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

Author

Listed:
  • Cankun Wang

    (The Ohio State University)

  • Diana Acosta

    (The Ohio State University)

  • Megan McNutt

    (The Ohio State University)

  • Jiang Bian

    (University of Florida)

  • Anjun Ma

    (The Ohio State University)

  • Hongjun Fu

    (The Ohio State University
    The Ohio State University)

  • Qin Ma

    (The Ohio State University)

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/ .

Suggested Citation

  • Cankun Wang & Diana Acosta & Megan McNutt & Jiang Bian & Anjun Ma & Hongjun Fu & Qin Ma, 2024. "A single-cell and spatial RNA-seq database for Alzheimer’s disease (ssREAD)," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49133-z
    DOI: 10.1038/s41467-024-49133-z
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    References listed on IDEAS

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    1. David Gate & Naresha Saligrama & Olivia Leventhal & Andrew C. Yang & Michael S. Unger & Jinte Middeldorp & Kelly Chen & Benoit Lehallier & Divya Channappa & Mark B. Los Santos & Alisha McBride & John , 2020. "Clonally expanded CD8 T cells patrol the cerebrospinal fluid in Alzheimer’s disease," Nature, Nature, vol. 577(7790), pages 399-404, January.
    2. Anjun Ma & Xiaoying Wang & Jingxian Li & Cankun Wang & Tong Xiao & Yuntao Liu & Hao Cheng & Juexin Wang & Yang Li & Yuzhou Chang & Jinpu Li & Duolin Wang & Yuexu Jiang & Li Su & Gang Xin & Shaopeng Gu, 2023. "Single-cell biological network inference using a heterogeneous graph transformer," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    3. Hansruedi Mathys & Jose Davila-Velderrain & Zhuyu Peng & Fan Gao & Shahin Mohammadi & Jennie Z. Young & Madhvi Menon & Liang He & Fatema Abdurrob & Xueqiao Jiang & Anthony J. Martorell & Richard M. Ra, 2019. "Author Correction: Single-cell transcriptomic analysis of Alzheimer’s disease," Nature, Nature, vol. 571(7763), pages 1-1, July.
    4. Andrew C. Yang & Ryan T. Vest & Fabian Kern & Davis P. Lee & Maayan Agam & Christina A. Maat & Patricia M. Losada & Michelle B. Chen & Nicholas Schaum & Nathalie Khoury & Angus Toland & Kruti Calcutta, 2022. "A human brain vascular atlas reveals diverse mediators of Alzheimer’s risk," Nature, Nature, vol. 603(7903), pages 885-892, March.
    5. Hansruedi Mathys & Jose Davila-Velderrain & Zhuyu Peng & Fan Gao & Shahin Mohammadi & Jennie Z. Young & Madhvi Menon & Liang He & Fatema Abdurrob & Xueqiao Jiang & Anthony J. Martorell & Richard M. Ra, 2019. "Single-cell transcriptomic analysis of Alzheimer’s disease," Nature, Nature, vol. 570(7761), pages 332-337, June.
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