Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer’s Disease(Dataset ID: STDS0000084)

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554
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1,767
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Spots: 19,160
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Genes: 47,298
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PMID: 32702314
Summary
Visualization
Data
Analysis results
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Dataset information
Contributors
Accessions
How to cite
Dataset information
Summary:
While complex inflammatory-like alterations are observed around the amyloid plaques of Alzheimer disease (AD), little is known about the molecular changes and cellular interactions that characterize this response. We investigate here in an AD mouse model the transcriptional changes occurring in tissue domains of 100 μm diameter around the amyloid plaques using spatial transcriptomics. We demonstrate early alterations in a gene co-expression network enriched for myelin and oligodendrocyte genes (OLIG), while a multicellular gene co- expression network of Plaque-Induced Genes (PIGs) involving the complement system, oxidative stress, lysosomes and inflammation is prominent in the later phase of the disease. We confirm the majority of the observed alterations at the cellular level using in situ sequencing on mouse and human brain sections. Genome-wide spatial transcriptomic analysis provides an unprecedented approach to untangle the dysregulated cellular network in the vicinity of pathogenic hallmarks of AD and other brain diseases.
Overall design:
In situ 2D-RNAseq via Spatial Transcriptomics on coronal section of AppNL-G-F KI mice and C57Bl/6J mice at 3,6,12 and 18 months of age.
Technology:
Spatial Transcriptomics
Platform:
GPL19057
Species:
Mus musculus(Ensembl 88)
Tissues:
Brain
Development stage:
3 months,6 months,12 months,18 months
Disease:
Alzheimer disease
Submission date: 2020-06-15Update date: 2020-07-22
DOI: To be continue
Contributors
Wei-Ting Chen,Ashley Lu,Katleen Craessaerts,Benjamin Pavie,Carlo S Frigerio,Nikky Corthout,Xiaoyan Q
Contact: bart.destrooper@kuleuven.vib.be
Accessions
GEO Series Accessions: GSE152506
How to cite
  • Cite database of STOmicsDB:
    [1] Xu, Zhicheng et al. "STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization." Nucleic acids research vol. 52,D1 (2024): D1053-D1061. doi: 10.1093/nar/gkad933'
  • Cite visualization dataset:
    [2] Wei-Ting Chen,Ashley Lu,Katleen Craessaerts,Benjamin Pavie,Carlo S Frigerio,Nikky Corthout,Xiaoyan Q. Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer’s Disease[DS/OL]. STOmicsDB, 2020[2020-06-15]. https://db.cngb.org/stomics/datasets/STDS0000084/. doi: xxxxxx
    #Format: {contributors}. {title}[DS/OL]. STOmicsDB, {the year of submission data}[{submission data}]. {dataset link}. doi: {doi ID}
  • Cite original data article:
    Citation: Chen, Wei-Ting et al. “Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer's Disease.” Cell vol. 182,4 (2020): 976-991.e19. doi:10.1016/j.cell.2020.06.038