Harmonized Single Nuclei Atlas of the Brain

03 May 2023

Brain Atlas

Accurately annotating cell types is a prerequisite for obtaining biologically robust results from single-cell transcriptomic data. To gain confidence in the analysis process, we curate compendia of single-cell studies from selected areas and combine multiple studies into a single statistical framework. This harmonization and statistical alignment of studies into atlases and cell-type references requires specialized expertise, which we have developed over the years. The Immunai single-cell curation team recently established a harmonized single nuclei atlas of the human brain.

Summary of the Immunai human brain atlas

The following 14 single-nuclei public studies (using GENEVESTIGATOR® IDS) were curated and harmonised: HS-04386, HS-04340, HS-03878, HS-03909, HS-03685, HS-04357, HS-04337, HS-04329, HS-03964, HS-03910, HS-03271, HS-03907, HS-03906, HS-03905. This resulted in a harmonized neuroscience atlas comprising:

  • Total cells harmonized: 1,336,998 cells
  • Unchanged cell type annotation: 493,311 cells
  • Changed cell type annotation (mainly deeper granularity): 826,248 cells
  • Removed: 17,439 cells
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Highlights of harmonization outcome:

  • Total of 98 identified cell types
  • 44 newly annotated subclasses of inhibitory neurons based on enriched genes
  • 18 newly annotated subclasses of excitatory neurons based on enriched genes
  • Improved neuron identification through assignment of cortical layers into anatomy section
  • Improved and more robust annotations of intermediate stages of oligodendroglial lineage (two types of newly-formed oligodendrocyte and two types of myelin-forming oligodendrocytes)
  • Discrimination of dural and arachnoidal fibroblast and identification of ectoderm barrier epithelium cell in arachnoidea (a.k.a. arachnoid barrier cells)
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Examples of how the Immunai brain atlas can be used

  1. Identification of disease-specific cell types and biomarkers: identify cell types and corresponding gene expression patterns that are specific to a particular disease or condition.
  2. Understanding the molecular basis of developmental processes: understand the molecular mechanisms that drive developmental processes, such as organogenesis and tissue differentiation.
  3. Drug target discovery: identify new drug targets by identifying cell types and gene expression patterns that are involved in disease progression.
  4. Drug candidate validation: validate the efficacy of drug candidates in preclinical models.

To arrange a more detailed presentation of our brain atlas, please contact sales@nebion.com.