,255)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/mycn/CHIPSEQ/NMYC-AB1-SJNBL054861_X1-MAST109.bw",
          "height": 15
        }
      }
    },
    "MYCN_NOD": {
      "config": {
        "pcolor": "0,51,255",
        "type": "bigwig",
        "height": 10
      },
      "SKNMM-ATRX_Mut": {
        "SKNMM-ATRX_Mut": {
          "pcolor": "rgb(0,0,255)",
          "pcolor2": "rgb(0,0,255)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/mycn/CHIPSEQ/NMYC-AB1-SJNBL054855_C1-MM-NMYC-No-DOX.bw",
          "height": 15
        }
      }
    },
    "MYCN_DOX": {
      "config": {
        "pcolor": "0,51,255",
        "type": "bigwig",
        "height": 10
      },
      "SKNMM-ATRX_Mut": {
        "SKNMM-ATRX_Mut": {
          "pcolor": "rgb(0,0,255)",
          "pcolor2": "rgb(0,0,255)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/mycn/CHIPSEQ/NMYC-AB1-SJNBL050758_C1-SKNMM-DOX.bw",
          "height": 15
        }
      },
      "SKNBE2-MYCN_Amp": {
        "SKNBE2-MYCN_Amp": {
          "pcolor": "rgb(0,0,255)",
          "pcolor2": "rgb(0,0,255)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/mycn/CHIPSEQ/NMYC-AB1-SJNBL054857_C1-BE-NMYC-DOX.bw",
          "height": 15
        }
      },
      "SKNFI-NF1Del": {
        "SKNFI-NF1Del": {
          "pcolor": "rgb(0,0,255)",
          "pcolor2": "rgb(0,0,255)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/mycn/CHIPSEQ/NMYC-AB1-SJNBL054858_C1-FI-NMYC-DOX.bw",
          "height": 15
        }
      }
    },
    "SuperEnhancer(SE)": {
      "config": {
        "pcolor": "0,0,255",
        "type": "bedj",
        "height": 10
      },
      "SJNBL030014.ATRX_Mut": {
        "SJNBL030014.ATRX_Mut": {
          "stackspace": 1,
          "sampleID": "SJNBL030014.ATRX_Mut",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.MAST126-ATRX_Mut.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "MAST126-ATRX_Mut SE"
        }
      },
      "CHLA90-ATRX_Mut": {
        "CHLA90-ATRX_Mut": {
          "stackspace": 1,
          "sampleID": "CHLA90-ATRX_Mut",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.CHLA90-ATRX_Mut.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "CHLA90-ATRX_Mut SE"
        }
      },
      "SKNMM-ATRX_Mut": {
        "SKNMM-ATRX_Mut": {
          "stackspace": 1,
          "sampleID": "SKNMM-ATRX_Mut",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.SKNMM-ATRX_Mut.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "SKNMM-ATRX_Mut SE"
        }
      },
      "SJNBL047443.ATRX_Mut-NF1Del": {
        "SJNBL047443.ATRX_Mut-NF1Del": {
          "stackspace": 1,
          "sampleID": "SJNBL047443.ATRX_Mut-NF1Del",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.MAST268-ATRX_Mut-NF1Del-ATRX_Mut-NF1Del.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "MAST268-ATRX_Mut-NF1Del SE"
        }
      },
      "FAM": {
        "FAM": {
          "stackspace": 1,
          "sampleID": "FAM",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.FAM.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "FAM SE"
        }
      },
      "SJNBL046.MYCN_Amp": {
        "SJNBL046.MYCN_Amp": {
          "stackspace": 1,
          "sampleID": "SJNBL046.MYCN_Amp",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.MAST3-MYCN_Amp.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "MAST3-MYCN_Amp SE"
        }
      },
      "SJNBL012407.MYCN_Amp": {
        "SJNBL012407.MYCN_Amp": {
          "stackspace": 1,
          "sampleID": "SJNBL012407.MYCN_Amp",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.MAST97-MYCN_Amp.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "MAST97-MYCN_Amp SE"
        }
      },
      "SJNBL013762.MYCN_Amp": {
        "SJNBL013762.MYCN_Amp": {
          "stackspace": 1,
          "sampleID": "SJNBL013762.MYCN_Amp",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.MAST109-MYCN_Amp.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "MAST109-MYCN_Amp SE"
        }
      },
      "SJNBL013763.MYCN_Amp": {
        "SJNBL013763.MYCN_Amp": {
          "stackspace": 1,
          "sampleID": "SJNBL013763.MYCN_Amp",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.MAST121-MYCN_Amp.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "MAST121-MYCN_Amp SE"
        }
      },
      "IMR32-MYCN_Amp": {
        "IMR32-MYCN_Amp": {
          "stackspace": 1,
          "sampleID": "IMR32-MYCN_Amp",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.IMR32-MYCN_Amp.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "IMR32-MYCN_Amp SE"
        }
      },
      "SKNBE2-MYCN_Amp": {
        "SKNBE2-MYCN_Amp": {
          "stackspace": 1,
          "sampleID": "SKNBE2-MYCN_Amp",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.SKNBE2-MYCN_Amp.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "SKNBE2-MYCN_Amp SE"
        }
      },
      "NBLS-MYCN_AmpLow": {
        "NBLS-MYCN_AmpLow": {
          "stackspace": 1,
          "sampleID": "NBLS-MYCN_AmpLow",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.NBLS-MYCN_AmpLow-NF1Mut-MYCN_AmpLow-NF1Mut.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "NBLS-MYCN_AmpLow SE"
        }
      },
      "NB5-MYCN_Amp-NF1Del": {
        "NB5-MYCN_Amp-NF1Del": {
          "stackspace": 1,
          "sampleID": "NB5-MYCN_Amp-NF1Del",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.NB5-MYCN_Amp-NF1Del-MYCN_Amp-NF1Del.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "NB5-MYCN_Amp-NF1Del SE"
        }
      },
      "SKNFI-NF1Del": {
        "SKNFI-NF1Del": {
          "stackspace": 1,
          "sampleID": "SKNFI-NF1Del",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.SKNFI-NF1Del.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "SKNFI-NF1Del SE"
        }
      },
      "LAN6-CDKN2ADel": {
        "LAN6-CDKN2ADel": {
          "stackspace": 1,
          "sampleID": "LAN6-CDKN2ADel",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.LAN6-CDKN2ADel.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "LAN6-CDKN2ADel SE"
        }
      },
      "SJNBL108.CDKN2ADel": {
        "SJNBL108.CDKN2ADel": {
          "stackspace": 1,
          "sampleID": "SJNBL108.CDKN2ADel",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.MAST11-CDKN2ADel.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "MAST11-CDKN2ADel SE"
        }
      },
      "SJNBL013761.WT": {
        "SJNBL013761.WT": {
          "stackspace": 1,
          "sampleID": "SJNBL013761.WT",
          "toppad": 1,
          "bottompad": 1,
          "file": "files/mycn/SE/SE.MAST78-AmpC.withK4me3.gz",
          "stackheight": 15,
          "type": "bedj",
          "onerow": 1,
          "name": "MAST78-AmpC SE"
        }
      },
      "SJNBL015724.WT": {
        "SJNBL015724.WT": {
          "stackspace": 1,
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});

Comparison of Epigenetic States in MYCN Amplified and ATRX Mutated Neuroblastomas

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