Single Cell Transcriptomics Classification

PI: John J. Ngai, Ngai Lab
University of California Berkeley
Title: “Classification of Cortical Neurons by Single Cell Transcriptomics”
BRAIN Category: Census of Cell Types (RFA MH-14-215)

To understand what makes neurons distinct, Dr. Ngai’s team will explore one major type of mouse brain cell, pinpointing genes responsible for differentiating them into subtypes and will also test whether each subtype has unique functions, using a new technique that labels them with tagged genes.

Cell Type Characterization Platform

PI: Hongkui Zeng, Allen Brain Atlases
Allen Institute for Brain Science
Title: “Establishing a Comprehensive and Standardized Cell Type Characterization Platform”
BRAIN Category: Census of Cell Types (RFA MH-14-215)

Dr. Zeng’s group will characterize cell types in brain circuits controlling sensations, such as vision and emotions, as a first step to better understand information processing across circuits. The data generated will be posted as a public online resource for the scientific community.

Combining genetics, genomics & anatomy

Principal Investigator: Sacha B. Nelson
Brandeis University
Title: Combining genetics, genomics, and anatomy to classify cell types across mammals”
BRAIN Category: Census of Cell Types (RFA MH-14-215)

To gain a deeper understanding of how cells have evolved specialized features, Dr. Nelson and colleagues will create transgenic strains of rats and mice that carry identical genetic modifications in many different cell types and see how the properties of these cells diverge across species.

Quantitative cell type-based mapping

Principal Investigator: Pavel Osten
Cold Spring Harbor Laboratory
Title: “Towards quantitative cell type-based mapping of the whole mouse brain”
BRAIN Category: Census of Cell Types (RFA MH-14-215)

The Osten team will develop an automated system to image different types of brain cells and their connections in mice, to pinpoint differences between males and females, across the lifespan.

Neuronal Subtypes By Cell Transcriptomics

Principal Investigator: Joshua R Sanes
Title: “Comprehensive Classification Of Neuronal Subtypes By Single Cell Transcriptomics”
BRAIN Category: Census of Cell Types (RFA MH-14-215)

Dr. Sanes and colleagues will use new methods of genetic screening to comprehensively catalog and distinguish different kinds of cells across species and brain regions.

Epigenomic mapping cell-type classification

Principal Investigator: Joseph R Ecker
Salk Institute for Biological Studies
Title: “Epigenomic mapping approaches for cell-type classification in the brain”
BRAIN Category: Census of Cell Types (RFA MH-14-215)

Dr. Ecker’s group will use signatures of epigenetics, the switching on-and-off of genes in response to experience, in mouse frontal cortex to help identify different classes of cells and understand their function.

Cell types in developing human fetal cortex

Principal Investigator: Daniel H Geschwind
UCLA Neuroscience
Title: “Defining cell types, lineage, and connectivity in developing human fetal cortex ”
BRAIN Category: Census of Cell Types (RFA MH-14-215)

Dr. Geschwind’s group will explore the diversity of cell types in the developing human brain, and will bring to bear state-of-the-art genetic and cellular visualization technology to map and trace the relationship between cell types across the cortex.

Cortical Neurons by Transcriptome

Principal Investigator: Massimo Scanziani
Title: “Classifying Cortical Neurons by Correlating Transcriptome with Function”
UC San Diego’s Neuroscience
BRAIN Category: Census of Cell Types (RFA MH-14-215)

Dr. Scanziani’s team will record neuronal responses to different visual stimuli to discover how individual brain cell activity is linked to expression of specific genes.

Massively Parallel Single Cell Analysis

Principal Investigator: Arnold Kriegstein
UCSF Neuroscience
Title: “Mapping the Developing Human Neocortex by Massively Parallel Single Cell Analysis”
BRAIN Category: Census of Cell Types (RFA MH-14-215)

By combining genetic, molecular and physiological techniques at the single cell level, Dr. Kriegstein and colleagues will classify diverse cell types in the prefrontal cortex of developing human brain tissue.

Cell-Type Classification in the Human Brain

Principal Investigator: Nenad Sestan
Yale Neuroscience
Title: “A Novel Approach for Cell-Type Classification and Connectivity in the Human Brain”
BRAIN Category: Census of Cell Types (RFA MH-14-215)

Dr. Sestan’s group will substantially advance the profiling of cell types – their molecular identities and connections – made possible by a new method of better preserving brain tissue to maintain cell integrity.

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