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For: Chen J, Cheung F, Shi R, Zhou H, Lu W; CHI Consortium. PBMC fixation and processing for Chromium single-cell RNA sequencing. J Transl Med 2018;16:198. [PMID: 30016977 DOI: 10.1186/s12967-018-1578-4] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 07/13/2018] [Indexed: 11/10/2022]  Open
Number Cited by Other Article(s)
1
Al Kadi M, Yamashita M, Shimojima M, Yoshikawa T, Ebihara H, Okuzaki D, Kurosu T. Cytokine storm and vascular leakage in severe dengue: insights from single-cell RNA profiling. Life Sci Alliance 2025;8:e202403008. [PMID: 40127923 PMCID: PMC11933670 DOI: 10.26508/lsa.202403008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 03/17/2025] [Accepted: 03/17/2025] [Indexed: 03/26/2025]  Open
2
Bjerre FA, Nielsen JV, Burton M, Dhumale P, Jørgensen MG, Hansen ST, Lund L, Thomassen M, Sørensen JA, Andersen DC, Jensen CH. Single-cell transcriptomics of clinical grade adipose-derived regenerative cells reveals consistency between donors independent of gender and BMI. Stem Cell Res Ther 2025;16:109. [PMID: 40038777 PMCID: PMC11881426 DOI: 10.1186/s13287-025-04234-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2025] [Accepted: 02/14/2025] [Indexed: 03/06/2025]  Open
3
Juzenas S, Goda K, Kiseliovas V, Zvirblyte J, Quintinal-Villalonga A, Siurkus J, Nainys J, Mazutis L. inDrops-2: a flexible, versatile and cost-efficient droplet microfluidic approach for high-throughput scRNA-seq of fresh and preserved clinical samples. Nucleic Acids Res 2025;53:gkae1312. [PMID: 39797728 PMCID: PMC11724362 DOI: 10.1093/nar/gkae1312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 11/28/2024] [Accepted: 12/26/2024] [Indexed: 01/13/2025]  Open
4
De Simone M, Hoover J, Lau J, Bennett H, Wu B, Chen C, Menon H, Au-Yeung A, Lear S, Vaidya S, Shi M, Lund J, Xavier-Magalhães A, Liang Y, Kurdoglu A, O’Gorman W, Modrusan Z, Le D, Darmanis S. A comprehensive analysis framework for evaluating commercial single-cell RNA sequencing technologies. Nucleic Acids Res 2025;53:gkae1186. [PMID: 39675380 PMCID: PMC11754665 DOI: 10.1093/nar/gkae1186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 11/08/2024] [Accepted: 11/14/2024] [Indexed: 12/17/2024]  Open
5
Utkina M, Shcherbakova A, Deviatiiarov R, Ryabova A, Loguinova M, Trofimov V, Kuznetsova A, Petropavlovskiy M, Salimkhanov R, Maksimov D, Albert E, Golubeva A, Asaad W, Urusova L, Bondarenko E, Lapshina A, Shutova A, Beltsevich D, Gusev O, Dzeranova L, Melnichenko G, Minniakhmetov I, Dedov I, Mokrysheva N, Popov S. Comparative evaluation of ACetic - MEthanol high salt dissociation approach for single-cell transcriptomics of frozen human tissues. Front Cell Dev Biol 2025;12:1469955. [PMID: 39839668 PMCID: PMC11748064 DOI: 10.3389/fcell.2024.1469955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Accepted: 11/20/2024] [Indexed: 01/23/2025]  Open
6
Lyu A, Fan Z, Clark M, Lea A, Luong D, Setayesh A, Starzinski A, Wolters R, Arias-Badia M, Allaire K, Wu K, Gurunathan V, Valderrábano L, Wei XX, Miller RA, Van Allen EM, Fong L. Evolution of myeloid-mediated immunotherapy resistance in prostate cancer. Nature 2025;637:1207-1217. [PMID: 39633050 PMCID: PMC11779626 DOI: 10.1038/s41586-024-08290-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 10/25/2024] [Indexed: 12/07/2024]
7
Mulet I, Grueso-Cortina C, Cortés-Cano M, Gerovska D, Wu G, Iakab SA, Jimenez-Blasco D, Curtabbi A, Hernansanz-Agustín P, Ketchum H, Manjarrés-Raza I, Wunderlich FT, Bolaños JP, Dawlaty MM, Hopf C, Enríquez JA, Araúzo-Bravo MJ, Tapia N. TET3 regulates terminal cell differentiation at the metabolic level. Nat Commun 2024;15:9749. [PMID: 39557858 PMCID: PMC11573987 DOI: 10.1038/s41467-024-54044-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 10/29/2024] [Indexed: 11/20/2024]  Open
8
