Genetics, Bioinformatics and Systems Biology Colloquium
Thursdays, 12:00 pm – 1:00 pm
UC San Diego, Powell-Focht Bioengineering Hall, Fung Auditorium
Complete schedule here

CRISPR Screening Workshop

Thursday, October 20, 2016 from 1:30 pm – 6:00 pm

Sanford Consortium for Regenerative Medicine


Organized by Olivier Harismendy, Kristen Jepsen and SDCSB

Sponsored by Illumina, Twist Bioscience, Flu’OMICS, and Agilent Technologies


Missed the event?

Review the pre-workshop installation guidelines here.
View and download the workshop slides here.


Pooled CRISPR based screens have become an important tool for functional genomics. Multiple laboratories in La Jolla are initiating screens and developing standard operating procedures for screen design, execution and analysis. The goal of the workshop is to provide attendees with the tools and knowledge to design, execute and analyze screens leading to reliable, reproducible and sensitive results.


Learning Goals
  • Design, execute and analyze a pooled CRISPR-based screen
  • Understand the limitations of CRISPR-based screens
  • Troubleshoot experimental steps
  • Control the quality of the reagents, libraries and resulting datasets
  • Identify significantly altered genes and pathways
  • Locate literature and online resources
  • Establish a network of users interested in CRISPR-screens and applications

Notably, the workshop will include a hands-on analysis session, which will require attendees to bring their own laptops, with R-Studio installed.


1:00 pm Registration
1:30 pm Welcome and introduction (Harismendy, Jepsen)
1:40 pm Library amplification and viral preparation (Bojorquez)
1:55 pm Popular designs of CRISPR pooled experiments (Shen)
2:15 pm Amplicon sequencing using Illumina instruments (Jepsen)
2:35 pm Library Preparation and quality control (Van Nostrand)
3:00 pm Break
3:15 pm Data QC and analysis – hands-on (Spahn, Harismendy)
5:00 pm Social happy hour and sponsors presentations


  • Ana Bojorquez – Research Associate – Trey Ideker’s Laboratory
  • John Paul Shen – Postdoctoral Fellow – Trey Ideker’s Laboratory
  • Olivier Harismendy – Assistant Professor – UC San Diego Moores Cancer Center
  • Philipp Spahn – Postdoctoral Fellow – Nathan Lewis’ Laboratory
  • Eric Van Nostrand – Postdoctoral Fellow – Gene Yeo’s Laboratory
  • Kristen Jepsen – Director – IGM Genomics Core


Teaching Assistant


  • Brian Tsui – Graduate Student – Hannah Carter’s Laboratory


No Show Policy

While we do not charge a fee to attend this event, these and our other events would be unsustainable unless those unable to attend cancelled their reservations no later than 2 days before the event. A no-show can limit your ability to book our events in the future. Thank you in advance for your cooperation.



Free parking at the Sanford Consortium’s east lot will be provided on a first-come, first-serve basis. Hourly parking is also available for purchase at the ticket booth. There is also additional parking near the Torrey Pines Gliderport, which is within walking distance.  The UCSD Shuttle Route has two drop off locations within walking distance to the Sanford Consortium.


Pictures of scientists having fun

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