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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)
Consensus Whole Mouse Brain dataset
Consensus Whole Mouse Brain single cell/nucleus transcriptomes
Consensus Whole Mouse Brain integrated taxonomy
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 snRNASeq data: clustering and annotations
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: spatial transcriptomics cells for each species
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
Consensus Mouse notebooks
Consensus Whole Mouse Brain #1: Clustering and Annotations
Consensus Whole Mouse Brain #2: 10X gene expression
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 snRNASeq analysis: clustering and annotations
Human-Mammalian Brain - Basal Ganglia 10X snRANSeq analysis: gene expression
Human-Mammalian Brain - Basal Ganglia spatial transcriptomic slab coordinates and annotation
Human-Mammalian Brain - Basal Ganglia spatial transcriptomics gene expression
ADDITIONAL RESOURCES
Resource Pages
Abbreviation lists
Cluster annotations
Gene lists
Parcellation annotations
Supplemental Metadata Descriptions
HMBA Basal Ganglia: Neuroglancer Views
Repository
Open issue
.md
.pdf
Abbreviation lists
Abbreviation lists
#
HMBA-BG-taxonomy-CCN20250428
