A Roadmap for the Human Gut Cell Atlas

Rooks, M. G. & Garrett, W. S. Gut microbiota, metabolites and host immunity. Nat. Rev. Immunol. 16, 341–352 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kolodziejczyk, A. A., Zheng, D. & Elinav, E. Diet-microbiota interactions and personalized nutrition. Nat. Rev. Microbiol. 17, 742–753 (2019).

Article  CAS  PubMed  Google Scholar 

Knight, R. et al. Best practices for analysing microbiomes. Nat. Rev. Microbiol. 16, 410–422 (2018).

Article  CAS  PubMed  Google Scholar 

Makki, K., Deehan, E. C., Walter, J. & Backhed, F. The impact of dietary fiber on gut microbiota in host health and disease. Cell Host Microbe 23, 705–715 (2018).

Article  CAS  PubMed  Google Scholar 

Khalili, H. et al. The role of diet in the aetiopathogenesis of inflammatory bowel disease. Nat. Rev. Gastroenterol. Hepatol. 15, 525–535 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Safi-Stibler, S. & Gabory, A. Epigenetics and the developmental origins of health and disease: parental environment signalling to the epigenome, critical time windows and sculpting the adult phenotype. Semin. Cell Dev. Biol. 97, 172–180 (2020).

Article  CAS  PubMed  Google Scholar 

Perrone, F. & Zilbauer, M. Biobanking of human gut organoids for translational research. Exp. Mol. Med. 53, 1451–1458 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Enns, R. A. et al. Clinical practice guidelines for the use of video capsule endoscopy. Gastroenterology 152, 497–514 (2017).

Article  PubMed  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 

Pilonis, N. D., Januszewicz, W. & di Pietro, M. Confocal laser endomicroscopy in gastro-intestinal endoscopy: technical aspects and clinical applications. Transl. Gastroenterol. Hepatol. 7, 7 (2022).

Article  PubMed  PubMed Central  Google Scholar 

Chen, W. C. & Wallace, M. B. Endoscopic management of mucosal lesions in the gastrointestinal tract. Expert. Rev. Gastroenterol. Hepatol. 10, 481–495 (2016).

Article  CAS  PubMed  Google Scholar 

Pensold, D. & Zimmer-Bensch, G. Methods for single-cell isolation and preparation. Adv. Exp. Med. Biol. 1255, 7–27 (2020).

Article  CAS  PubMed  Google Scholar 

Regev, A. et al. The human cell atlas. eLife 6, e27041 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Rozenblatt-Rosen, O., Stubbington, M. J. T., Regev, A. & Teichmann, S. A. The human cell atlas: from vision to reality. Nature 550, 451–453 (2017).

Article  CAS  PubMed  Google Scholar 

Skinnider, M. A., Squair, J. W. & Courtine, G. Enabling reproducible re-analysis of single-cell data. Genome Biol. 22, 215 (2021).

Article  PubMed  PubMed Central  Google Scholar 

Füllgrabe, A. et al. Guidelines for reporting single-cell RNA-seq experiments. Nat. Biotechnol. 38, 1384–1386 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Burger, A. et al. Towards a clinically-based common coordinate framework for the human gut cell atlas: the gut models. BMC Med. Inform. Decis. Mak. 23, 36 (2023).

Article  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 

Lee, S. S. J. The ethics of consent in a shifting genomic ecosystem. Annu. Rev. Biomed. Data Sci. 4, 145–164 (2021).

Article  PubMed  PubMed Central  Google Scholar 

EUR-Lex, The European Parliament and the Council of the European Union. General Data Protection Regulation (EU) 2016/679 (GDPR) https://eur-lex.europa.eu/eli/reg/2016/679/oj (2016).

Bledsoe, M. J. & Grizzle, W. E. Use of human specimens in research: the evolving United States regulatory, policy, and scientific landscape. Diagn. Histopathol. 19, 322–330 (2013).

Article  Google Scholar 

Shore, N. et al. Understanding community-based processes for research ethics review: a national study. Am. J. Public Health 101, S359–S364 (2011).

Article  PubMed  PubMed Central  Google Scholar 

Editorial. Tackling helicopter research. Nat. Geosci. 15, 597 (2022).

Article  Google Scholar 

Mikesell, L., Bromley, E. & Khodyakov, D. Ethical community-engaged research: a literature review. Am. J. Public Health 103, e7–e14 (2013).

Article  PubMed  PubMed Central  Google Scholar 

Elmentaite, R. et al. Cells of the human intestinal tract mapped across space and time. Nature 597, 250–255 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Camp, J. G., Platt, R. & Treutlein, B. Mapping human cell phenotypes to genotypes with single-cell genomics. Science 365, 1401–1405 (2019).

Article  CAS  PubMed  Google Scholar 

Macaulay, I. C. et al. G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nat. Methods 12, 519–522 (2015).

Article  CAS  PubMed  Google Scholar 

Lareau, C. A. et al. Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility. Nat. Biotechnol. 37, 916–924 (2019).

Article  CAS  PubMed  Google Scholar 

Smallwood, S. A. et al. Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity. Nat. Methods 11, 817–820 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hao, Y. H. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–357 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pott, S. Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells. eLife https://doi.org/10.7554/eLife.23203 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Clark, S. J. et al. scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells. Nat. Commun. 9, 781 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Drokhlyansky, E. et al. The human and mouse enteric nervous system at single-cell resolution. Cell 182, 1606–1622.e23 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Setliff, I. et al. High-throughput mapping of B cell receptor sequences to antigen specificity. Cell 179, 1636–1646.e15 (2019).

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 

Wu, S. Z. et al. A single-cell and spatially resolved atlas of human breast cancers. Nat. Genet. 53, 1334–1347 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Xia, C., Babcock, H. P., Moffitt, J. R. & Zhuang, X. Multiplexed detection of RNA using MERFISH and branched DNA amplification. Sci. Rep. 9, 7721 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Black, S. et al. CODEX multiplexed tissue imaging with DNA-conjugated antibodies. Nat. Protoc. 16, 3802–3835 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Haniffa, M. et al. A roadmap for the human developmental cell atlas. Nature 597, 196–205 (2021).

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