<oai_dc:dc xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
  <dc:creator>Yu J</dc:creator>
  <dc:creator>Ciaudo C</dc:creator>
  <dc:date>2017</dc:date>
  <dc:description xmlns:ns0="xml" ns0:lang="en">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/).</dc:description>
  <dc:format>application/pdf</dc:format>
  <dc:identifier>https://sonar.ch/global/documents/254280</dc:identifier>
  <dc:language>eng</dc:language>
  <dc:relation>info:eu-repo/semantics/altIdentifier/doi/10.1038/srep44736</dc:relation>
  <dc:relation>info:eu-repo/semantics/altIdentifier/pmid/28303933</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:source>Scientific reports. - 2017</dc:source>
  <dc:subject xmlns:ns1="xml" ns1:lang="en">Animals</dc:subject>
  <dc:subject xmlns:ns2="xml" ns2:lang="en">Databases as Topic</dc:subject>
  <dc:subject xmlns:ns3="xml" ns3:lang="en">Gene Regulatory Networks</dc:subject>
  <dc:subject xmlns:ns4="xml" ns4:lang="en">Genetic Techniques</dc:subject>
  <dc:subject xmlns:ns5="xml" ns5:lang="en">Genetic Vectors</dc:subject>
  <dc:subject xmlns:ns6="xml" ns6:lang="en">Haploidy</dc:subject>
  <dc:subject xmlns:ns7="xml" ns7:lang="en">Humans</dc:subject>
  <dc:subject xmlns:ns8="xml" ns8:lang="en">Mammals</dc:subject>
  <dc:subject xmlns:ns9="xml" ns9:lang="en">Mice</dc:subject>
  <dc:subject xmlns:ns10="xml" ns10:lang="en">Molecular Sequence Annotation</dc:subject>
  <dc:subject xmlns:ns11="xml" ns11:lang="en">Phenotype</dc:subject>
  <dc:subject xmlns:ns12="xml" ns12:lang="en">Promoter Regions, Genetic</dc:subject>
  <dc:subject xmlns:ns13="xml" ns13:lang="en">ROC Curve</dc:subject>
  <dc:subject xmlns:ns14="xml" ns14:lang="en">Reproducibility of Results</dc:subject>
  <dc:subject xmlns:ns15="xml" ns15:lang="en">Sequence Analysis, DNA</dc:subject>
  <dc:subject xmlns:ns16="xml" ns16:lang="en">Transcriptome</dc:subject>
  <dc:title xmlns:ns17="xml" ns17:lang="en">Vector Integration Sites Identification for Gene-Trap Screening in Mammalian Haploid Cells.</dc:title>
  <dc:type>http://purl.org/coar/resource_type/c_6501</dc:type>
</oai_dc:dc>