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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.

Rnaseq intro image

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. Detailed protocols describing experimental methods and analysis steps are described in the Transcriptomics Overview technical whitepaper.


Cell Diversity in the Human Cortex

RNA-Seq Data Summary

Rnaseq human image

Middle Temporal Gyrus (MTG):

This RNA-Seq data set is created from intact nuclei derived from frozen human brain specimens, to survey cell type diversity in the human middle temporal gyrus (MTG). In total, 15,928 nuclei from 8 human tissue donors ranging in age from 24-66 years were analyzed. Analysis of these transcriptional profiles reveals approximately 75 transcriptionally distinct cell types, subdivided into 45 inhibitory neuron types, 24 excitatory neuron types, and 6 non-neuronal types.

Primary Visual Cortex (V1) and Anterior Cingulate Cortex (ACC):

Addition of a total of 16,281 nuclei from two new brain regions from the same donors provides a means to investigate the diversity of cell types across the human neocortex. Data from matched brain regions in mouse will also allow for direct comparison of cell types across mammalian species. Analysis of these data sets is still in progress, and cell type calls are expected in the next public release.

Download

Brain Region Number of Cells or Nuclei Downloadable RNA-Seq data files
Middle Temporal Gyrus (MTG) 15,928 nuclei

Gene-level (exonic and intronic) read count values for all samples (zip)

.gtf File

Primary Visual Cortex (V1) 8,998 nuclei

Gene-level (exonic and intronic) read count values for all samples (zip)

.gtf File

Anterior Cingulate Cortex (ACC) 7,283 nuclei

Gene-level (exonic and intronic) read count values for all samples (zip)

.gtf File

Browse the Data: Middle Temporal Gyrus (MTG)

The RNA-Seq Data Navigator provides flexible analysis tools for viewing rich transcriptional data, at the level of gene and in a taxonomy derived from analysis of the whole data set. Selected transcripts can be viewed based on similarity of expression pattern, or comparisons of specimen metrics.

Some examples to explore:

  • Use this tool to explore transcriptional markers for cells that are enriched in a cortical layer.
  • Find genes differentially expressed between two user-defined groups of cells or cell types.
  • Explore which cell types express your favorite gene using the Sample Heatmaps view, or find other genes with similar expression patterns.
  • View a 2D projection of the data using t-SNE plots or see the hierarchy of how clusters are related in our navigator overview to understand more about the relationships between different cell types.
  • Analyze specific metrics for properties across different cell types using River Plots or Specimen Metadata views.

Cell Diversity in the Mouse Cortex

RNA-Seq Data Summary

Rnaseq mouse image

Primary Visual Cortex (VISp) and Anterior Lateral Motor Area (ALM):

To investigate the diversity of cell types across the mouse neocortex at the transcriptional level, 15,413 cells were profiled from the primary visual cortex (VISp), and 10,068 cells from the anterior lateral motor cortex (ALM). These two regions represent distant poles of the neocortex and perform distinct functions. Analysis of these transcriptional profiles reveals 133 transcriptomic cell types, divided into 61 GABAergic neuron types and 16 non-neuronal types, most of which are shared across both cortical areas, and 56 glutamatergic neuron types, most of which segregate by cortical region.

Primary Motor Area (MOp) and Anterior Cingulate Area (ACA):

The addition of 9,944 cells from two more areas will provide insight into whether similar glutamatergic cell types at both cortical poles represent distinct types or two ends of a developmental gradient, and will provide increased resolution of GABAergic interneuron diversity. Data from matched brain regions in human will also allow for direct comparison of cell types across mammalian species. Analysis of these data sets is still in progress, and cell type calls are expected in the next public release.

Nuclei from Primary Motor Area (MOp):

For a more unbiased selection of cell types, 6,847 nuclei were profiled from mouse MOp. These data will allow a direct comparison between cells and nuclei from the same cortical area, providing an accurate assessment of the proportion different cell types in MOp. As the only available data set on mouse nuclei, these samples will also provide insight into the source of gene expression differences identified between human nuclei and mouse cells. Analysis of these data sets is still in progress, and cell type calls are expected in the next public release.

Additional RNA-Seq data is available as part of the Brain Cell Data Center (BCDC) portal.

