Brain PFC Atlas

A large-scale integrated atlas of single-cell RNA-Seq data from aging and eight common central nervous system diseases

Our work provides a multi-disease cell atlas based on large-scale snRNA-seq data and analyses the disease and sex heterogeneity of neurotransmitter system (NTS), which provides new insights into the mechanisms of multiple central nervous system (CNS) diseases and provides a reference for disease precision therapy against NTS.

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Brain aging and development atlas

Human PFC ExN subtype atlas

The dataset comprises 389,031 excitatory neuron (ExN) cells categorized into 12 distinct subtypes.

Human PFC InN subtype atlas

There are 180,310 inhibitory neuron (InN) cells divided into 13 subtypes.

Human PFC Non-neuron atlas

There are 315,636 mature oligodendrocytes (MOL), 45,378 oligodendrocyte precursor cells (OPCs), 89,936 astrocytes, and 32,743 microglia. Furthermore, the analysis identifies a total of 10,754 blood vessel-related cells.

Human HIP atlas

A single-nucleus transcriptomic atlas of human hippocampus aging containing 173,453 nuclei.

Human ACC atlas

A single-nucleus transcriptomic atlas of human anterior cingulate cortex aging containing 62,704 nuclei.

Human AMY atlas

A single-nucleus transcriptomic atlas of human amygdaloid nucleus aging containing 57,344 nuclei.

Human EC atlas

A single-nucleus transcriptomic atlas of human entorhinal cortex aging containing 48,058 nuclei.

Human MB atlas

A single-nucleus transcriptomic atlas of human midbrain aging containing 33,713 nuclei.

Human SC atlas

A single-nucleus transcriptomic atlas of human spinal cord aging containing 57,274 nuclei.

Human multiregion aging atlas

A single-nucleus transcriptomic atlas of seven different CNS regions in the human brain, covering 1 million cells from 235 post-mortem human brain samples across 200 individuals aged 19-101 years without neuropsychiatric disease.

TS HIP atlas

A single-nucleus transcriptomic atlas of tree shrew hippocampus spanning postnatal life, detailing the dynamics and diversity of the neurogenic lineage, oligodendrocytes, microglia, and endothelial cells (Please cite: Xiong, Liu-Lin et al. Cross-Species Insights from Single-Nucleus Sequencing Highlight Aging-Related Hippocampal Features in Tree Shrew. Molecular biology and evolution vol. 42,2 (2025): msaf020. doi:10.1093/molbev/msaf020).

Human DS PFC-STP atlas

Mid-gestational cell-type-specific transcriptomic signatures in the prefrontal and superior temporal cortex in Down syndrome (Please cite: Niu, Rui-Ze et al. Mid-gestational cell-type-specific transcriptomic signatures in the prefrontal and superior temporal cortex in Down syndrome. Nature communications vol. 16,1 11249. 11 Dec. 2025, doi:10.1038/s41467-025-66109-9).

Other atlas

Single‐cell transcriptome unveils unique transcriptomic signatures of human organ‐specific endothelial cells.

The atlas of > 210,000 ECs derived from 38 regions across 24 human tissues(Please cite: Niu, Rui-Ze et al. Single-cell transcriptome unveils unique transcriptomic signatures of human organ-specific endothelial cells. Basic research in cardiology vol. 119,6 (2024): 973-999. doi:10.1007/s00395-024-01087-5).

Aging Plasma Proteome(Please cite: Lehallier et al. Undulating changes in human plasma proteome profiles across the lifespan. Nature medicine, 2019, 25, 1843-1850).

Get in touch

The processed expression matrices used and/or analysed during the current study and corresponding code for this research available from the author on reasonable request.

niuruize1@kmmu.edu.cn
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Kunming, Yunnan