Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Jan 8;49(D1):D1029-D1037.
doi: 10.1093/nar/gkaa762.

STAB: a spatio-temporal cell atlas of the human brain

Liting Song  1 , Shaojun Pan  1 , Zichao Zhang  1 , Longhao Jia  1 , Wei-Hua Chen  2 , Xing-Ming Zhao  1   3   4
Affiliations

STAB: a spatio-temporal cell atlas of the human brain

Liting Song et al. Nucleic Acids Res. .

Abstract

The human brain is the most complex organ consisting of billions of neuronal and non-neuronal cells that are organized into distinct anatomical and functional regions. Elucidating the cellular and transcriptome architecture underlying the brain is crucial for understanding brain functions and brain disorders. Thanks to the single-cell RNA sequencing technologies, it is becoming possible to dissect the cellular compositions of the brain. Although great effort has been made to explore the transcriptome architecture of the human brain, a comprehensive database with dynamic cellular compositions and molecular characteristics of the human brain during the lifespan is still not available. Here, we present STAB (a Spatio-Temporal cell Atlas of the human Brain), a database consists of single-cell transcriptomes across multiple brain regions and developmental periods. Right now, STAB contains single-cell gene expression profiling of 42 cell subtypes across 20 brain regions and 11 developmental periods. With STAB, the landscape of cell types and their regional heterogeneity and temporal dynamics across the human brain can be clearly seen, which can help to understand both the development of the normal human brain and the etiology of neuropsychiatric disorders. STAB is available at http://stab.comp-sysbio.org.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Schematic overview of functionalities provided by STAB.
Figure 2.
Figure 2.
Landscape of cell subtypes with their marker genes. (A) The identified cell subtypes. (B) The expression of classical marker genes for major cell types. (C) Expression of layer-specific marker genes in excitatory (left) and inhibitory (right) neuron subtypes. The size and color of the dot denote the percentage of cells expressing corresponding layer-specific marker genes and the expression value of the gene averaged over a certain cell subtype, respectively. (D) Heatmap of expression levels for marker genes associated with sub-pallial origins (MGE, CGE) and neurotransmitter for inhibitory neuron cell subtypes.
Figure 3.
Figure 3.
Spatiotemporal heterogeneity of cell (sub)types. (A) The cell type (left) and subtype (right) composition of each brain region at period 6 (late mid-fetal). (B) Expression of CD68 in different cell types across brain regions at P6. (C) The dynamic cellular compositions with the development of PFC. (D–E) The expression trajectories of SYP and VIP genes within different cell subtypes along the development of DFC. The shaded bands denote 95% confidence intervals.
Figure 4.
Figure 4.
Cell subtypes associated with brain disorders. (A) The distribution of cell types associated with neurodegenerative and neuropsychiatric diseases. (B) The heatmap of expression of high confident ASD genes across various cell (sub)types. (C andD) The expression dynamics of DSCAM within different cell subtypes in PFC and DFC along with development.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

  • scMD facilitates cell type deconvolution using single-cell DNA methylation references.
    Cai M, Zhou J, McKennan C, Wang J. Cai M, et al. Commun Biol. 2024 Jan 2;7(1):1. doi: 10.1038/s42003-023-05690-5. Commun Biol. 2024. PMID: 38168620 Free PMC article.
  • STalign: Alignment of spatial transcriptomics data using diffeomorphic metric mapping.
    Clifton K, Anant M, Aihara G, Atta L, Aimiuwu OK, Kebschull JM, Miller MI, Tward D, Fan J. Clifton K, et al. Nat Commun. 2023 Dec 8;14(1):8123. doi: 10.1038/s41467-023-43915-7. Nat Commun. 2023. PMID: 38065970 Free PMC article.
  • Mutation of key signaling regulators of cerebrovascular development in vein of Galen malformations.
    Zhao S, Mekbib KY, van der Ent MA, Allington G, Prendergast A, Chau JE, Smith H, Shohfi J, Ocken J, Duran D, Furey CG, Hao LT, Duy PQ, Reeves BC, Zhang J, Nelson-Williams C, Chen D, Li B, Nottoli T, Bai S, Rolle M, Zeng X, Dong W, Fu PY, Wang YC, Mane S, Piwowarczyk P, Fehnel KP, See AP, Iskandar BJ, Aagaard-Kienitz B, Moyer QJ, Dennis E, Kiziltug E, Kundishora AJ, DeSpenza T Jr, Greenberg ABW, Kidanemariam SM, Hale AT, Johnston JM, Jackson EM, Storm PB, Lang SS, Butler WE, Carter BS, Chapman P, Stapleton CJ, Patel AB, Rodesch G, Smajda S, Berenstein A, Barak T, Erson-Omay EZ, Zhao H, Moreno-De-Luca A, Proctor MR, Smith ER, Orbach DB, Alper SL, Nicoli S, Boggon TJ, Lifton RP, Gunel M, King PD, Jin SC, Kahle KT. Zhao S, et al. Nat Commun. 2023 Nov 17;14(1):7452. doi: 10.1038/s41467-023-43062-z. Nat Commun. 2023. PMID: 37978175 Free PMC article.
  • NCBI GEO: archive for gene expression and epigenomics data sets: 23-year update.
    Clough E, Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Lee H, Zhang N, Serova N, Wagner L, Zalunin V, Kochergin A, Soboleva A. Clough E, et al. Nucleic Acids Res. 2024 Jan 5;52(D1):D138-D144. doi: 10.1093/nar/gkad965. Nucleic Acids Res. 2024. PMID: 37933855 Free PMC article.
  • SCAN: Spatiotemporal Cloud Atlas for Neural cells.
    Deng Y, Lu Y, Li M, Shen J, Qin S, Zhang W, Zhang Q, Shen Z, Li C, Jia T, Chen P, Peng L, Chen Y, Zhang W, Liu H, Zhang L, Rong L, Wang X, Chen D. Deng Y, et al. Nucleic Acids Res. 2024 Jan 5;52(D1):D998-D1009. doi: 10.1093/nar/gkad895. Nucleic Acids Res. 2024. PMID: 37930842 Free PMC article.
See all "Cited by" articles

References

    1. Saunders A., Macosko E.Z., Wysoker A., Goldman M., Krienen F.M., de Rivera H., Bien E., Baum M., Bortolin L., Wang S.Y. et al. .. Molecular diversity and specializations among the cells of the adult mouse brain. Cell. 2018; 174:1015–1031. - PMC - PubMed
    1. Fan X., Dong J., Zhong S., Wei Y., Wu Q., Yan L., Yong J., Sun L., Wang X., Zhao Y. et al. .. Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis. Cell Res. 2018; 28:730–745. - PMC - PubMed
    1. Lake B.B., Ai R., Kaeser G.E., Salathia N.S., Yung Y.C., Liu R., Wildberg A., Gao D., Fung H.L., Chen S. et al. .. Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain. Science. 2016; 352:1586–1590. - PMC - PubMed
    1. Zhong S., Zhang S., Fan X., Wu Q., Yan L., Dong J., Zhang H., Li L., Sun L., Pan N. et al. .. A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex. Nature. 2018; 555:524–528. - PubMed
    1. Hill R.S., Walsh C.A.. Molecular insights into human brain evolution. Nature. 2005; 437:64–67. - PubMed

Publication types

MeSH terms