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PASPLG LMO2 Enhancer SNV/Indel

Mullighan Lab

27 4

Oct 6, 2023

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Whole Genome Sequencing

RNA Sequencing

ATAC Sequencing

HiChIP

Depiction of H3K27ac HiChIP, H3K27ac coverage, diagnostic/germline sample WGS and WTS coverage in a T-ALL patient, showcasing enhancer generation by Enhancer SNV/Indel upstream of LMO2. The heatmap represent interactions between genomic loci, with color coding denoting interaction strength.

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{
  "host": "https://proteinpaint.stjude.org/",
  "parseurl": true,
  "nobox": true,
  "noheader": true,
  "genome": "hg38",
  "nativetracks": "RefGene",
  "block": true,
  "position": "chr11:33850351-33903951",
  "tracks": [
    {
      "type": "hicstraw",
      "file": "ppolonen/hg38/HICHIP/H3K27ac_HiChIP_PASPLG.hic",
      "name": "HiChIP",
      "percentile_max": 95,
      "mincutoff": 0,
      "pyramidup": 1,
      "enzyme": ""
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/HICHIP/2543807_H3K27ac_PASPLG_S4_L004.coverage.bw",
      "name": "H3K27ac HiChIP",
      "scale": {
        "min": 0,
        "max": 900
      },
      "pcolor": "#FF2600"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/ATAC/2580207_PASPLG.nuc.bw",
      "name": "ATAC-nuc",
      "scale": {
        "min": 0,
        "max": 15
      },
      "pcolor": "#40A5EE"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/ATAC/2580207_PASPLG.free.bw",
      "name": "ATAC-free",
      "scale": {
        "min": 0,
        "max": 15
      },
      "pcolor": "#40A5EE"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/WGS/SJALL069839_D1-PASPLG_D.bw",
      "name": "WGS-D",
      "scale": {
        "min": 0,
        "max": 150
      },
      "pcolor": "#113F91"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/WGS/SJALL069839_G1-PASPLG_G.bw",
      "name": "WGS-G",
      "scale": {
        "min": 0,
        "max": 150
      },
      "pcolor": "#113F91"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/RNA/SJALL069839_D1-PASPLG_D.STAR.Signal.UniqueMultiple.str1.out.bw",
      "name": "RNA-D-str1",
      "pcolor": "#195C37"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/RNA/SJALL069839_D1-PASPLG_D.STAR.Signal.UniqueMultiple.str2.out.bw",
      "name": "RNA-D-str2",
      "pcolor": "#195C37"
    }
  ]
}

Visualization Code

{
  "host": "https://proteinpaint.stjude.org/",
  "parseurl": true,
  "nobox": true,
  "noheader": true,
  "genome": "hg38",
  "nativetracks": "RefGene",
  "block": true,
  "position": "chr11:33850351-33903951",
  "tracks": [
    {
      "type": "hicstraw",
      "file": "ppolonen/hg38/HICHIP/H3K27ac_HiChIP_PASPLG.hic",
      "name": "HiChIP",
      "percentile_max": 95,
      "mincutoff": 0,
      "pyramidup": 1,
      "enzyme": ""
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/HICHIP/2543807_H3K27ac_PASPLG_S4_L004.coverage.bw",
      "name": "H3K27ac HiChIP",
      "scale": {
        "min": 0,
        "max": 900
      },
      "pcolor": "#FF2600"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/ATAC/2580207_PASPLG.nuc.bw",
      "name": "ATAC-nuc",
      "scale": {
        "min": 0,
        "max": 15
      },
      "pcolor": "#40A5EE"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/ATAC/2580207_PASPLG.free.bw",
      "name": "ATAC-free",
      "scale": {
        "min": 0,
        "max": 15
      },
      "pcolor": "#40A5EE"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/WGS/SJALL069839_D1-PASPLG_D.bw",
      "name": "WGS-D",
      "scale": {
        "min": 0,
        "max": 150
      },
      "pcolor": "#113F91"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/WGS/SJALL069839_G1-PASPLG_G.bw",
      "name": "WGS-G",
      "scale": {
        "min": 0,
        "max": 150
      },
      "pcolor": "#113F91"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/RNA/SJALL069839_D1-PASPLG_D.STAR.Signal.UniqueMultiple.str1.out.bw",
      "name": "RNA-D-str1",
      "pcolor": "#195C37"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/RNA/SJALL069839_D1-PASPLG_D.STAR.Signal.UniqueMultiple.str2.out.bw",
      "name": "RNA-D-str2",
      "pcolor": "#195C37"
    }
  ]
}

PASPLG LMO2 Enhancer SNV/Indel

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Visualization Code