Single Cell Workshop 2014





Single-Cell RNA-sequencing Workshop


Thursday, October 2, 2014, 9:00am to Friday, October 3, 2014, 5:00pm


Harvard University, Sherman Fairchild 268, 7 Divinity Ave., Cambridge, MA

falseThe two‐day workshop will provide attendees with an opportunity to gain detailed information on several current methods for single‐cell transcriptome analysis.

The speakers have either developed a particular method or extensively used it in their own research. The workshop will focus on the theory and key technical elements of each method (including practical demonstrations) and discuss their pros and cons depending on experimental design. The data analysis part will include a hands‐on session on data quality assurance, differential expression analysis and subpopulation analysis steps.


Registration is now CLOSED as we have reached our capacity.  Confirmation of registration was sent via email the week of 9/15/14.

Faculty Organizers

Lev Silberstein ( and Peter Kharchenko (

Program: Day One

AM: Lectures

  • Lev Silberstein and Peter Kharchenko - Introduction and overview of the workshop
  • Sunney Xie (Harvard) - Single‐cell RNA‐Seq using multiple annealing and looping‐based amplification cycles (MALBAC)
  • Saiful Islam (Stanford) - Single‐cell RNA‐Seq using unique molecular identifiers
  • John Trombetta and Chloe Villani (Broad Institute/Regev & Hacohen Labs) - Single‐cell RNA‐Seq with Smart‐Seq
  • Je Hyuk Lee and Evan Daugharthy (Harvard) - FISSEQ for in situ transcriptional profiling
  • Jim Eberwine (UPenn) - Single‐cell transcriptomics—in fixed cells, live cell culture and live slices

Break for lunch

PM: Practical Demonstrations (group rotations)

  • Jim Eberwine (UPenn) - Interpretation of the bioanalyzer data following single-cell cDNA amplification
  • Je Hyuk Lee and Evan Daugharthy (Harvard) - FISSEQ demonstration
  • Saiful Islam (Stanford) - Cell isolation for single‐cell RNA‐Seq and UMI protocol overview
  • John Trombetta and Chloe Villani (Broad) - Smart‐Seq: Key experimental steps

Program: Day Two

AM: Presentations and Discussion

  • Manisha Ray (Fluidigm) - Using the C1 System to automate mRNA‐Seq of single cells: Introduction and implementation
  • Ken Livak (Fluidigm) - Driving genomics to the single‐cell level: Data analysis and implementing multiple RNA‐Seq protocols on the C1 System
  • Roundtable Discussion: Which single‐cell RNA‐Seq method should I choose for my experiment?

Break for lunch

PM: Computational Analysis of Single-Cell Data*

  • Peter Kharchenko (Harvard) - Overview of single‐cell RNA‐Seq analysis methods
  • Guo Chen Yuan (DFCI) - Mapping cellular hierarchy by single‐cell gene expression analysis
  • Data Analysis Practicum -  Alignment/QC/Normalization/Differential Expression/Cell and Gene Networks/Subpopulation Analysis

* at Northwest B129 computer lab

For questions about the program, please contact Claudia Rizzini ( or tel: 617.495.4388)

This workshop is co-sponsored by the Harvard Stem Cell Institute and Harvard Catalyst.

Computational workshop online tutorials:

single-cell_rna-seq_workshop_october_2014_0.pdf290 KB