Course Details

  • Date: November 14th, 2017 - November 14th, 2017
  • Time: 9:30 am - 5:00 pm
  • Location: NIH B37, Rm 6041 and 4041
  • Presenter(s): Vishal Koparde (CCBR)

The CCR Office of Science and Technology Resources (OSTR), along with the Bioinformatics Training and Education Program (BTEP), are pleased to organize this event for the CCR scientific community.

The primary goal of single cell sequencing is to investigate individual cells using optimized next generation sequencing (NGS) technologies, with the goal of resolving cellular differences to better understand the function of an individual cell in the context of its microenvironment. The event will provide an overview of this emerging field, and speakers will talk about technology platforms, the best practices for sample preparation, and bioinformatics approaches for analysis of sc-RNAseq data.

Date:            Tuesday, November 14, 2017

Time:           Session I B37, Rm 4041/4107 (9:30-11:00 am)

Session II B37, Rm 6041/6107 (2:00-5:00pm)

Scroll further down for WebEx information


Session I (B37, Rm 4041/4107)

9:30 am – 11:00 am        Introduction to Single Cell Genomics

                                     Speaker: Michael Kelly, Ph.D., NIDCD

  • Key Concepts in Single Cell Genomics
  • Current Challenges & Limitations
  • Experimental Design Considerations
  • Platform Selection Considerations
  • “Established” and Emerging Applications


Session II (B37, Rm 6041/6107)

2:15 pm – 2:45 pm         Overview of Single Cell Technologies at CCR Cores

     Speaker: Xaolin Wu, Ph.D., CCR Genomics Technology Lab

  • BD Rhapsody Single Cell Analysis for RNA and Proteins
  • Chromium Single Cell 3′ Solutiom=n
  • DEP Array Technology Rare Cell Isolation
  • Fluidigm C1 for Single Cell Genomics


2:45 pm – 3:45 pm       Single Cell RNA-Seq at CCR-SF: Best practices using 10X Genomics

   Speaker: Monika Mehta, Ph.D., CCR-SF (ATRF)

  • Current production systems
  • New methods being tested
  • Optimal experimental design
  • Sample requirements, prep and QC
  • Highlights from range of projects at SF


3:45 pm – 4:45 pm          Overview of single cell RNA-Seq analysis

      Speaker: Vishal Koparde, Ph.D., CCBR

  • How is single cell data different from bulk RNASeq?
  • Options for filtering, normalization and visualization
  • Current popular analysis tools

In-person attendance is encouraged. For convenience, the talks will be on WebEx (link below):

Meeting number/Access Code: 858 626 079

Audio connection: 1-650-479-3207 Call-in toll number (US/Canada)