Virtual Conference Agenda

Advances in Single Cell Genomics to Study Brain Cell Types

Society for Neuroscience Member-Only Virtual Conference

June 4, 2018 | 9 a.m. – 5 p.m. EDT

Session 1 | Deciphering the Cellular Landscape of the Brain Using Single Cell Transcriptomics

9:00 a.m. – 10:00 a.m. EDT


Evan Macosko             Bosiljka Tasic             Naomi Habib   

Single cell/nucleus transcriptomics has emerged as a powerful approach to classify cell types and dynamic cell states in any multicellular organ or organism. By measuring gene expression in single cells in a genome-wide manner, one obtains a highly multidimensional molecular signature of each cell, which enables identification of cellular diversity and dynamic changes in the healthy and diseased brain.

Evan Macosko, Bosiljka Tasic, and Naomi Habib will present various methods to perform single cell and nucleus RNA-sequencing in brain tissue, computational approaches to analyze the data, and examples of applications in the mouse and human brain. A short Q&A will follow presentations.

Networking Break

10:00 a.m. – 10:15 a.m. EDT

Session 2 | Single Cell Epigenomics Uncovers Gene Regulatory Diversity in Mammalian Brains

10:15 a.m. – 11:15 a.m. EDT


  Chongyuan Luo         Sebastian Preissl

The epigenome is an ensemble of chemical modifications to DNA and chromatin that affects gene regulation. Genome-wide mapping of epigenomic signatures is one of the most effective approaches for identifying gene regulatory elements, such as enhancer sequences.

Chongyuan Luo and Sebastian Preissl will introduce the utility of single cell epigenomic approaches — such as DNA methylation profiling and chromatin accessibility profiling — that have demonstrated robust classifications of brain cell types and enabled the mapping of the regulatory landscape for virtually all brain cell populations. These approaches provide opportunities to determine the cell-type specific functions of non-coding sequences and decipher their contribution to brain diseases. A short Q&A will follow presentations.

Networking Break

11:15 a.m. – 11:30 a.m. EDT

Session 3 | Spatial Transcriptomics of Neurons and Brain Circuits

11:30 a.m. – 12:30 p.m. EDT


       Ed Boyden                   Long Cai                  Mats Nilsson     

Brain cells have complex morphologies and are organized into complex networks in order to compute sensations, actions, decisions, and emotions. To understand this spatial organization and how it goes awry in brain disorder states, it is important to map transcripts — ideally at omic scale — throughout neurons and intact brain circuits in species such as mice and humans.

Ed Boyden, Long Cai, and Mats Nilsson will discuss cutting edge techniques, such as FISH and other sequencing technologies facilitated by strategies that de-crowd transcripts in dense tissues to permit the accurate assessment and mapping of transcripts in neurons in brain tissue. Such technologies enable the connection between the molecular world of cell types and cell states and the systems world of networks and circuits. These connections are key to understanding how brain computations are implemented, and how they might be repaired in states of disease. A short Q&A will follow presentations.

Networking Break

12:30 p.m. – 1:30 p.m. EDT

Session 4 | Multi-Feature Analysis and Integration for the Functional Dissection of Brain Cell Types

1:30 p.m. – 2:30 p.m. EDT


     Josh Huang               Jonathan Ting            Andreas Tolias   

Understanding the diversity of brain cell types and the roles of cell types within brain circuits is an immense challenge in modern neuroscience. Recent progress in the field of single cell biology and transcriptomics has enabled unprecedented resolution of cell types, including delineation of previously unrecognized types and subtypes in the mammalian brain.

Josh Huang, Jonathan Ting, and Andreas Tolias will explore how cutting-edge and highly integrative experimental approaches are being leveraged for multi-feature analysis at the single cell level. Speakers will also address how these datasets support cell type classification efforts, increasingly precise tool development, and the functional dissection of mouse and human brain cell types. A short Q&A will follow presentations.

Networking Break

2:30 p.m. – 2:45 p.m. EDT

Session 5 | Single Cell RNA Sequencing Reveals Dynamic Developmental Trajectories During Mammalian Brain Development

2:45 p.m. – 3:45 p.m. EDT


      Alex Pollen           Tom Nowakowski        Giorgia Quadrato        Gioele La Manno

The development of the nervous system is a complex and branched dynamical process. These features pose important challenges to determining how the vast heterogeneity of the nervous system arises. Single cell RNA sequencing (RNA Seq) technologies offer an important tool to study developmental processes. However, analysis of these data are further complicated by the superposition of several sources of biological variability, including differentiation, maturation, and regional diversity. Early-stage investigators will highlight possibilities unlocked by single cell RNA sequencing techniques and technical challenges that remain.

Alex Pollen and Tom Nowakowski will present different strategies adopted to address sources of variation and complexity, including by using a comprehensive single cell survey of the developing human brain across five years, 48 individuals, and multiple stages of development and brain regions. Giorgia Quadrato will address the potential and limitations of modeling human disease progression and developmental trajectory using human organoids, and describe how single cell RNA sequencing can be used to asses organoids heterogeneity and similarity to their in vivo counterparts. Gioele La Manno will present a new method of “RNA velocity,” that can be used to study nervous system development and other dynamical processes. They will also highlight how this approach can be extended to obtain lineage tracing-like data from human embryonic tissue specimens. A panel discussion and Q&A will follow presentations.

Networking Break

3:45 p.m. – 4:00 p.m. EDT

Session 6 | Reconstructing Brain Evolution with Single Cell RNA Sequencing Data

4:00 p.m. – 5:00 p.m. EDT


                  Trygve Bakken     Maria Antonietta Tosches       

The stunning complexity of the brain is the result of evolutionary processes. Changes of brain size or connectivity are not sufficient to explain the diversity of vertebrate brains. Neuron types also change over evolutionary time, but elucidating their evolution has been challenging. Single cell and single nucleus RNA sequencing enable comparisons of neural cell types across species in an unbiased and quantitative way.

Trygve Bakken will describe the extent to which transcriptomic cell types are conserved in mouse and human cortex. Maria Antonietta Tosches will present how the comparison of reptilian and mammalian single cell RNA sequencing data inform us on the evolution of the cerebral cortex. A short Q&A will follow presentations.

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