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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
• Denisovan
• Neanderthal

H1ESC

• Reference
• Denisovan
• Neanderthal

HFFC6

• Reference
• Denisovan
• Neanderthal

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

GM12878

• GM12878 vs GM12878 with Denisovan SVs
• GM12878 vs GM12878 with Neanderthal SVs

H1ESC

• H1ESC vs H1ESC with Denisovan SVs
• H1ESC vs H1ESC with Neanderthal SVs

HFFC6

• HFFC6 vs HFFC6 with Denisovan SVs
• HFFC6 vs HFFC6 with Neanderthal SVs

2. Modern Human Cell Lines

GM12878

• CTCF 3+ (.bedpe)
• Enhancers (.bed)
• Chromatin States (.bb)

H1ESC

• CTCF 3+ (.bedpe)
• Enhancers (.bed)
• Chromatin States (.bb)

HFFC6

• CTCF 3+ (.bedpe)
• Enhancers (.bed)
• Chromatin States (.bb)