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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)
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)
Consensus Whole Mouse Brain dataset (Macosko, Zeng)
- Consensus Whole Mouse Brain single cell/nucleus transcriptomes
- Consensus Whole Mouse Brain integrated taxonomy
Developing Mouse - Visual Cortex
- Developing Mouse - Visual Cortex single cell transcriptomes
- Developing Mouse - Visual Cortex taxonomy
Human whole-brain transcriptomic cell type atlas (Kimberly Siletti)
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
SEA-AD datasets

NOTEBOOKS

Mouse whole-brain transcriptomic cell type atlas (Hongkui Zeng)
Consensus Mouse notebooks
- Consensus Whole Mouse Brain #1: Clustering and Annotations
- Consensus Whole Mouse Brain #2: 10X gene expression
Developing Mouse - Visual Cortex notebooks
- Developing Mouse - Visual Cortex 10X scRNASeq analysis: clustering and annotations
- Developing Mouse - Visual Cortex: 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
ASAP Human Postmortem-Derived Brain Sequencing Collection (ASAP-PMDBS) Notebooks
Human-Mammalian Brain - Basal Ganglia: Notebooks
SEA-AD - notebooks

ADDITIONAL RESOURCES

Resource Pages

Repository
Open issue

.md

Cluster annotations

Cluster annotations#

WMB-taxonomy (CCN20230504)
WMB-taxonomy (CCN20230722)
Consensus WMB integrated taxonomy (CCN20251031)
Developing Mouse - Visual Cortex (CCN20230722+CCN20260131)
Zeng-Aging-Mouse-WMB-taxonomy (CCN20230722+CS20241021)
WHB-taxonomy
SEAAD-taxonomy
SEA-AD-Multiregion-taxonomy (CCN20260630)
SEA-AD-CaH-taxonomy (CCN20260701)
HMBA-BG-taxonomy-CCN20250428

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Abbreviation lists

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Gene lists

By Allen Institute

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