bioRxiv preprint doi: https://doi.org/10.1101/558130; this version posted February 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Pooled CRISPR Inverse PCR sequencing (PCIP-seq): simultaneous sequencing of retroviral insertion points and the associated provirus in thousands of cells with long reads Maria Artesi1,2,7, Vincent Hahaut1,2,7, Fereshteh Ashrafi1,3, Ambroise Marçais4, Olivier Hermine4, Philip Griebel5, Natasa Arsic5, Frank van der Meer6, Arsène Burny2, Dominique Bron2, Carole Charlier1, Michel Georges1, Anne Van den Broeke1,2,8,*, Keith Durkin1,2,8,* 1Unit of Animal Genomics, GIGA-R, Université de Liège (ULiège), Avenue de l’Hôpital 11, B34, Liège 4000, Belgium. 2Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Boulevard de Waterloo 121, Brussels 1000, Belgium. 3Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran 4Service d’hématologie, Hôpital Universitaire Necker, Université René Descartes, Assistance Publique Hôpitaux de Paris, Paris, France. 5Vaccine and Infectious Disease Organization, VIDO-Intervac, University of Saskatchewan, 120 Veterinary Road, Saskatoon, Canada S7N 5E3, 6Faculty of Veterinary Medicine: Ecosystem and Public Health, Calgary, AB, Canada, 7These authors contributed equally: Maria Artesi, Vincent Hahaut, 8These authors jointly supervised the work: Anne Van den Broeke, Keith Durkin, *corresponding authors, email:
[email protected],
[email protected] Abstract Retroviral infections create a large population of cells, each defined by a unique proviral insertion site. Methods based on short-read high throughput sequencing can identify thousands of insertion sites, but the proviruses within remain unobserved.