Alías-Segura S, Pazos F, Chagoyen M. Differential expression and co-expression reveal cell types relevant to genetic disorder phenotypes. Bioinformatics 2024;40:btae646. [PMID: 39468724 PMCID: PMC11549017 DOI: 10.1093/bioinformatics/btae646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 10/22/2024] [Accepted: 10/25/2024] [Indexed: 10/30/2024]  Open
9
Ellman DG, Bjerre FA, Bak ST, Mathiesen SB, Harvald EB, Jensen CH, Andersen DC. Protocol to achieve high-resolution single-cell transcriptomics of cardiomyocytes in multiple species. STAR Protoc 2024;5:103194. [PMID: 39096494 PMCID: PMC11345562 DOI: 10.1016/j.xpro.2024.103194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/17/2024] [Accepted: 06/21/2024] [Indexed: 08/05/2024]  Open
10
Mo X, Wang C, Pu Q, Zhang Z, Wu D. Revealing genetic causality between blood-based biomarkers and major depression in east Asian ancestry. Front Psychiatry 2024;15:1424958. [PMID: 39323965 PMCID: PMC11423294 DOI: 10.3389/fpsyt.2024.1424958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 08/26/2024] [Indexed: 09/27/2024]  Open
11
Redd PS, Merting AD, Klement JD, Poschel DB, Yang D, Liu K. In vitro antibody-mediated SARS-CoV-2 infection suppression through human ACE2 receptor blockade. Immunol Lett 2024;268:106887. [PMID: 38925442 PMCID: PMC11256821 DOI: 10.1016/j.imlet.2024.106887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/23/2024] [Accepted: 06/22/2024] [Indexed: 06/28/2024]
12
Bernadskaya YY, Kuan A, Tjärnberg A, Brandenburg J, Zheng P, Wiechecki K, Kaplan N, Failla M, Bikou M, Madilian O, Wang W, Christiaen L. Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604718. [PMID: 39091743 PMCID: PMC11291048 DOI: 10.1101/2024.07.23.604718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
13
Mattar P, Reginato A, Lavados C, Das D, Kalyani M, Martinez-Lopez N, Sharma M, Skovbjerg G, Skytte JL, Roostalu U, Subbarayan R, Picarda E, Zang X, Zhang J, Guha C, Schwartz G, Rajbhandari P, Singh R. Insulin and leptin oscillations license food-entrained browning and metabolic flexibility. Cell Rep 2024;43:114390. [PMID: 38900636 PMCID: PMC11562929 DOI: 10.1016/j.celrep.2024.114390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/23/2024] [Accepted: 06/06/2024] [Indexed: 06/22/2024]  Open
14
Huang S, Shi W, Li S, Fan Q, Yang C, Cao J, Wu L. Advanced sequencing-based high-throughput and long-read single-cell transcriptome analysis. LAB ON A CHIP 2024;24:2601-2621. [PMID: 38669201 DOI: 10.1039/d4lc00105b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
15
Laisné M, Rodgers B, Benlamara S, Wicinski J, Nicolas A, Djerroudi L, Gupta N, Ferry L, Kirsh O, Daher D, Philippe C, Okada Y, Charafe-Jauffret E, Cristofari G, Meseure D, Vincent-Salomon A, Ginestier C, Defossez PA. A novel bioinformatic approach reveals cooperation between Cancer/Testis genes in basal-like breast tumors. Oncogene 2024;43:1369-1385. [PMID: 38467851 PMCID: PMC11065691 DOI: 10.1038/s41388-024-03002-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 03/13/2024]
16
Zelikson N, Ben S, Caspi M, Tarabe R, Shaleve Y, Pri-Paz Basson Y, Tayer-Shifman O, Goldberg E, Kivity S, Rosin-Arbesfeld R. Wnt signaling regulates chemokine production and cell migration of circulating human monocytes. Cell Commun Signal 2024;22:229. [PMID: 38622714 PMCID: PMC11020454 DOI: 10.1186/s12964-024-01608-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 04/09/2024] [Indexed: 04/17/2024]  Open
17
Coulter EM, Bewicke-Copley F, Mossner M, Graham TA, Fitzgibbon J, Okosun J. Defining an Optimized Workflow for Enriching and Analyzing Residual Tumor Populations Using Intracellular Markers. J Mol Diagn 2024;26:245-256. [PMID: 38280422 DOI: 10.1016/j.jmoldx.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 12/12/2023] [Accepted: 01/11/2024] [Indexed: 01/29/2024]  Open
18
