Single Cell Genomics Day: A (Virtual) Practical Workshop


When:Friday March 4, 2022 10:00 AM to 5:00 PM EDT
Livestream:All talks will be openly livestreamed on this website and Youtube. Registration is not required.
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10:00 — 10:40 AM (EST)Rahul Satija New York Genome Center (NYGC) and New York University (NYU)
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Single-cell genomics: Recent advances and future directions
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10:40 — 11:20 AMSarah Teichmann Wellcome Sanger Institute
Mapping the human body: Locating cells in time and space
11:20 — 11:40 AMIvan Raimondi New York Genome Center, Technology Innovation Lab
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Multifactorial chromatin profiling at single-cell resolution
11:40 AM — 12:00 noonCoffee Break
12:00 — 12:20 PMKaiyi Jiang MIT, Abudayyeh-Gootenberg Lab
Programmable eukaryotic protein expression with RNA sensors
12:20 — 12:40 PMJoseph Replogle Whitehead Institute, Weissman Lab
Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq
12:40 — 1:00 PMHarm Wessels, Carol Dalgarno New York Genome Center, Satija Lab
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New technologies and opportunities for single-cell perturbation screens
1:00 — 1:40 PMLunch Break
1:40 — 2:00 PMAmy Chen Stanford University, Greenleaf Lab
NEAT-seq: Simultaneous profiling of intra-nuclear proteins, chromatin accessibility, and gene expression in single cells
2:00 — 2:40 PMXiao Wang MIT, Broad Institute
Multimodal in situ analysis of single-cell transcriptomic states
2:40 — 3:00 PMYuhan Hao NYGC/NYU, Satija Lab
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Cross-modality integration of single cell data
3:00 — 3:20 PMCoffee Break
3:20 — 4:00 PMBing Ren UC San Diego
Single cell analysis of epigenome in health and disease
4:00 — 4:20 PMJasper Janssens VIB-KU Leuven, Aerts Lab
Decoding gene regulation in the fly brain
4:20 PM — 4:40 PMYanxiang Deng Yale University, Fan Lab
Spatial CUT&TAG: Spatially resolved chromatin modification profiling at the cellular level


Recent developments in molecular biology, microfluidics, and computational biology have transformed the field of single cell genomics, and have widespread biological applications. 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 sixth annual Single Cell Genomics Day on Friday, March 4, 2022. This workshop will begin with an overview of exciting developments in the field over the past year, followed by in-depth presentations on exciting methods and techniques. Our goal is to empower you to utilize single cell genomics in your work. The workshop is free and open to beginners and experts alike.

Come to:

  • Learn about cutting-edge molecular technologies including: multimodal profiling of chromatin state in single cells, measuring cellular gene expression and electrophysiology in-situ, and performing combinatorial and genome-wide single cell CRISPR screens.
  • Discover powerful new computational approaches including: tools to assemble and map to multimodal reference ‘atlases’, techniques to interpret non-coding genetic variants using single-cell chromatin accessibility data, and methods for integrating spatially-resolved gene expression measurements with single-cell RNA-seq datasets.
  • Share ideas, troubleshoot experiments, and ask questions.

Due to the COVID-19 pandemic, Single Cell Genomics Day will take place virtually in 2022. We are able to make all talks freely available via livestream thanks to support from the National Human Genome Research Institute to the Center for Integrated Cellular Analysis.

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.

Integrative single-cell analysis. (Stuart and Satija., 2019) [PubMed]
Our recent overview of multi-modal technologies and computational integration methods for single-cell data.

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.