CCMI - Workshop

CRISPR Screening Workshop

Speaker's slides and video recordings from the workshop are provided below. 

Organized by Olivier Harismendy and Kristen Jepsen.

Sponsored by Agilent, FluOMICSIllumina, MilliporeSigma and Synthego.

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

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


  • 12:30 pm – Registration
  • 1:00 pm – Welcome and introduction (Harismendy, Jepsen) Slides | YouTube
  • 1:10 pm – Library amplification and viral preparation (Bojorquez) Slides | YouTube
  • 1:25 pm – Popular designs of CRISPR pooled experiments (Shen) Slides | YouTube
  • 1:45 pm – Library Preparation and Quality Control (Van Nostrand, Jepsen) Slides 1 | Slides 2 | YouTube 
  • 2:30 pm – Break
  • 3:00 pm – Screen Analysis with PinAPL-Py (Spahn) Slides | YouTube  
  • 4:20 pm – Use Case #1: CRISPR-Cas9 Dissection of Heparan Sulfate (Ryan Weiss, PhD) Slides | YouTube
  • 4:40 pm – Use Case #2 : Identification of pancreatic cancer stem cell dependencies using a genome-wide CRISPR screen (Nikki Lytle, PhD) (slides n/a)
  • 5:00 pm – Closing remarks (Harismendy) YouTube 
  • Social happy hour and sponsors presentations including raffles

For more info on PinAPL-Py, visit PinAPL-Py's homepage and check out the tutorial on Github.


  • Ana Flores-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 

Sponsored Raffle Prizes

Agilent's SureVector Library Cloning Kit. The library cloning kit uses Agilent’s SureVector chemistry to allow the rapid generation of plasmid libraries from an amplified oligo pool. Included in the kit are Agilent’s linearized pSGLenti vector backbone, competent cells, media and all buffers and reagents required to clone Agilent’s pooled ready-to-clone or ready-to-amplify libraries. Each kit contains sufficient amounts of the above materials to generate four plasmid libraries of 60,000 guides.

Illumina will be raffling off its newest option in DNA library prep, Nextera Flex. The Nextera DNA Flex Library Prep Kit uses a fast, user-friendly workflow. On-bead tagmentation chemistry reduces total library prep time to ~3.5 hours, from DNA extraction to library normalization. The Nextera DNA Flex workflow supports a broad DNA input range (1–500 ng), multiple sample types, and both small and large genomes. The workflow includes DNA extraction from blood, saliva, or dried blood spots or bacterial colonies.

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 canceled 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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