Manu Setty
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Wiley Online Library,
Genome Biology,
BioRxiv,
Cell Press,
The Journal of Immunology
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Articles by Manu Setty
Author Correction: Age-related epithelial defects limit thymic function and regeneration
Correction to: Nature Immunology https://doi.org/10.1038/s41590-024-01915-9, published online 7 August 2024. In the version of this article initially published, in Extended Data Fig. 7a, due to a figure assembly mistake, the images shown as “Mouse 1, 2, 3” on the right-hand panel were mistakenly images representing regions 1–3 from one representative mouse. The images have been replaced with correct data from three different aged reporter mice.
Molecular profiling of adult C. elegans glia across sexes by single-nuclear RNA-seq
Keywords glia snRNA-seq glial transcriptome sexual dimorphism dense core vesicles C.
Single-cell analysis of bidirectional reprogramming between early embryonic states identify mechanisms of differential lineage plasticities in mice
Keywords epiblast primitive endoderm ES cells XEN cells pluripotency extra-embryonic endoderm reprogramming lineage plasticity single-cell analysis blastocyst Get full text access Log in, subscribe or purchase for full access. References 1. Chazaud, C. ∙ Yamanaka, Y. Lineage specification in the mouse preimplantation embryo Development. 2016; 143:1063-1074 2. Schrode, N. ∙ Xenopoulos, P. ∙ Piliszek, A. ...
Age-related epithelial defects limit thymic function and regeneration - Nature Immunology
Abstract The thymus is essential for establishing adaptive immunity yet undergoes age-related involution that leads to compromised immune responsiveness. The thymus is also extremely sensitive to acute insult and although capable of regeneration, this capacity declines with age for unknown reasons.
Signals that control MAIT cell function in healthy and inflamed human tissues
CONFLICT OF INTEREST STATEMENT The authors declare no conflict of interest. REFERENCES 1, , , . Analysis of T cell antigen receptor (TCR) expression by human peripheral blood CD4-8- alpha/beta T cells demonstrates preferential use of several V beta genes and an invariant TCR alpha chain. J Exp Med. 1993; 178(1): 1-16. 2, , , et al. An invariant T cell receptor alpha chain defines a novel TAP-independent major histocompatibility complex class Ib-restricted alpha/beta T cell subpopulation in mammals.
Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities
Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website.
SEACells infers transcriptional and epigenomic cellular states from single-cell genomics data - Nature Biotechnology
Abstract Metacells are cell groupings derived from single-cell sequencing data that represent highly granular, distinct cell states. Here we present single-cell aggregation of cell states (SEACells), an algorithm for identifying metacells that overcome the sparsity of single-cell data while retaining heterogeneity obscured by traditional cell clustering.
Simultaneous CUT&Tag profiling of the accessible and silenced regulome in single cells
New Results Derek H. Janssens, View ORCID ProfileDominik J. Otto, Michael P. Meers, View ORCID ProfileManu Setty, View ORCID ProfileKami Ahmad, View ORCID ProfileSteven Henikoff doi: https://doi.org/10.1101/2021.12.19.473377 Summary Cleavage Under Targets & Tagmentation (CUT&Tag) is an antibody-directed transposase tethering strategy for in situ chromatin profiling in small samples and single cells.
Reversal of lineage plasticity in RB1/TP53-deleted prostate cancer through FGFR and Janus kinase inhibition
Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website.
Fully defined human pluripotent stem cell-derived microglia and tri-culture system model C3 production in Alzheimer’s disease
Abstract Aberrant inflammation in the CNS has been implicated as a major player in the pathogenesis of human neurodegenerative disease. We developed a new approach to derive microglia from human pluripotent stem cells (hPSCs) and built a defined hPSC-derived tri-culture system containing pure populations of hPSC-derived microglia, astrocytes, and neurons to dissect cellular cross-talk along the neuroinflammatory axis in vitro.
Single-Cell Transcriptomics Reveals Early Emergence of Liver Parenchymal and Non-parenchymal Cell Lineages
Highlights • Single-cell analyses provide a comprehensive atlas of liver cell lineage emergence • A distinct, migratory, hepatomesenchymal hybrid cell type is identified • Liver endothelial and mesenchymal progenitors emerge during early hepatogenesis • Candidate cell-cell interactions are identified within the primitive liver sinusoid Summary The cellular complexity and scale of the early liver have constrained analyses examining its emergence during organogenesis.
Author Correction: Characterization of cell fate probabilities in single-cell data with Palantir
Affiliations Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA Manu Setty , Vaidotas Kiseliovas , Jacob Levine , Adam Gayoso , Linas Mazutis & Dana Pe’er Authors Search for Manu Setty in: Search for Vaidotas Kiseliovas in: Search for Jacob Levine in: Search for Adam Gayoso in: Search for Linas Mazutis in: Search for Dana Pe’er in: Corresponding author Correspondence to Dana Pe’er.
The emergent landscape of the mouse gut endoderm at single-cell resolution
Abstract To delineate the ontogeny of the mammalian endoderm, we generated 112,217 single-cell transcriptomes representing all endoderm populations within the mouse embryo until midgestation.
Characterization of cell fate probabilities in single-cell data with Palantir
Abstract Single-cell RNA sequencing studies of differentiating systems have raised fundamental questions regarding the discrete versus continuous nature of both differentiation and cell fate. Here we present Palantir, an algorithm that models trajectories of differentiating cells by treating cell fate as a probabilistic process and leverages entropy to measure cell plasticity along the trajectory.
Multiparameter mass cytometry of T cell development and selection
T cell development and selection in the thymus play key roles in shaping the adaptive immune system and maintaining self-tolerance. Previous studies characterizing thymic development have largely relied on genetic perturbations and subsequent cell sorting that invariably perturb specific developmental compartments.
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