A subscription to JoVE is required to view this content. Sign in or start your free trial.
Chapters
- 00:05Title
- 00:39Generation of Retroviral Stock
- 02:20Viral Infection of HEK293T Cells
- 04:30Genomic DNA Fragmentation
- 05:33Ligation of Linker Oligonucleotide to Fragmented Genomic DNA
- 06:58Amplification of Viral LTR-host Genomic DNA Junctions by Semi-nested PCR
- 08:02Results: Sequence Logos Depicting HIV-1 Base Preferences from Representative Experiment Libraries
- 08:52Conclusion
We describe a protocol for amplifying retroviral integration sites from the genomic DNA of infected cells, sequencing the amplified virus-host junctions, and then mapping these sequences to a reference genome. We also describe techniques to quantify the distribution of integration sites relative to various genomic annotations using BEDTools.
