Stem Cells & Gene Editing Workshop

Genome engineering in stem cells has tremendous scientific potential, but beginning your work in this field can be daunting. The Allen Institute for Cell Science has developed systematic workflows for endogenous gene tagging in human induced pluripotent stem cells (hiPSCs), as well as best practices along the way. Using these methods we have created a collection of fluorescently tagged hiPSC lines as described on and in our publication in MBoC.

Apply to join us on Wednesday, March 27 to learn the ins and outs of working with stem cells and performing endogenous gene tagging using CRISPR/Cas9 directly from our scientists.


We’ll open the workshop with interactive seminars about endogenous gene tagging for both expressed and non-expressed genes including a hands-on session on the use of basic bioinformatics tools for designing crRNAs and donor plasmids for gene tagging as well as the genomic and cell biological QC assays and workflows we use to generate high quality clonal cell lines. In the afternoon, step into our labs for live, in-depth demonstrations of many aspects of stem cell maintenance and characterization. We’ll wrap up the afternoon with a discussion session with our scientists that specialize in gene editing, cardiomyocyte differentiation, microscopy, image analysis, and modeling. A detailed list of topics is available below.

Due to the hands-on nature of this workshop and focused, small group discussions, we have limited the number of participants to 25. We encourage trainees and bench scientists interested in gene editing in stem cells to apply (no more than one per lab).  We are eager to host a diverse audience at this workshop and will be providing travel awards to a few attendees based on scientific area of interest and financial need. Applications for this workshop are now closed.

Workshop Topics

Gene Editing

  • crRNA and donor molecule design for knock-in
  • Practical workflows for generating clonal hiPSC lines
  • Tips, tricks, and best practices for identifying precisely edited, healthy hiPSC clones

Stem Cells

  • Passaging, thawing and cryopreserving hiPSC
  • Identifying good hiPSC morphology
  • Passaging and cryopreserving hiPSC clones in 96-well plates
  • Best practices for flow analysis and sorting of hiPSC


Draft Schedule


Registration and breakfast (provided)


Gene Editing Part I


AM Break


Gene Editing Part II


Lunch (provided)


Preparation for lab demos


Groups rotate through lab demonstrations


PM Break


Roundtable discussions with Institute scientists