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Cell Types Database: RNA-Seq Data

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Protocols  |  Background

M1 - 10x genomics (2020)

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Multiple Cortical Areas - SMART-seq (2019)

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MTG - SMART-seq (2018)

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V1, ACC - SMART-seq (2018)


MTG - 10x SEA-AD (2022)

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Protocols  |  Background

NOTE As of 10/21/2021: The Mouse CTX-HPF datasets have been updated to reflect the final taxonomy and cell type annotations from the May 2021 paper in Cell here

Whole Cortex & Hippocampus - 10x genomics (2020)
with 10x-SMART-seq taxonomy (2021)

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Whole Cortex & Hippocampus - SMART-seq (2019)
with 10x-SMART-seq taxonomy (2021)

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V1 & ALM - SMART-seq (2018)

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ACA and MOp - SMART-seq (2018)



Protocols  |  Background

Mouse, Human, Macaque - LGN (2018)




Background: Profiling Cellular Diversity in the Brain

The mammalian brain is composed of many cell populations that differ based on their molecular, morphological, electrophysiological and functional characteristics. Classifying these cells into types is one of the essential approaches to defining the diversity of the brain's building blocks. This project seeks to characterize cortical diversity at the cellular level for several neuroanatomical areas in both mouse and human. Additional data will be released regularly, building toward a complete picture of cellular diversity of the brain and how this diversity is conserved across species.


Transcriptional profiling: RNA-Seq Data

Single cell (or single nucleus) RNA sequencing (RNA-Seq) is a scalable approach to provide genome-wide expression profiles for thousands of cells. This data set includes single cell and nuclear transcriptomic profiles, assayed from human and mouse brain regions. Anatomical specificity is achieved by microdissecting tissue from defined brain areas, such as cortical layers or cell groups in LGd.


Cell Diversity in the Human Cortex

To investigate the cellular diversity across human cortex, a low-bias approach to profile cell-type diversity was sought, constrained by the challenge of working with precious and limited tissue sources. Individual layers of cortex were dissected from tissues covering the middle temporal gyrus (MTG), anterior cingulate gyrus (CgGr), primary visual cortex (V1C), primary motor cortex (M1C), primary somatosensory cortex (S1C) and primary auditory cortex (A1C) derived from human brain, and nuclei were dissociated and sorted using the neuronal marker NeuN. Nuclei were sampled from postmortem and neurosurgical (MTG only) donor brains and expression was profiled with SMART-Seq v4 or 10x Genomics Chromium Single Cell 3' v3 RNA-sequencing.

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Cell Diversity in the Mouse Cortex and Hippocampus

Our goal is to define cell types in the adult mouse brain using large-scale single-cell transcriptomics. Towards that goal, we have generated a dataset that includes single-cell transcriptomes from multiple cortical areas and the hippocampal formation. Samples were collected from dissections of brain regions from ~8 week-old male and female mice, from a variety of transgenic lines. For most brain regions, we isolated labeled cells from pan-GABAergic, pan-glutamatergic, and pan-neuronal transgenic lines. For primary visual cortex (VISp) and anterolateral motor cortex (ALM), we sampled additional cells using driver lines that label more specific and rare types. To investigate the correspondence between transcriptomic types and neuronal projection properties, we collected cells labeled from retrograde injections for select combinations of target injection sites and dissection regions. Labeled cells were collected by fluorescence activated sorting (FACS) of single cells. We also collected cells without fluorescent labeling to sample non-neuronal cell types. Isolated single cells were processed for RNA sequencing using SMART-Seq v4 and 10x Chromium v2. This dataset reveals the molecular architecture of the neocortex and hippocampal formation, with a wide range of shared and unique cell types across areas. It provides the basis for comparative studies of cellular diversity in development, evolution, and diseases.  

RNA-Seq data generated as part of the Brain Initiative Cell Census Network (BICCN) are available as part of the Brain Cell Data Center (BCDC) portal.

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Comparative cellular anatomy in the thalamus (LGN)

Abundant anatomical and physiological evidence supports the presence of at least 3 distinct types of principal or relay neurons in the dorsal lateral geniculate nucleus (dLGN), the brain region that conveys visual information from the mammalian retina to the primary visual cortex. This data set provides detailed transcriptional profiles of cells from this area, available for download. Cells derived from this area were compared across 3 species (human, macaque, and mouse) to assess cross-species correspondence based on transcriptional profiles.


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