Ismail KA, Mukherjee M, Kareta MS, Lopez SMC. Enabling methanol fixation of pediatric nasal wash during respiratory illness for single cell sequencing in comparison with fresh samples. Pediatr Res 2024;95:835-842. [PMID: 37758866 DOI: 10.1038/s41390-023-02780-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/21/2023] [Accepted: 07/24/2023] [Indexed: 09/29/2023]
19
Hume AJ, Olejnik J, White MR, Huang J, Turcinovic J, Heiden B, Bawa PS, Williams CJ, Gorham NG, Alekseyev YO, Connor JH, Kotton DN, Mühlberger E. Heat Inactivation of Nipah Virus for Downstream Single-Cell RNA Sequencing Does Not Interfere with Sample Quality. Pathogens 2024;13:62. [PMID: 38251369 PMCID: PMC10818917 DOI: 10.3390/pathogens13010062] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/23/2024]  Open
20
Wyler E. Single-Cell RNA-Sequencing of RVFV Infection. Methods Mol Biol 2024;2824:361-372. [PMID: 39039423 DOI: 10.1007/978-1-0716-3926-9_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
21
Mai D, Jahn A, Murray T, Morikubo M, Lim PN, Cervantes MM, Pham LK, Nemeth J, Urdahl K, Diercks AH, Aderem A, Rothchild AC. Exposure to Mycobacterium remodels alveolar macrophages and the early innate response to Mycobacterium tuberculosis infection. PLoS Pathog 2024;20:e1011871. [PMID: 38236787 PMCID: PMC10796046 DOI: 10.1371/journal.ppat.1011871] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/27/2023] [Indexed: 01/22/2024]  Open
22
Madaci L, Gard C, Nin S, Sarrabay A, Baier C, Venton G, Rihet P, Puthier D, Loriod B, Costello R. Single-Cell Transcriptome Analysis of Acute Myeloid Leukemia Cells Using Methanol Fixation and Cryopreservation. Diseases 2023;12:1. [PMID: 38275564 PMCID: PMC10814800 DOI: 10.3390/diseases12010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/08/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024]  Open
23
Kostic M, Raymond JJ, Freyre CAC, Henry B, Tumkaya T, Khlghatyan J, Dvornik J, Li J, Hsiao JS, Cheon SH, Chung J, Sun Y, Dolmetsch RE, Worringer KA, Ihry RJ. Patient Brain Organoids Identify a Link between the 16p11.2 Copy Number Variant and the RBFOX1 Gene. ACS Chem Neurosci 2023;14:3993-4012. [PMID: 37903506 PMCID: PMC10655044 DOI: 10.1021/acschemneuro.3c00442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/14/2023] [Indexed: 11/01/2023]  Open
24
Nakanishi T, Willett J, Farjoun Y, Allen RJ, Guillen-Guio B, Adra D, Zhou S, Richards JB. Alternative splicing in lung influences COVID-19 severity and respiratory diseases. Nat Commun 2023;14:6198. [PMID: 37794074 PMCID: PMC10550956 DOI: 10.1038/s41467-023-41912-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 09/21/2023] [Indexed: 10/06/2023]  Open
25
Sánchez-Carbonell M, Jiménez Peinado P, Bayer-Kaufmann C, Hennings JC, Hofmann Y, Schmidt S, Witte OW, Urbach A. Effect of methanol fixation on single-cell RNA sequencing of the murine dentate gyrus. Front Mol Neurosci 2023;16:1223798. [PMID: 37860083 PMCID: PMC10582346 DOI: 10.3389/fnmol.2023.1223798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023]  Open
26
Bageritz J, Krausse N, Yousefian S, Leible S, Valentini E, Boutros M. Glyoxal as an alternative fixative for single-cell RNA sequencing. G3 (BETHESDA, MD.) 2023;13:jkad160. [PMID: 37494060 PMCID: PMC10542564 DOI: 10.1093/g3journal/jkad160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/27/2023]
27
Dhumale P, Nielsen JV, Hansen ACS, Burton M, Beck HC, Jørgensen MG, Toyserkani NM, Haahr MK, Hansen ST, Lund L, Thomassen M, Sørensen JA, Andersen DC, Jensen CH, Sheikh SP. CD31 defines a subpopulation of human adipose-derived regenerative cells with potent angiogenic effects. Sci Rep 2023;13:14401. [PMID: 37658225 PMCID: PMC10474028 DOI: 10.1038/s41598-023-41535-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023]  Open
28
Yi PC, Zhuo L, Lin J, Chang C, Goddard A, Yoon OK. Impact of delayed PBMC processing on functional and genomic assays. J Immunol Methods 2023:113514. [PMID: 37353001 DOI: 10.1016/j.jim.2023.113514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/08/2023] [Accepted: 06/08/2023] [Indexed: 06/25/2023]
29
