Experiments are done in Hek293. HCT-116 cell data is available but difficult. ChIP-seq data (Phillip) conflicts based on cell type (Hek vs HCT). Many more usable reads in Hek than HCT. Likely the experiments were bad, not the cell type.

Potential transcriptional regulators in HPV

Proteins:

• E2
• E6
• E7

Similar to EBV paper (Phillip and Lee)

• EBV paper is simpler (fewer risk factors)
• What make HPV-16 a high risk strain.

MultiQC

Kraken

• Percentage of reads that align with the top species (usually human)

Picard

• Fragment length
• nucleosome free region (150)

Deeptools

• fingerprint plot should be non-linear (curve closer to 0)
• line with slope of 1 represents random

ENCODE

• IDR = peak calling

Definitions

HCT-116

• colon cancer cell line.
• Flippin reagents work in only a small number of cell types (including HCT-116).
• HPV literature uses HCT-116

HPV-16

• A high risk strain of human papilloma virus

Hek293 Cells

• Hek293 cells (not a great model of specific cell types). Useful for making proteins.