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Cited by 73Single-cell and spatial transcriptomicsAlzheimer's disease research and treatmentsDementia and Cognitive Impairment Research

A single-cell and spatial RNA-seq database for Alzheimer’s disease (ssREAD)

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Wang, Cankun, Acosta, Diana, McNutt, Megan, Bian, Jiang, Ma, Anjun, Fu, Hongjun, Ma, Qin·2024·Nature Communications
DOI 10.1038/s41467-024-49133-zPMC PMC11156951
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Abstract

Alzheimer’s Disease (AD) pathology has been increasingly explored through single-cell and single-nucleus RNA-sequencing (scRNA-seq & snRNA-seq) and spatial transcriptomics (ST). However, the surge in data demands a comprehensive, user-friendly repository. Addressing this, we introduce a single-cell and spatial RNA-seq database for Alzheimer’s disease (ssREAD). It offers a broader spectrum of AD-related datasets, an optimized analytical pipeline, and improved usability. The database encompasses 1,053 samples (277 integrated datasets) from 67 AD-related scRNA-seq & snRNA-seq studies, totaling 7,332,202 cells. Additionally, it archives 381 ST datasets from 18 human and mouse brain studies. Each dataset is annotated with details such as species, gender, brain region, disease/control status, age, and AD Braak stages. ssREAD also provides an analysis suite for cell clustering, identification of differentially expressed and spatially variable genes, cell-type-specific marker genes and regulons, and spot deconvolution for integrative analysis. ssREAD is freely available at https://bmblx.bmi.osumc.edu/ssread/.

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    “We analyzed human astrocyte transcriptomes taken from four published single-nuclei transcriptomic datasets to determine whether genotype-specific lipid droplet proteome changes are reflected in post-mortem brain samples51–54.”

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Cited by

Sorted by citations

Authors
Wang, C., Acosta, D., McNutt, M., Bian, J., Ma, A., Fu, H., & Ma, Q.
Affiliations
  • The Ohio State University (US)
  • University of Florida Health (US)
Corresponding author
  • Fu, Hongjun
  • Ma, Qin
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2024-06-06
Volume
15
Issue
1
Pages
4710-4710
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-024-49133-z
PMC
PMC11156951
OpenAlex
W4399388096
Cited by
73
References
16
Citations by year
2026: 31 · 2025: 31 · 2024: 10
FWCI
9.30
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion, cc-by)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • U.S. Department of Health and Human Services (R21HG012482)
  • National Institutes of Health (1r01gm152585-01)
  • National Institute on Aging (R01AG075092)
  • National Human Genome Research Institute (R21HG012482)
  • National Institute of General Medical Sciences (R01-GM152585)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
  • Health Sciences › Medicine › Psychiatry and Mental health › Dementia and Cognitive Impairment Research
Keywords
Alzheimer's disease, single-cell RNA sequencing, single-nucleus RNA sequencing, spatial transcriptomics, brain transcriptomics, cell clustering, differentially expressed genes, spatially variable genes, cell type markers, regulon, Braak stages, mouse brain

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