Vector Integration Sites Identification for Gene-Trap Screening in Mammalian Haploid Cells
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Date
2017-03-17
Publication Type
Journal Article
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yes
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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 parameters on the performance. Finally, we developed: VISITs, a dedicated pipeline for analyzing PhiT-seq data
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published
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Journal / series
Volume
7
Pages / Article No.
44736
Publisher
Nature
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Edition / version
Methods
Software
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Date collected
Date created
Subject
high-throughput screening; Software
Organisational unit
03983 - Ciaudo, C. (ehemalig) / Ciaudo, C. (former)
03983 - Ciaudo, C. (ehemalig) / Ciaudo, C. (former)