Denisenko, E. et al. Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows. Genome Biol. 21, 130 (2020).
Article CAS PubMed PubMed Central Google Scholar
Slyper, M. et al. A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Nat. Med. 26, 792–802 (2020).
Article CAS PubMed PubMed Central Google Scholar
Heng, T. S. P. et al. The Immunological Genome Project: networks of gene expression in immune cells. Nat. Immunol. 9, 1091–1094 (2008).
Article CAS PubMed Google Scholar
Schulte-Schrepping, J. et al. Severe COVID-19 is marked by a dysregulated myeloid cell compartment. Cell 182, 1419–1440.e23 (2020).
Article CAS PubMed PubMed Central Google Scholar
Grieshaber-Bouyer, R. et al. The neutrotime transcriptional signature defines a single continuum of neutrophils across biological compartments. Nat. Commun. 12, 2856 (2021).
Article ADS CAS PubMed PubMed Central Google Scholar
Ballesteros, I. et al. Co-option of neutrophil fates by tissue environments. Cell 183, 1282–1297.e18 (2020).
Article CAS PubMed Google Scholar
Huang, J. et al. Single-cell transcriptome profiling reveals neutrophil heterogeneity and functional multiplicity in the early stage of severe burn patients. Front. Immunol. 12, 792122 (2021).
Article CAS PubMed Google Scholar
Miyake, K. et al. Single cell transcriptomics clarifies the basophil differentiation trajectory and identifies pre-basophils upstream of mature basophils. Nat. Commun. 14, 2694 (2023).
Article ADS CAS PubMed PubMed Central Google Scholar
Wechsler, M. E. et al. Eosinophils in health and disease: a state-of-the-art review. Mayo Clin. Proc. 96, 2694–2707 (2021).
Article CAS PubMed Google Scholar
Gurtner, A. et al. Active eosinophils regulate host defence and immune responses in colitis. Nature 615, 151–157 (2023).
Article ADS CAS PubMed Google Scholar
Shah, K., Ignacio, A., McCoy, K. D. & Harris, N. L. The emerging roles of eosinophils in mucosal homeostasis. Mucosal Immunol. 13, 574–583 (2020).
Article CAS PubMed Google Scholar
Mao, H. et al. Mechanisms of Siglec-F-induced eosinophil apoptosis: a role for caspases but not for SHP-1, Src kinases, NADPH oxidase or reactive oxygen. PLoS ONE 8, e68143 (2013).
Article ADS CAS PubMed PubMed Central Google Scholar
Knuplez, E. et al. Frontline science: superior mouse eosinophil depletion in vivo targeting transgenic Siglec-8 instead of endogenous Siglec-F: mechanisms and pitfalls. J. Leukoc. Biol. 108, 43–58 (2020).
Article CAS PubMed Google Scholar
Shamri, R. et al. CCL11 elicits secretion of RNases from mouse eosinophils and their cell-free granules. FASEB J. 26, 2084–2093 (2012).
Article CAS PubMed PubMed Central Google Scholar
Rosenberg, H. F. Eosinophil-derived neurotoxin (EDN/RNase 2) and the mouse eosinophil-associated RNases (mEars): expanding roles in promoting host defense. Int. J. Mol. Sci. 16, 15442–15455 (2015).
Article CAS PubMed PubMed Central Google Scholar
Shum, E. Y., Walczak, E. M., Chang, C. & Christina Fan, H. in Single Molecule and Single Cell Sequencing. (ed. Suzuki, Y.) 63–79 (Springer, 2019).
Fan, H. C., Fu, G. K. & Fodor, S. P. A. Combinatorial labeling of single cells for gene expression cytometry. Science 347, 1258367 (2015).
Dent, L. A., Strath, M., Mellor, A. L. & Sanderson, C. J. Eosinophilia in transgenic mice expressing interleukin 5. J. Exp. Med. 172, 1425–1431 (1990).
Article CAS PubMed Google Scholar
Dyer, K. D. et al. Functionally competent eosinophils differentiated ex vivo in high purity from normal mouse bone marrow. J. Immunol. 181 4004–4009 (2008).
