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Allen Brain Cell Atlas - Data Access
INTRODUCTION
Getting started
Accessing 10x RNA-seq 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
Cluster groups and neighborhood specific UMAP embeddings
Allen Mouse Common Coordinate Framework (2020 version)
MERFISH CCF mapped coordinates
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
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)
Cluster neighborhoods and embeddings
Cell type neighborhood gallery
Allen Mouse Common Coordinate Framework (2020 version)
MERFISH CCF mapped coordinates
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)
ADDITIONAL RESOURCES
Resource Pages
Gene lists
Cluster annotations
Parcellation annotations
Repository
Open issue
.md
.pdf
Parcellation annotations
Parcellation annotations
#
Allen-CCF-2020
