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Normal Healthy Controls

Mullighan Lab

Oct 6, 2023

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ChIP Sequencing

HiChIP

Healthy normal Double Positive (DP) and CD34+ HSPCs H3K27ac HiChIP (GSE165209) raw interactions as heatmaps, with corresponding H3K27ac coverage is shown. H3K27ac ChIPseq from different healthy thymic T-cells and in CD34+ cells is also shown from GSE151081.

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{
  "host": "https://proteinpaint.stjude.org/",
  "parseurl": true,
  "nobox": true,
  "noheader": true,
  "genome": "hg38",
  "nativetracks": "RefGene",
  "block": true,
  "position": "chr14:97381247-99375146",
  "tracks": [
	   {
    "type": "hicstraw",
    "file": "ppolonen/hg38/HICHIP/CD34_5M.hic",
    "name": "CD34: HiChIP",
    "percentile_max": 90,
    "mincutoff": 0,
    "pyramidup": 1,
    "enzyme": ""
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/HICHIP/CD34_5M.coverage.bw",
    "name": "CD34: H3K27ac HiChIP",
    "scale": {
      "min": 0,
      "max": 100
    },
    "pcolor": "#FF2600"
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/HICHIP/2604157_DP_Mat_Thy6_S112_L003.coverage.bw",
    "name": "DP: H3K27ac HiChIP",
    "scale": {
      "min": 0,
      "max": 100
    },
    "pcolor": "#FF2600"
  },
  {
    "type": "hicstraw",
    "file": "ppolonen/hg38/HICHIP/2604157_DP_Mat_Thy6_S112_L003.hic",
    "name": "DP: HiChIP",
    "percentile_max": 90,
    "mincutoff": 0,
    "pyramidup": 0,
    "enzyme": ""
  },
 
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/HICHIP/CD34_Goodell_CTCF.bw",
    "name": "CD34 CTCF",
    "scale": {
      "min": 0,
      "max": 50
    },
    "pcolor": "#40A5EE"
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/CHIP_ATLAS/SRX8383368.bw",
    "name": "H3K27ac CD34+ CD1+",
    "scale": {
      "min": 0,
      "max": 1
    },
    "pcolor": "#40A5EE"
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/CHIP_ATLAS/SRX8383367.bw",
    "name": "H3K27ac CD34+ CD1-",
    "scale": {
      "min": 0,
      "max": 1
    },
    "pcolor": "#40A5EE"
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/CHIP_ATLAS/SRX8383369.bw",
    "name": "H3K27ac CD34+ CD4+",
    "scale": {
      "min": 0,
      "max": 1
    },
    "pcolor": "#40A5EE"
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/CHIP_ATLAS/SRX8383372.bw",
    "name": "H3K27ac DP CD3+",
    "scale": {
      "min": 0,
      "max": 1
    },
    "pcolor": "#40A5EE"
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/CHIP_ATLAS/SRX8383371.bw",
    "name": "H3K27ac DP CD3-",
    "scale": {
      "min": 0,
      "max": 1
    },
    "pcolor": "#40A5EE"
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/CHIP_ATLAS/SRX8383373.bw",
    "name": "H3K27ac SP CD4+",
    "scale": {
      "min": 0,
      "max": 1
    },
    "pcolor": "#40A5EE"
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/CHIP_ATLAS/SRX8383374.bw",
    "name": "H3K27ac SP CD8+",
    "scale": {
      "min": 0,
      "max": 1
    },
    "pcolor": "#40A5EE"
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/CHIP_ATLAS/SRX8383370.bw",
    "name": "H3K27ac ISP CD28+",
    "scale": {
      "min": 0,
      "max": 1
    },
    "pcolor": "#40A5EE"
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/CHIP_ATLAS/SRX8383376.bw",
    "name": "H3K27ac ISP CD28+",
    "scale": {
      "min": 0,
      "max": 1
    },
    "pcolor": "#40A5EE"
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/CHIP_ATLAS/SRX8383375.bw",
    "name": "H3K27ac ISP CD28+",
    "scale": {
      "min": 0,
      "max": 1
    },
    "pcolor": "#40A5EE"
  }
]
}

