Droplet-based single-cell total RNA-seq reveals differential non-coding expression and splicing patterns during mouse development

Autor: Hollfelder, Florian, Salmen, F, De Jonghe, Joachim, Kaminski, T, Alemany, A, Parada, G, Verity-Legg, Joe, Yanagida, A, Kohler, Timo, Battich, N, Van Den Brekel, Floris, Ellermann, A, Martinez Arias, A, Nichols, J, Hemberg, M, Van Oudenaarden, A

In recent years, single-cell transcriptome sequencing has revolutionized biology, allowing for the unbiased characterization of cellular subpopulations. However, most methods amplify the termini of polyadenylated transcripts capturing only a small fr

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::47c4f7e4e2a5b6e6c9f62a5d1214bfa2

High-throughput total RNA sequencing in single cells using VASA-seq.

Autor: Salmen F; Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, Netherlands.; Oncode Institute, Utrecht, Netherlands., De Jonghe J; Department of Biochemistry, University of Cambridge, Cambridge, UK.; Francis Crick Institute, London, UK., Kaminski TS; Department of Biochemistry, University of Cambridge, Cambridge, UK.; Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland., Alemany A; Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, Netherlands.; Oncode Institute, Utrecht, Netherlands., Parada GE; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK., Verity-Legg J; Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, Netherlands.; Oncode Institute, Utrecht, Netherlands., Yanagida A; Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, Japan., Kohler TN; Department of Biochemistry, University of Cambridge, Cambridge, UK.; Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Cambridge, UK., Battich N; Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, Netherlands.; Oncode Institute, Utrecht, Netherlands., van den Brekel F; Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, Netherlands.; Oncode Institute, Utrecht, Netherlands., Ellermann AL; Department of Biochemistry, University of Cambridge, Cambridge, UK., Arias AM; Systems Bioengineering, DCEXS, Universidad Pompeu Fabra, Doctor Aiguader 88 ICREA (Institució Catalana de Recerca i Estudis Avançats), Barcelona, Spain., Nichols J; Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Cambridge, UK.; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK., Hemberg M; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA., Hollfelder F; Department of Biochemistry, University of Cambridge, Cambridge, UK. fh111@cam.ac.uk., van Oudenaarden A; Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, Netherlands. a.vanoudenaarden@hubrecht.eu.; Oncode Institute, Utrecht, Netherlands. a.vanoudenaarden@hubrecht.eu.

Publikováno v: Nature biotechnology [Nat Biotechnol] 2022 Dec; Vol. 40 (12), pp. 1780-1793. Date of Electronic Publication: 2022 Jun 27.

Storm: Incorporating transient stochastic dynamics to infer the RNA velocity with metabolic labeling information.

Autor: Peng, Qiangwei¹ (AUTHOR), Qiu, Xiaojie^2,3,4,5 (AUTHOR) xiaojie@stanford.edu, Li, Tiejun^1,6 (AUTHOR) tieli@pku.edu.cn

Publikováno v: PLoS Computational Biology. 11/18/2024, Vol. 20 Issue 11, p1-38. 38p.

UNSEG: unsupervised segmentation of cells and their nuclei in complex tissue samples.

Autor: Kochetov, Bogdan^1,2, Bell, Phoenix D.^3,4, Garcia, Paulo S.³, Shalaby, Akram S.⁵, Raphael, Rebecca^1,2, Raymond, Benjamin⁶, Leibowitz, Brian J.^2,7, Schoedel, Karen³, Brand, Rhonda M.^8,9, Brand, Randall E.^2,8, Yu, Jian¹⁰, Zhang, Lin¹⁰, Diergaarde, Brenda^2,11, Schoen, Robert E.⁸, Singhi, Aatur³, Uttam, Shikhar^1,2 shf28@pitt.edu

Publikováno v: Communications Biology. 8/30/2024, Vol. 7 Issue 1, p1-14. 14p.

Living in a noisy world-origins of gene expression noise and its impact on cellular decision-making.

Autor: Pal S; Department of Bioscience and Biotechnology, IIT Kharagpur, India., Dhar R; Department of Bioscience and Biotechnology, IIT Kharagpur, India.

Publikováno v: FEBS letters [FEBS Lett] 2024 Jul; Vol. 598 (14), pp. 1673-1691. Date of Electronic Publication: 2024 May 09.