Cited by 157

Integrative in situ mapping of single-cell transcriptional states and tissue histopathology in a mouse model of Alzheimer’s disease

Zeng, Hu, Huang, Jiahao, Zhou, Haowen, Meilandt, William J., Dejanovic, Borislav, Zhou, Yiming, Bohlen, Christopher J., Lee, Seung-Hye +7 more·2023·Nature Neuroscience

Published version of a preprint

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41593-022-01251-x

Cites

37 of 37 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • AD DEGs were consistent with published results both for region-specific DEGs and for DEGs computed jointly over all regions for multiple AD variables, and were further corroborated by comparisons with various independent studies.

    “AD DEGs were consistent with published results both for region-specific DEGs and for DEGs computed jointly over all regions for multiple AD variables, and were further corroborated by comparisons with various independent studies11,12,15,19,47–53”

    From Single-cell multiregion dissection of Alzheimer’s disease (2024) · cites this paper as [52]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 30

  1. [1]Masters CL Alzheimer’s disease. Nat. Rev. Dis. Prim. 1, 15056 (2015). 27188934
  2. [3]Busche MA & Hyman BT Synergy between amyloid-β and tau in Alzheimer’s disease. Nat. Neurosci. 23, 1183– 1193 (2020). 32778792 PMC11831977
  3. [5]Beach TG, Walker R. & McGeer EG Patterns of gliosis in Alzheimer’s disease and aging cerebrum. Glia 2, 420– 436 (1989). 2531723
  4. [6]Butt AM, De La Rocha IC & Rivera A. Oligodendroglial cells in Alzheimer’s disease. Adv. Exp. Med. Biol. 1175, 325– 333 (2019). 31583593
  5. [7]Henstridge CM, Hyman BT & Spires-Jones TL Beyond the neuron–cellular interactions early in Alzheimer disease pathogenesis. Nat. Rev. Neurosci. 20, 94– 108 (2019). 30643230 PMC6545070
  6. [9]Habib N. Disease-associated astrocytes in Alzheimer’s disease and aging. Nat. Neurosci. 23, 701– 706 (2020). 32341542 PMC9262034
  7. [11]Lau S-F, Cao H, Fu AKY & Ip NY Single-nucleus transcriptome analysis reveals dysregulation of angiogenic endothelial cells and neuroprotective glia in Alzheimer’s disease. Proc. Natl Acad. Sci. USA 117, 25800– 25809 (2020). 32989152 PMC7568283
  8. [12]Mathys H. Single-cell transcriptomic analysis of Alzheimer’s disease. Nature 570, 332– 337 (2019). 31042697 PMC6865822
  9. [18]Lewcock JW Emerging microglia biology defines novel therapeutic approaches for Alzheimer’s disease. Neuron 108, 801– 821 (2020). 33096024
  10. [22]Liddelow SA & Barres BA Reactive astrocytes: production, function, and therapeutic potential. Immunity 46, 957– 967 (2017). 28636962
  11. [24]Sofroniew MV Astrocyte reactivity: subtypes, states, and functions in CNS innate immunity. Trends Immunol. 41, 758– 770 (2020). 32819810 PMC7484257
  12. [25]Yun SP Block of A1 astrocyte conversion by microglia is neuroprotective in models of Parkinson’s disease. Nat. Med. 24, 931– 938 (2018). 29892066 PMC6039259
  13. [26]van den Brink SC Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations. Nat. Methods 14, 935– 936 (2017). 28960196
  14. [30]Chen KH, Boettiger AN, Moffitt JR, Wang S. & Zhuang X. RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348, aaa6090 (2015). 25858977 PMC4662681
  15. [31]Rodriques SG Slide-seq: a scalable technology for measuring genome-wide expression at high spatial resolution. Science 363, 1463– 1467 (2019). 30923225 PMC6927209
  16. [33]Stuart T. & Satija R. Integrative single-cell analysis. Nat. Rev. Genet. 20, 257– 272 (2019). 30696980
  17. [35]Qian X. Probabilistic cell typing enables fine mapping of closely related cell types in situ. Nat. Methods 17, 101– 106 (2020). 31740815 PMC6949128
  18. [36]Alon S. Expansion sequencing: spatially precise in situ transcriptomics in intact biological systems. Science 371, eaax2656 (2021). 33509999 PMC7900882
  19. [37]Liu S. Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses. Nucleic Acids Res. 49, e58 (2021). 33693773 PMC8191787
  20. [42]Koopmans F. SynGO: an evidence-based, expert-curated knowledge base for the synapse. Neuron 103, 217– 234 (2019). 31171447 PMC6764089
  21. [46]Zamanian JL Genomic analysis of reactive astrogliosis. J. Neurosci. 32, 6391– 6410 (2012). 22553043 PMC3480225
  22. [48]Cao J. The single-cell transcriptional landscape of mammalian organogenesis. Nature 566, 496– 502 (2019). 30787437 PMC6434952
  23. [49]Feregrino C. & Tschopp P. Assessing evolutionary and developmental transcriptome dynamics in homologous cell types. Dev. Dyn. 251, 1472– 1489 (2022). 34114716 PMC9545966
  24. [51]Raudvere U. g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). Nucleic Acids Res. 47, W191– W198 (2019). 31066453 PMC6602461
  25. [53]Pease-Raissi SE & Chan JR Building a (w)rapport between neurons and oligodendroglia: reciprocal interactions underlying adaptive myelination. Neuron 109, 1258– 1273 (2021). 33621477 PMC8068592
  26. [54]Dejanovic B. Complement C1q-dependent excitatory and inhibitory synapse elimination by astrocytes and microglia in Alzheimer’s disease mouse models. Nat. Aging 2, 837– 850 (2022). 37118504 PMC10154216
  27. [56]Schmidt U, Weigert M, Broaddus C. & Myers G. Medical Image Computing and Computer Assisted Intervention—MICCAI 2018 265– 273 (Springer International Publishing, 2018).
  28. [59]Johnson WE, Li C. & Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8, 118– 127 (2007). 16632515
  29. [61]Pau G, Fuchs F, Sklyar O, Boutros M. & Huber W. EBImage–an R package for image processing with applications to cellular phenotypes. Bioinformatics 26, 979– 981 (2010). 20338898 PMC2844988
  30. [62]Gu Z, Eils R. & Schlesner M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32, 2847– 2849 (2016). 27207943

Cited by

Sorted by citations

Authors
Zeng, H., Huang, J., Zhou, H., Meilandt, W. J., Dejanovic, B., Zhou, Y., Bohlen, C. J., Lee, S.-H., Ren, J., Liu, A., Tang, Z., Sheng, H., Liu, J., Sheng, M., & Wang, X.
Venue
Nature Neuroscience
Published
2023-02-02
Volume
26
Issue
3
Pages
430-446
ISSN
  • 1097-6256
  • 1546-1726
Cited by
157
References
37
Language
en
Funders
U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (1DP2GM146245-01)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review