title: CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation.
abstract: The CRISPR/Cas9 system was recently developed as a powerful and flexible technology for targeted genome engineering, including genome editing (altering the genetic sequence) and gene regulation (without altering the genetic sequence). These applications require the design of single guide RNAs (sgRNAs) that are efficient and specific. However, this remains challenging, as it requires the consideration of many criteria. Several sgRNA design tools have been developed for gene editing, but currently there is no tool for the design of sgRNAs for gene regulation. With accumulating experimental data on the use of CRISPR/Cas9 for gene editing and regulation, we implement a comprehensive computational tool based on a set of sgRNA design rules summarized from these published reports. We report a genome-wide sgRNA design tool and provide an online website for predicting sgRNAs that are efficient and specific. We name the tool CRISPR-ERA, for clustered regularly interspaced short palindromic repeat-mediated editing, repression, and activation (ERA).
  
  
  METHODS
  http://CRISPR-ERA.stanford.edu.
  
  
  BACKGROUND
  stanley.qi@stanford.edu or xwwang@tsinghua.edu.cn
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Bioinformatics Division, Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China, Stanford Chemistry, Engineering & Medicine for Human Health (ChEM-H).
authors.forename: Honglei
authors.initials: H
authors.lastname: Liu
authors.affiliation: Bioinformatics Division, Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Wei
authors.affiliation: Department of Bioengineering and.
authors.forename: Antonia
authors.initials: A
authors.lastname: Dominguez
authors.affiliation: Bioinformatics Division, Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China.
authors.forename: Yanda
authors.initials: Y
authors.lastname: Li
authors.affiliation: Bioinformatics Division, Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China.
authors.forename: Xiaowo
authors.initials: X
authors.lastname: Wang
authors.affiliation: Stanford Chemistry, Engineering & Medicine for Human Health (ChEM-H), Department of Bioengineering and Department of Chemical and Systems Biology, Stanford University, 443 Via Ortega, Shriram Center 376, Stanford, CA 94305-4125, USA.
authors.forename: Lei S
authors.initials: LS
authors.lastname: Qi
mesh_terms: D000818:Animals; D064112:Clustered Regularly Interspaced Short Palindromic Repeats / Q000235:genetics*; D005786:Gene Expression Regulation; D006801:Humans; D017393:RNA Editing / Q000235:genetics*; D012984:Software