Wang, L. et al. Single-cell transcriptomic analysis reveals the immune landscape of lung in steroid-resistant asthma exacerbation. Proc. Natl Acad. Sci. USA 118, e2005590118 (2021).
Article CAS PubMed PubMed Central Google Scholar
Tang, W. et al. Single-cell RNA-sequencing in asthma research. Front. Immunol. 13, 988573 (2022).
Article CAS PubMed PubMed Central Google Scholar
Smillie, C. S. et al. Intra- and inter-cellular rewiring of the human colon during ulcerative colitis. Cell 178, 714–730.e22 (2019).
Article CAS PubMed PubMed Central Google Scholar
Martin, J. C. et al. Single-cell analysis of Crohn’s disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy. Cell 178, 1493–1508.e20 (2019).
Article CAS PubMed PubMed Central Google Scholar
Elmentaite, R. et al. Single-cell sequencing of developing human gut reveals transcriptional links to childhood Crohn’s disease. Dev. Cell 55, 771–783.e5 (2020).
Article CAS PubMed PubMed Central Google Scholar
Kong, L. et al. The landscape of immune dysregulation in Crohn’s disease revealed through single-cell transcriptomic profiling in the ileum and colon. Immunity 56, 444–458.e5 (2023).
Article CAS PubMed PubMed Central Google Scholar
Fawkner-Corbett, D. et al. Spatiotemporal analysis of human intestinal development at single-cell resolution. Cell 184, 810–826.e23 (2021).
Article CAS PubMed PubMed Central Google Scholar
Ho, Y.-T. et al. Longitudinal single-cell transcriptomics reveals a role for Serpina3n-mediated resolution of inflammation in a mouse colitis model. Cell Mol. Gastroenterol. Hepatol. 12, 547–566 (2021).
Article CAS PubMed PubMed Central Google Scholar
Cui, A. et al. Single-cell atlas of the liver myeloid compartment before and after cure of chronic viral hepatitis. J. Hepatol. https://doi.org/10.1016/j.jhep.2023.02.040 (2023).
Salcher, S. et al. High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer. Cancer Cell 40, 1503–1520.e8 (2022).
Article CAS PubMed PubMed Central Google Scholar
Schwarzfischer, M. et al. TiO2 nanoparticles abrogate the protective effect of the Crohn’s disease-associated variation within the PTPN22 gene locus. Gut https://doi.org/10.1136/gutjnl-2021-325911 (2022).
Gao, C., Zhang, M. & Chen, L. The comparison of two single-cell sequencing platforms: BD Rhapsody and 10x Genomics Chromium. Curr. Genomics 21, 602–609 (2020).
Article CAS PubMed PubMed Central Google Scholar
Mayer, A. T. et al. A tissue atlas of ulcerative colitis revealing evidence of sex-dependent differences in disease-driving inflammatory cell types and resistance to TNF inhibitor therapy. Sci. Adv. 9, eadd1166 (2023).
Article PubMed PubMed Central Google Scholar
Lafzi, A. et al. Identifying spatial co-occurrence in healthy and inflamed tissues (ISCHIA). Mol. Syst. Biol. 20, 98–119 (2024).
Article PubMed PubMed Central Google Scholar
Bock, C. et al. High-content CRISPR screening. Nat. Rev. Methods Prim. 2, 1–23 (2022).
Shi, H., Doench, J. G. & Chi, H. CRISPR screens for functional interrogation of immunity. Nat. Rev. Immunol. https://doi.org/10.1038/s41577-022-00802-4 (2022).
Parnas, O. et al. A genome-wide CRISPR screen in primary immune cells to dissect regulatory networks. Cell 162, 675–686 (2015).
Article CAS PubMed PubMed Central Google Scholar
Yeung, A. T. Y. et al. A genome-wide knockout screen in human macrophages identified host factors modulating Salmonella infection. mBio 10, e02169–19 (2019).
Comments (0)