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1. Archaic and Modern Human Comparison

Structural Variants (SVs)

• Denisovan SVs (.bed)
• Neanderthal SVs (.bed)

Analyzed Regions

• Analyzed Regions in Denisovian vs Modern Human (.bed)
• Analyzed Regions in Neanderthal vs Modern Human (.bed)

CTCF 3+ Interactions (ChIA-PET)

GM12878

• Reference (.bedpe)
• Denisovan (.bedpe)
• Neanderthal (.bedpe)

H1ESC

• Reference (.bedpe)
• Denisovan (.bedpe)
• Neanderthal (.bedpe)

HFFC6

• Reference (.bedpe)
• Denisovan (.bedpe)
• Neanderthal (.bedpe)

Chromatin 3D models

GM12878

• Reference (.cif)
• Denisovan (.cif)
• Neanderthal (.cif)

H1ESC

• Reference (.cif)
• Denisovan (.cif)
• Neanderthal (.cif)

HFFC6

• Reference (.cif)
• Denisovan (.cif)
• Neanderthal (.cif)

Enhancer–Promoter 3D distances (Archaic vs Modern Human)

GM12878

• GM12878 vs GM12878 with Denisovan SVs (.tsv)
• GM12878 vs GM12878 with Neanderthal SVs (.tsv)

H1ESC

• H1ESC vs H1ESC with Denisovan SVs (.tsv)
• H1ESC vs H1ESC with Neanderthal SVs (.tsv)

HFFC6

• HFFC6 vs HFFC6 with Denisovan SVs (.tsv)
• HFFC6 vs HFFC6 with Neanderthal SVs (.tsv)

2. Modern Human Cell Lines

GM12878

• CTCF 3+ (.bedpe)
• Enhancers (.bed)
• Chromatin States (.bb)
• Chromatin Contact Domains (CCDs) (.bed)
• Chromatin 3D models (.cif)

H1ESC

• CTCF 3+ (.bedpe)
• Enhancers (.bed)
• Chromatin States (.bb)
• Chromatin Contact Domains (CCDs) (.bed)
• Chromatin 3D models (.cif)

HFFC6

• CTCF 3+ (.bedpe)
• Enhancers (.bed)
• Chromatin States (.bb)
• Chromatin Contact Domains (CCDs) (.bed)
• Chromatin 3D models (.cif)

Cross Cell Line Comparisons

• GM12878 vs H1ESC
  • Cross cell line comparison (.tsv)
  • CCDs intersection (.bed)
• GM12878 vs HFFC6
  • Cross cell line comparison (.tsv)
  • CCDs intersection (.bed)
• H1ESC vs HFFC6
  • Cross cell line comparison (.tsv)
  • CCDs intersection (.bed)