Sant P, Rippe K, Mallm JP. Approaches for single-cell RNA sequencing across tissues and cell types. Transcription 2023;14:127-145. [PMID: 37062951 PMCID: PMC10807473 DOI: 10.1080/21541264.2023.2200721] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/30/2023] [Indexed: 04/18/2023]  Open
30
Gutiérrez-Franco A, Ake F, Hassan MN, Cayuela NC, Mularoni L, Plass M. Methanol fixation is the method of choice for droplet-based single-cell transcriptomics of neural cells. Commun Biol 2023;6:522. [PMID: 37188816 DOI: 10.1038/s42003-023-04834-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 04/12/2023] [Indexed: 05/17/2023]  Open
31
Scully T, Klein A. A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538465. [PMID: 37163054 PMCID: PMC10168337 DOI: 10.1101/2023.04.26.538465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
32
Oder B, Chatzidimitriou A, Langerak AW, Rosenquist R, Österholm C. Recent revelations and future directions using single-cell technologies in chronic lymphocytic leukemia. Front Oncol 2023;13:1143811. [PMID: 37091144 PMCID: PMC10117666 DOI: 10.3389/fonc.2023.1143811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/22/2023] [Indexed: 04/08/2023]  Open
33
Characterization of bone marrow heterogeneity in NK-AML (M4/M5) based on single-cell RNA sequencing. Exp Hematol Oncol 2023;12:25. [PMID: 36879313 PMCID: PMC9987113 DOI: 10.1186/s40164-023-00391-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/21/2023] [Indexed: 03/08/2023]  Open
34
Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data. Proc Natl Acad Sci U S A 2023;120:e2217868120. [PMID: 36719923 PMCID: PMC9963017 DOI: 10.1073/pnas.2217868120] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]  Open
35
Ru B, Huang J, Zhang Y, Aldape K, Jiang P. Estimation of cell lineages in tumors from spatial transcriptomics data. Nat Commun 2023;14:568. [PMID: 36732531 PMCID: PMC9895078 DOI: 10.1038/s41467-023-36062-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 01/13/2023] [Indexed: 02/04/2023]  Open
36
Patil AR, Schug J, the HPAP Consortium, Naji A, Kaestner KH, Faryabi RB, Vahedi G. Computational workflow and interactive analysis of single-cell expression profiling of islets generated by the Human Pancreas Analysis Program. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.522578. [PMID: 36711819 PMCID: PMC9881881 DOI: 10.1101/2023.01.03.522578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
37
Han JL, Song YX, Yao WJ, Zhou J, Du Y, Xu T. Follicle-Stimulating Hormone Provokes Macrophages to Secrete IL-1β Contributing to Atherosclerosis Progression. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023;210:25-32. [PMID: 36368721 DOI: 10.4049/jimmunol.2200475] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/06/2022] [Indexed: 02/17/2024]
38
Teng X, Mou DC, Li HF, Jiao L, Wu SS, Pi JK, Wang Y, Zhu ML, Tang M, Liu Y. SIGIRR deficiency contributes to CD4 T cell abnormalities by facilitating the IL1/C/EBPβ/TNF-α signaling axis in rheumatoid arthritis. Mol Med 2022;28:135. [DOI: 10.1186/s10020-022-00563-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 10/28/2022] [Indexed: 11/19/2022]  Open
39
Single-cell sequencing unveils key contributions of immune cell populations in cancer-associated adipose wasting. Cell Discov 2022;8:122. [PMCID: PMC9663454 DOI: 10.1038/s41421-022-00466-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022]  Open
40
Bosch-Camós L, Alonso U, Esteve-Codina A, Chang CY, Martín-Mur B, Accensi F, Muñoz M, Navas MJ, Dabad M, Vidal E, Pina-Pedrero S, Pleguezuelos P, Caratù G, Salas ML, Liu L, Bataklieva S, Gavrilov B, Rodríguez F, Argilaguet J. Cross-protection against African swine fever virus upon intranasal vaccination is associated with an adaptive-innate immune crosstalk. PLoS Pathog 2022;18:e1010931. [PMID: 36350837 PMCID: PMC9645615 DOI: 10.1371/journal.ppat.1010931] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/17/2022] [Indexed: 11/11/2022]  Open
