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

  • Yu J Swiss Federal Institute of Technology Zurich, Department of Biology, Institute of Molecular Health Sciences, Chair of RNAi and Genome Integrity, Zurich, Switzerland.
  • Ciaudo C Swiss Federal Institute of Technology Zurich, Department of Biology, Institute of Molecular Health Sciences, Chair of RNAi and Genome Integrity, Zurich, Switzerland.
  • 2017-03-18
Published in:
  • Scientific reports. - 2017
Animals
Databases as Topic
Gene Regulatory Networks
Genetic Techniques
Genetic Vectors
Haploidy
Humans
Mammals
Mice
Molecular Sequence Annotation
Phenotype
Promoter Regions, Genetic
ROC Curve
Reproducibility of Results
Sequence Analysis, DNA
Transcriptome
English 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 (https://sourceforge.net/projects/visits/).
Language
  • English
Open access status
gold
Identifiers
Persistent URL
https://sonar.ch/global/documents/254280
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