Visualization Code

{
  "host": "https://proteinpaint.stjude.org/",
  "parseurl": true,
  "nobox": true,
  "noheader": true,
  "genome": "hg38",
  "nativetracks": "RefGene",
  "block": true,
  "position": "chr14:97381247-99375146",
  "tracks": [
	   {
    "type": "hicstraw",
    "file": "ppolonen/hg38/HICHIP/CD34_5M.hic",
    "name": "CD34: HiChIP",
    "percentile_max": 90,
    "mincutoff": 0,
    "pyramidup": 1,
    "enzyme": ""
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/HICHIP/CD34_5M.coverage.bw",
    "name": "CD34: H3K27ac HiChIP",
    "scale": {
      "min": 0,
      "max": 100
    },
    "pcolor": "#FF2600"
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/HICHIP/2604157_DP_Mat_Thy6_S112_L003.coverage.bw",
    "name": "DP: H3K27ac HiChIP",
    "scale": {
      "min": 0,
      "max": 100
    },
    "pcolor": "#FF2600"
  },
  {
    "type": "hicstraw",
    "file": "ppolonen/hg38/HICHIP/2604157_DP_Mat_Thy6_S112_L003.hic",
    "name": "DP: HiChIP",
    "percentile_max": 90,
    "mincutoff": 0,
    "pyramidup": 0,
    "enzyme": ""
  },
 
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/HICHIP/CD34_Goodell_CTCF.bw",
    "name": "CD34 CTCF",
    "scale": {
      "min": 0,
      "max": 50
    },
    "pcolor": "#40A5EE"
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/CHIP_ATLAS/SRX8383368.bw",
    "name": "H3K27ac CD34+ CD1+",
    "scale": {
      "min": 0,
      "max": 1
    },
    "pcolor": "#40A5EE"
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/CHIP_ATLAS/SRX8383367.bw",
    "name": "H3K27ac CD34+ CD1-",
    "scale": {
      "min": 0,
      "max": 1
    },
    "pcolor": "#40A5EE"
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/CHIP_ATLAS/SRX8383369.bw",
    "name": "H3K27ac CD34+ CD4+",
    "scale": {
      "min": 0,
      "max": 1
    },
    "pcolor": "#40A5EE"
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/CHIP_ATLAS/SRX8383372.bw",
    "name": "H3K27ac DP CD3+",
    "scale": {
      "min": 0,
      "max": 1
    },
    "pcolor": "#40A5EE"
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/CHIP_ATLAS/SRX8383371.bw",
    "name": "H3K27ac DP CD3-",
    "scale": {
      "min": 0,
      "max": 1
    },
    "pcolor": "#40A5EE"
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/CHIP_ATLAS/SRX8383373.bw",
    "name": "H3K27ac SP CD4+",
    "scale": {
      "min": 0,
      "max": 1
    },
    "pcolor": "#40A5EE"
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/CHIP_ATLAS/SRX8383374.bw",
    "name": "H3K27ac SP CD8+",
    "scale": {
      "min": 0,
      "max": 1
    },
    "pcolor": "#40A5EE"
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/CHIP_ATLAS/SRX8383370.bw",
    "name": "H3K27ac ISP CD28+",
    "scale": {
      "min": 0,
      "max": 1
    },
    "pcolor": "#40A5EE"
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/CHIP_ATLAS/SRX8383376.bw",
    "name": "H3K27ac ISP CD28+",
    "scale": {
      "min": 0,
      "max": 1
    },
    "pcolor": "#40A5EE"
  },
  {
    "type": "bigwig",
    "file": "ppolonen/hg38/CHIP_ATLAS/SRX8383375.bw",
    "name": "H3K27ac ISP CD28+",
    "scale": {
      "min": 0,
      "max": 1
    },
    "pcolor": "#40A5EE"
  }
]
}

Normal Healthy Controls

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Visualization Code