41
Lee H, Joo JY, Sohn DH, Kang J, Yu Y, Park HR, Kim YH. Single-cell RNA sequencing reveals rebalancing of immunological response in patients with periodontitis after non-surgical periodontal therapy. J Transl Med 2022;20:504. [PMID: 36329504 PMCID: PMC9635198 DOI: 10.1186/s12967-022-03702-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/05/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]  Open
42
Roos K, Rooda I, Keif RS, Liivrand M, Smolander OP, Salumets A, Velthut-Meikas A. Single-cell RNA-seq analysis and cell-cluster deconvolution of the human preovulatory follicular fluid cells provide insights into the pathophysiology of ovarian hyporesponse. Front Endocrinol (Lausanne) 2022;13:945347. [PMID: 36339426 PMCID: PMC9635625 DOI: 10.3389/fendo.2022.945347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/22/2022] [Indexed: 11/13/2022]  Open
43
Shih AJ, Adelson RP, Vashistha H, Khalili H, Nayyar A, Puran R, Herrera R, Chatterjee PK, Lee AT, Truskinovsky AM, Elmaliki K, DeFranco M, Metz CN, Gregersen PK. Single-cell analysis of menstrual endometrial tissues defines phenotypes associated with endometriosis. BMC Med 2022;20:315. [PMID: 36104692 PMCID: PMC9476391 DOI: 10.1186/s12916-022-02500-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 07/27/2022] [Indexed: 01/15/2023]  Open
44
Verhoeven BM, Mei S, Olsen TK, Gustafsson K, Valind A, Lindström A, Gisselsson D, Fard SS, Hagerling C, Kharchenko PV, Kogner P, Johnsen JI, Baryawno N. The immune cell atlas of human neuroblastoma. Cell Rep Med 2022;3:100657. [PMID: 35688160 PMCID: PMC9245004 DOI: 10.1016/j.xcrm.2022.100657] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 01/26/2022] [Accepted: 05/17/2022] [Indexed: 12/03/2022]
45
De Alwis R, Hansson J, Lindgren D, Schoch S, Tejera A, Scholtz B, Elfving P, Möller C, Nilsson H, Johansson M, Axelson H. Size‑based isolation and detection of renal carcinoma cells from whole blood. Mol Clin Oncol 2022;16:101. [PMID: 35463211 PMCID: PMC9022084 DOI: 10.3892/mco.2022.2534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/18/2022] [Indexed: 11/25/2022]  Open
46
Arora D, Robey PG. Recent updates on the biological basis of heterogeneity in bone marrow stromal cells/skeletal stem cells. BIOMATERIALS TRANSLATIONAL 2022;3:3-16. [PMID: 35837340 PMCID: PMC9255791 DOI: 10.12336/biomatertransl.2022.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/17/2022] [Accepted: 03/20/2022] [Indexed: 11/15/2022]
47
M Ascensión A, Ibáñez-Solé O, Inza I, Izeta A, Araúzo-Bravo MJ. Triku: a feature selection method based on nearest neighbors for single-cell data. Gigascience 2022;11:giac017. [PMID: 35277963 PMCID: PMC8917514 DOI: 10.1093/gigascience/giac017] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/24/2021] [Indexed: 01/03/2023]  Open
48
Cho I, Chang JB. Simultaneous expansion microscopy imaging of proteins and mRNAs via dual-ExM. Sci Rep 2022;12:3360. [PMID: 35233025 PMCID: PMC8888644 DOI: 10.1038/s41598-022-06903-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 02/03/2022] [Indexed: 11/08/2022]  Open
49
Kleino I, Nowlan K, Kotimaa J, Kekäläinen E. Optimising protein detection with fixable custom oligo-labelled antibodies for single-cell multi-omics approaches. Biotechnol J 2022;17:e2100213. [PMID: 35174641 DOI: 10.1002/biot.202100213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 02/06/2022] [Accepted: 02/12/2022] [Indexed: 11/11/2022]
50
Rauschmeier R, Reinhardt A, Gustafsson C, Glaros V, Artemov AV, Dunst J, Taneja R, Adameyko I, Månsson R, Busslinger M, Kreslavsky T. Bhlhe40 function in activated B and TFH cells restrains the GC reaction and prevents lymphomagenesis. J Exp Med 2021;219:212923. [PMID: 34919144 PMCID: PMC8689665 DOI: 10.1084/jem.20211406] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/01/2021] [Accepted: 11/23/2021] [Indexed: 12/22/2022]  Open
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