Single Cell Analysis
June 26 - July 11, 2020
Application & Materials Deadline: March 15, 2020


David Chenoweth, University of Pennsylvania
Michael McConnell, 
Lieber Institute for Brain Development
Sydney Shaffer, University of Pennsylvania
Gene Yeo, University of California, San Diego


COVID-19: We are closely monitoring the COVID-19 situation as it evolves, following CDC guidelines to ensure the safety and well-being of our participants and staff. Advisory

As of March 3rd, CSHL has postponed or canceled all upcoming scientific conferences and courses bringing participants to campus through April 5th, and we are evaluating future events on a rolling basis. 

Participants from CDC Warning Level 3 countries are being advised to cancel their participation unless they can demonstrate having departed the area at least two weeks prior to their visit to CSHL. 

We anticipate making a decision about this course and communicating to all participants soon.

Travel Plans: If you have not already made travel arrangements, we would recommend holding off on that until after our decision is announced. 

Travel Insurance Tip: CSHL recommends that all participants look into the possibility of extended travel insurance, for example, Cancel for Any Reason Travel Insurance (CFAR).


See the roll of honor - who's taken the course in the past.

Video about the course.

The goal of this two-week course is to teach students cutting-edge wet-lab approaches for single cell analysis, and to provide familiarity with basic bioinformatic approaches to single cell data. Modules of the course will be taught by scientists with expertise in distinct areas of single cell analysis. Topics to be covered include quantitative single cell analysis by RNAseq, genomic DNA analysis, proteomics, and metabolomics. 

  • Droplet- and microwell based single cell isolation
  • Single cell RNA seq library preparation
  • Single molecule FISH
  • Single cell peptidomics with Mass Spec
  • Single cell western blot
  • Photoactivatable single cell probes
  • Single cell mass spectrometry 
  • Soft X-ray tomography
  • Introductory single cell sequencing analysis

2019 Speakers and Module Leaders Included:

Nancy Allbritton, University of North Carolina
James Eberwine, University of Pennsylvania
Amy Herr, University of California Berkeley
Kristin Knouse, Whitehead Institute/Massachusetts Institute of Technology
Carolyn Larabell, University of California, San Francisco
Arjun Raj, University of Pennsylvania 
Elena Romanova, University of Illinois
Stas Rubakhin, University of Illinois
Carsten Schultz, Oregon Health & Science University
Peter Sims, Columbia University
Jonathan Sweedler, University of Illinois

This course is supported with funds provided by: National Institute of General Medical Sciences, Howard Hughes Medical Institute and Helmsley Charitable Trust.

We would like to acknowledge the following companies that provided invaluable equipment support:
Agilent Technologies, Eppendorf North America, Hamamatsu Photonics, Molecular Devices, ProteinSimple, Inc, Sutter Instrument Company, Thermo Fisher Scientific

Cost (including board and lodging): $4,480

No fees are due until you have completed the full application process and are accepted into the course.

Students accepted into the course should plan to arrive by early evening on June 25 and plan to depart after breakfast on July 11.

Students are further expected to bring a laptop computer with specified bioinformatic packages pre-installed.

Before applying, ensure you have:
  1. Personal statement/essay;
  2. Letter(s) of recommendation;
  3. Curriculum vitae/resume (optional);
  4. Financial aid request (optional).
    More details.

If you are not ready to fully apply but wish to express interest in applying, receive a reminder two weeks prior to the deadline, and tell us about your financial aid requirements, click below: