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Allen Brain Cell Atlas - Data Access - Home
  • Allen Brain Cell Atlas - Data Access

INTRODUCTION

  • Getting started
  • Accessing 10x RNA-seq gene expression data
  • Using cells selected in the ABC Atlas with Gene Expression data.

DATA

  • Mouse whole-brain transcriptomic cell type atlas (Hongkui Zeng)
    • Whole mouse brain 10Xv2 single cell transcriptomes
    • Whole mouse brain 10Xv3 single cell transcriptomes
    • Whole mouse brain 10XMulti single cell transcriptomes
    • Clustering analysis of whole adult mouse brain 10X single cell transcriptomes
    • Whole adult mouse brain taxonomy of cell types
    • MERFISH spatial transcriptomics dataset of a single adult mouse brain
    • Imputed MERFISH spatial transcriptomics of a single adult mouse brain
    • Cluster groups and neighborhood specific UMAP embeddings
    • Allen Mouse Common Coordinate Framework (2020 version)
    • MERFISH CCF mapped coordinates
  • Aging Mouse dataset (Hongkui Zeng)
    • Zeng Aging Mouse 10Xv3 single cell transcriptomes
    • Zeng Aging Mouse clustering and mapping to the WMB taxonomy of cell types
  • A molecularly defined and spatially resolved cell atlas of the whole mouse brain (Xiaowei Zhuang)
    • MERFISH spatial transcriptomics dataset of a single adult mouse brain (Zhuang-ABCA-1)
    • MERFISH spatial transcriptomics dataset of a single adult mouse brain (Zhuang-ABCA-2)
    • MERFISH spatial transcriptomics dataset of a single adult mouse brain (Zhuang-ABCA-3)
    • MERFISH spatial transcriptomics dataset of a single adult mouse brain (Zhuang-ABCA-4)
  • Human whole-brain transcriptomic cell type atlas (Kimberly Siletti)
    • Human brain 10Xv3 single nucleus transcriptomes
    • Clustering analysis of whole human brain 10X single nucleus transcriptomes
    • Human brain taxonomy of cell types
  • ASAP Human Postmortem-Derived Brain Sequencing Collection (ASAP-PMDBS)
    • ASAP Human Postmortem-Derived Brain Sequencing Collection (PMDBS): Data Overview
    • ASAP Human Postmortem-Derived Brain Sequencing Collection (PMDBS): Mapping to the Whole Human Brain (WHB) and Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) Taxonomies
  • Human-Mammalian Brain - Basal Ganglia: Data
    • Human-Mammalian Brain - Basal Ganglia 10X snRANSeq data: Aligned gene expression across species
    • Human-Mammalian Brain - Basal Ganglia 10X snRANSeq data: Individual species gene expression
    • Human-Mammalian Brain - Basal Ganglia 10X snRANSeq data: clustering and annotations

NOTEBOOKS

  • Mouse whole-brain transcriptomic cell type atlas (Hongkui Zeng)
    • 10x RNA-seq clustering analysis and annotation (CCN20230722)
    • 10x scRNA-seq gene expression data
      • 10x RNA-seq gene expression data (part 1)
      • 10x RNA-seq gene expression data (part 2a)
      • 10x RNA-seq gene expression data (part 2b)
    • MERFISH whole brain spatial transcriptomics
      • MERFISH whole brain spatial transcriptomics (part 1)
      • MERFISH whole brain spatial transcriptomics (part 2a)
      • MERFISH whole brain spatial transcriptomics (part 2b)
      • MERFISH whole brain spatial transcriptomics cells with imputed genes
    • Cluster neighborhoods and embeddings
    • Cell type neighborhood gallery
    • Allen Mouse Common Coordinate Framework (2020 version)
    • MERFISH CCF mapped coordinates
  • Aging Mouse Notebooks (Hongkui Zeng)
    • Mouse Aging clustering analysis and annotation
    • Mouse Aging 10X RNA-seq gene expression
  • A molecularly defined and spatially resolved cell atlas of the whole mouse brain (Xiaowei Zhuang)
    • MERFISH whole mouse brain spatial transcriptomics (Xiaowei Zhuang)
  • Whole Human Brain 10x scRNA-seq gene expression data
    • Whole Human Brain 10x RNA-seq clustering analysis and annotation
    • Whole Human Brain (WHB) 10x RNA-seq gene expression data (part 1)
    • Whole Human Brain 10x RNA-seq gene expression data (part 2)
  • ASAP Human Postmortem-Derived Brain Sequencing Collection (ASAP-PMDBS) Notebooks
    • ASAP Human Postmortem-Derived Brain Sequencing Collection (PMDBS): Data Overview
    • ASAP Human Postmortem-Derived Brain Sequencing Collection (PMDBS): Mapping to the Whole Human Brain Taxonomy
    • ASAP Human Postmortem-Derived Brain Sequencing Collection (PMDBS): Mapping to the SEA-AD Taxonomy
    • ASAP Human Postmortem-Derived Brain Sequencing Collection (PMDBS): Gene Expression
  • Human-Mammalian Brain - Basal Ganglia: Notebooks
    • Human-Mammalian Brain - Basal Ganglia 10X snRANSeq analysis: clustering and annotations
    • Human-Mammalian Brain - Basal Ganglia 10X snRANSeq analysis: gene expression

ADDITIONAL RESOURCES

  • Resource Pages
    • Abbreviation lists
    • Cluster annotations
    • Gene lists
    • Parcellation annotations
  • Repository
  • Open issue
  • .md

Cluster annotations

Cluster annotations#

  • WMB-taxonomy (CCN20230504)

  • WMB-taxonomy (CCN20230722)

  • Zeng-Aging-Mouse-WMB-taxonomy (CCN20230722+CS20241021)

  • WHB-taxonomy

  • SEAAD-taxonomy

  • HMBA-BG-taxonomy-CCN20250428

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Abbreviation lists

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Gene lists

By Allen Institute

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