Single Cell Genomics Day: A Practical Workshop

Recent developments in molecular biology, microfluidics, and computational biology have transformed the field of single cell genomics. However, the breathtaking pace of technology development has given rise to a multitude of molecular protocols, commercial systems, and computational challenges.

The Satija Lab is excited to host the Second Annual Single Cell Genomics Day on Friday, January 19, 2018. This workshop will begin with an overview of exciting developments in the field over the past year, followed by in-depth presentations with an emphasis on practical details and considerations. Our goal is not to fully describe the details of each method, but instead to highlight the intuition and key use cases that can help motivate new users to get started.

Single Cell Genomics Day will be held at the NYU Center for Genomics and Systems Biology, with check in beginning at 9:00 AM. Please register in advance to attend in person. The workshop is free for all participants, thanks to generous support from the NYU Biology department and Center for Genomics and Systems Biology.

We thank the Chan Zuckerberg Initiative for supporting a livestream of the presentation. The livestream has ended and is not available for viewing.


9:30 am — 10:00 am Rahul Satija NYGC/NYU
Download Slides, Summary and References
Single Cell Genomics: Recent Advances and Future Directions
View the talk here
10:00 am — 10:30 am Marlon Stoeckius NYGC Technology Innovation Lab
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Simultaneous Measurement of mRNA and Protein in Single Cells
Topics: CITE-Seq, Abseq, REAP-Seq
10:30 am — 11:00 am Shiwei Zheng NYGC/NYU
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Multiplexing Strategies for Single Cell Sequencing
Topics: Genetic Demultiplexing, Cell 'Hashing'
11:00 am — 11:15 am Coffee Break
11:15 am — 12:00 pm Evan Macosko Broad Institute
Keynote: Molecular Exploration of the Brain at Single Cell Resolution
12:00 pm — 12:30 pm Kasandra Burgos 10X Genomics
Expanding the Range of Applications for Single Cell RNA-Seq
Topics: Sample Fixation, 5' Sequencing, Nuclear Profiling
12:30 pm — 1:30 pm Lunch
1:30 pm — 2:00 pm Jan Slabbaert NYGC/NYU
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Applying Single Cell Sequencing for Lineage Reconstruction
Topics: GESTALT, CRISPR scars
2:00 pm — 2:45 pm Peter Kharchenko Harvard Medical School
Keynote: Transcriptional Dynamics in Single Cells
2:45 pm — 3:00 pm Coffee Break
3:00 pm — 3:25 pm Andrew Butler NYGC/NYU
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Batch Correction and Data Integration for Single Cell Transcriptomics
3:25 pm — 3:50 pm Efthymia Papalexi NYGC/NYU
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Combining CRISPR Screens with Single Cell RNA-Seq
Topics: Perturb-Seq, CROP-Seq, CRISP-seq


Additional resources

Below, we list a few useful resources for those who would like to a brief introduction to the field prior to the workshop.

A practical guide to single cell RNA-seq for biomedical research and clinical applications. (Haque et al., 2017) [PubMed]
An excellent overview of single cell genomics, for those new to the field.

Choosing a single cell technology. (Satija Lab) [PDF Slides]
From our first single cell genomics day. Covers the strengths, weaknesses, and ideal uses cases for common technology platforms.

Computational and analytical challenges in single-cell transcriptomics. (Stegle, Teichmann, and Marioni, 2015) [PubMed]
A broad and comprehensive discussion of analytical challenges for single cell analysis.

Power analysis of single-cell RNA-sequencing experiments. (Svensson et al., 2017) [PubMed]
A comprehensive technical benchmarking of single cell technologies.

Methods and challenges in the analysis of single-cell RNA-sequencing data. (Camara, 2017) [Link]
A concise overview, focusing on recent analytical developments in the field.