Single Cell Genomics Day: A (Virtual) Practical Workshop


When:Friday March 26, 2021 10:00 AM to 5:00 PM EDT
Livestream:All talks will be openly livestreamed on this website. Registration is not required.


10:00 — 10:40 AM (EDT)Rahul Satija New York Genome Center (NYGC) and New York University (NYU)
Summary and References
Single-cell genomics: Recent advances and future directions
View the talk here
10:40 — 11:00 AMHattie Chung Broad Institute
Jointly profiling nuclear proteins and RNA in single cells in vivo
11:00 — 11:40 AMCole Trapnell University of Washington
Studying developmental robustness at whole-embryo scale and single-cell resolution
11:40 AM — 12:00 noonCoffee Break
12:00 — 12:20 PMShila Ghazanfar Cambridge Institute
Integrating molecule-resolved spatial gene expression and single cell RNA-sequencing data
12:20 — 12:40 PMPaul Datlinger Austrian Academy of Sciences
Ultra-high throughput single-cell RNA sequencing and perturbation screening by combinatorial fluidic indexing
12:40 — 1:00 PMJaison Jain New York Genome Center
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Reference-based mapping for single-cell analysis
1:00 — 1:40 PMLunch Break
1:40 — 2:00 PMSarah Pierce Stanford University School of Medicine
Spear-ATAC: Pooled, droplet-based, single-cell chromatin accessibility CRISPR screens.
2:00 — 2:40 PMDana Pe'er Memorial Sloan Kettering Cancer Center
Trajectories of plasticity in development and cancer
2:40 — 3:00 PMSaket Choudhary NYGC/NYU
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Count models for normalization of single-cell RNA-seq data
3:00 — 3:20 PMCoffee Break
3:20 — 4:00 PMFei Chen Broad Institute
Next Generation Tools for Spatial and Temporal Genomics
4:00 — 4:20 PMXin Jin Harvard University
In vivo Perturb-seq: studying gene function in developing tissues
4:20 PM — 4:40 PMBingjie Zhang NYGC/NYU
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Integrated epigenomic analysis with single-cell CUT&TAG
4:40 PM — 5:00 PMEfthymia Papalexi NYGC/NYU
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Analytical strategies for single-cell pooled CRISPR screens


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 fifth annual Single Cell Genomics Day on Friday, March 26, 2021. 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: profiling chromatin state and transcription factor binding in single cells, perform in-vivo CRISPR screens with single-cell readouts, and conducting single-cell sequencing in-situ.
  • Discover powerful new computational approaches including: algorithms for trajectory inference and single-cell ‘fate mapping’, tools to ‘map’ query datasets onto curated ‘atlases’, and methods for integrating spatially-resolved gene expression measurements with single-cell RNA-seq datasets.
  • Learn about strategies for massively multiplexed experimental design, and new approaches for statistical modeling and comparisons of single-cell datasets between healthy and diseased states.
  • Share ideas, troubleshoot experiments, and ask questions.
  • Hear presentations from:
    • Dana Pe’er Sloan Kettering Institute
    • Fei Chen Broad Institute
    • Cole Trapnell University of Washington
    • Hattie Chung (Regev/Chen Labs) Broad Institute
    • Shila Ghazanfar (Marioni Lab) EMBL/EBI
    • Xin Jin (Regev/Zhang/Arlotta Labs) Broad Institute
    • Sarah Pierce (Greenleaf/Winslow Labs) Stanford University
    • Paul Datlinger (Bock Lab) CeMM Vienna

Due to the COVID-19 pandemic, Single Cell Genomics Day will take place virtually in 2021. 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.