Download

Brain Region Number of Cells or Nuclei Downloadable RNA-Seq data files
Primary Visual Cortex (VISp) 15,413 cells

Gene-level (exonic and intronic) read count values for all samples (zip)

.gtf File

Anterior Lateral Motor Area (ALM) 10,068 cells

Gene-level (exonic and intronic) read count values for all samples (zip)

.gtf File

Anterior Cingulate Area (ACA) 5,028 cells

Gene-level (exonic and intronic) read count values for all samples (zip)

.gtf File

Primary Motor Area (MOp) 4,916 cells

Gene-level (exonic and intronic) read count values for all samples (zip)

.gtf File

Primary Motor Area (MOp) 6,847 nuclei

Gene-level (exonic and intronic) read count values for all samples (zip)

.gtf File

Browse the Data: Primary Visual Cortex (VISp) and Anterior Lateral Motor Area (ALM)

The RNA-Seq Data Navigator provides flexible analysis tools for viewing rich transcriptional data, at the level of gene and in a taxonomy derived from analysis of the whole data set. Selected transcripts can be viewed based on similarity of expression pattern, or comparisons of specimen metrics.

Some examples to explore:

  • Use this tool to explore transcriptional markers for cells that are enriched in a cortical layer.
  • Find genes differentially expressed between two user-defined groups of cells or cell types.
  • Explore which cell types express your favorite gene using the Sample Heatmaps view, or find other genes with similar expression patterns.
  • View a 2D projection of the data using t-SNE plots or see the hierarchy of how clusters are related in our navigator overview to understand more about the relationships between different cell types.
  • Analyze specific metrics for properties across different cell types using River Plots or Specimen Metadata views.

Comparative cellular anatomy in the thalamus

RNA-Seq Data Summary: Lateral Geniculate (LGN)

Rnaseq 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.

Download

Species Brain Region Number of Cells or Nuclei Downloadable RNA-Seq data files
Human Human Lateral Geniculate Nucleus (LGN) 1,576 nuclei

Gene-level (exonic and intronic) read count values for all samples (zip)

.gtf File

Mouse Dorsolateral Geniculate Complex (LGd) 1,996 cells

Gene-level (exonic and intronic) read count values for all samples (zip)

.gtf File

Macaque Lateral Geniculate Nucleus (LGN) 1,092 nuclei

Gene-level (exonic and intronic) read count values for all samples (zip)

.gtf File


RNA-Seq Process Controls

To monitor for consistent, high-quality sampling of single-cell and single-nucleus RNA-Seq data, eight controls (4 negative and 4 positive) were included in each Amplification set (8 controls + 88 samples). A control strip included 2 wells without cells (termed ERCC for External RNA Controls Consortium, negative), 2 wells without cells or ERCC (termed NTC for No Template Control, negative), 2 wells with 10 pg Control RNA (mouse) provided in the Takara SMART-Seq v4 kit (termed Control RNA, positive), and 2 wells with either 10 pg of Mouse Whole Brain Total RNA (termed MouseWhole, Zyagen MR-201, positive) or 10 pg of Human Universal Reference Total RNA (termed UHR, Takara 636538, positive). Controls for mouse and human data is available to download via the links below, and detailed methods are described in the Technical Whitepapers.

Note that separate control sets are available for samples released in June 2018 and October 2018.

Download

Species Cortical Area Downloadable RNA-Seq data files
Human MTG

Controls Data | .gtf File

Human VISp, ACC

Controls Data | .gtf File

Mouse VISp, ALM

Controls Data | .gtf File

Mouse ACA, MOp (cells and nuclei) Controls Data | .gtf File

Previously Published RNA-Seq Data Files

Earlier data generated for the Cell Types project have been updated with newer, more comprehensive collections. Previously released transcriptional data from single cell and nuclear RNA-Seq assays from human and mouse brain regions are available for download via the links below. RNA-Seq data released in October 2017 differed from current data in the following ways. First, alignment and quantification algorithms used for mouse data now use STAR instead of bowtie + RSEM. Second, gene expression is now presented for introns as well as exons, and is not scaled by transcript length, with CPM quantification replacing FPKM and TPM quantification. Third, metadata values for each cell or nucleus have been updated. Most notably, the cell type classification has been updated for mouse LGd, and is provided for other data sets. Finally, the RNA-Seq heatmap for LGd has been deprecated, and replaced with a richer analysis tool, the RNA-Seq Data Navigators for human and mouse. A detailed description of how this archived data was processed is described in the technical whitepapers, in Documentation.

Download

Species Brain Region Number of Cells or Nuclei Downloadable RNA-Seq data files (from October 2017)
Human Middle Temporal Gyrus (MTG) 15,928 nuclei

Gene-level (exonic and intronic) CPM values for all samples (zip)

Mouse Primary Visual Cortex (VISp) 8,329 cells

Gene-level FPKM values for all samples (zip)

URL to file with expected counts, FPKM and TPM values for each sample. (csv)

Mouse Anterior Lateral Motor Area (ALM) 5,992 cells

Gene-level FPKM values for all samples (zip)

URL to file with expected counts, FPKM and TPM values for each sample. (csv)

Mouse Dorsal Lateral Geniculate Complex (LGd) 1,772 cells

RNA-Seq heatmap for LGd

Gene-level FPKM values for all samples (zip)