Vector Integration Sites Identification for Gene-Trap Screening in Mammalian Haploid Cells.

ABSTRACT: Forward genetic screens using retroviral (or transposon) gene-trap vectors in a haploid genome revolutionized the investigation of molecular networks in mammals. However, the sequencing data generated by Phenotypic interrogation followed by Tag sequencing (PhiT-seq) were not well characterized. The analysis of human and mouse haploid screens allowed us to describe PhiT-seq data and to define quality control steps. Moreover, we identified several blind spots in both haploid genomes where gene-trap vectors can hardly integrate. Integration of transcriptomic data improved the performance of candidate gene identification. Furthermore, we experimented with various statistical tests to account for biological replicates in PhiT-seq and investigated the effect of normalization methods and other pa

SUBMITTER: Yu J 

PROVIDER: S-EPMC5356192 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature