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scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation.
E Madissoon, A Wilbrey-Clark, R J Miragaia, K Saeb-Parsy, K T Mahbubani, N Georgakopoulos, P Harding, K Polanski, N Huang, K Nowicki-Osuch, R C Fitzgerald, K W Loudon, J R Ferdinand, M R Clatworthy, A Tsingene, S van Dongen, M Dabrowska, M Patel, M J T Stubbington, S A Teichmann, O Stegle, K B Meyer
Feb 02, 2020
BACKGROUND:The Human Cell Atlas is a large international collaborative effort to map all cell types of the human body. Single-cell RNA sequencing can generate high-quality data for the delivery of such an atlas. However, delays...
Published by: Genome biology, volume 21, issue 1
scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation.
E Madissoon, A Wilbrey-Clark, RJ Miragaia, K Saeb-Parsy, KT Mahbubani, N Georgakopoulos, P Harding, K Polanski, N Huang, K Nowicki-Osuch, RC Fitzgerald, KW Loudon, JR Ferdinand, MR Clatworthy, A Tsingene, S van Dongen, M Dabrowska, M Patel, MJT Stubbington, SA Teichmann, O Stegle, KB Meyer
Jan 06, 2020
BACKGROUND: The Human Cell Atlas is a large international collaborative effort to map all cell types of the human body. Single-cell RNA sequencing can generate high-quality data for the delivery of such an atlas. However, delays...
Single-cell transcriptome analyses reveal novel targets modulating cardiac neovascularization by resident endothelial cells following myocardial infarction.
Ziwen Li, Emmanouil G Solomonidis, Marco Meloni, Richard S Taylor, Rodger Duffin, Ross Dobie, Marlene S Magalhaes, Beth EP Henderson, Pieter A Louwe, Gabriela D'Amico, Kairbaan M Hodivala-Dilke, Ajay M Shah, Nicholas L Mills, Benjamin D Simons, Gillian A Gray, Neil C Henderson, Andrew H Baker, Mairi Brittan
Jun 10, 2019
AIMS: A better understanding of the pathways that regulate regeneration of the coronary vasculature is of fundamental importance for the advancement of strategies to treat patients with heart disease. Here, we aimed to...
Cell Proliferation Endothelial Cells Lineage tracing Myocardial Infarction single-cell RNA sequencing Therapeutic angiogenesis Animals Cell Proliferation Endothelial Cells Gene Expression Profiling Humans Mice Mice Transgenic Myocardial Infarction Myocardium Neovascularization Physiologic Single-Cell Analysis Transcriptome
Enteroendocrine cell lineages that differentially control feeding and gut motility.
Marito Hayashi, Judith A Kaye, Ella R Douglas, Narendra R Joshi, Fiona M Gribble, Frank Reimann, Stephen D Liberles
Mar 24, 2023
scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation
E. Madissoon, A. Wilbrey-Clark, R. J. Miragaia, K. Saeb-Parsy, K. T. Mahbubani, N. Georgakopoulos, P. Harding, K. Polanski, N. Huang, K. Nowicki-Osuch, R. C. Fitzgerald, K. W. Loudon, J. R. Ferdinand, M. R. Clatworthy, A. Tsingene, S. van Dongen, M. Dabrowska, M. Patel, M. J. T. Stubbington, S. A. Teichmann, O. Stegle, K. B. Meyer
Jun 06, 2020
Abstract: Background: The Human Cell Atlas is a large international collaborative effort to map all cell types of the human body. Single-cell RNA sequencing can generate high-quality data for the delivery of such an atlas....
scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation
E. Madissoon, A. Wilbrey-Clark, R. J. Miragaia, K. Saeb-Parsy, K. T. Mahbubani, N. Georgakopoulos, P. Harding, K. Polanski, N. Huang, K. Nowicki-Osuch, R. C. Fitzgerald, K. W. Loudon, J. R. Ferdinand, M. R. Clatworthy, A. Tsingene, S. van Dongen, M. Dabrowska, M. Patel, M. J. T. Stubbington, S. A. Teichmann, O. Stegle, K. B. Meyer
Dec 30, 2020
Abstract: Background: The Human Cell Atlas is a large international collaborative effort to map all cell types of the human body. Single-cell RNA sequencing can generate high-quality data for the delivery of such an atlas....
Cell Atlas technologies and insights into tissue architecture.
Since Robert Hooke first described the existence of 'cells' in 1665, scientists have sought to identify and further characterise these fundamental units of life. While our understanding of cell location, morphology and function...
Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data.
Bayesian immune activation single-cell RNA sequencing statistics transcriptional noise variability Animals Biological Variation Population CD4-Positive T-Lymphocytes Cell Differentiation Cell Lineage Computer Simulation Gene Expression Regulation Immunity Lymphocyte Activation Mice Mice Inbred C57BL Models Theoretical Sequence Analysis RNA Single-Cell Analysis Transcriptome
Comparative analysis of sequencing technologies for single-cell transcriptomics.
Kedar Nath Natarajan, Zhichao Miao, Miaomiao Jiang, Xiaoyun Huang, Hongpo Zhou, Jiarui Xie, Chunqing Wang, Shishang Qin, Zhikun Zhao, Liang Wu, Naibo Yang, Bo Li, Yong Hou, Shiping Liu, Sarah A Teichmann
May 16, 2019
Single-cell RNA-seq technologies require library preparation prior to sequencing. Here, we present the first report to compare the cheaper BGISEQ-500 platform to the Illumina HiSeq platform for scRNA-seq. We generate a resource...
Hematopoietic stem cells retain functional potential and molecular identity in hibernation cultures.
Caroline A Oedekoven, Miriam Belmonte, Daniel Bode, Fiona K Hamey, Mairi S Shepherd, James Lok Chi Che, Grace Boyd, Craig McDonald, Serena Belluschi, Evangelia Diamanti, Hugo P Bastos, Katherine S Bridge, Berthold Göttgens, Elisa Laurenti, David G Kent
Apr 12, 2021
Advances in the isolation and gene expression profiling of single hematopoietic stem cells (HSCs) have permitted in-depth resolution of their molecular program. However, long-term HSCs can only be isolated to near purity from...
Cell Cycle Hematopoietic Stem Cells quiescence single-cell RNA sequencing single-cell assays Stem Cell Niche Transplantation Animals Arylsulfotransferase Bone Marrow Transplantation Cell Culture Techniques Cell Cycle Cell Differentiation Cells Cultured Cytokines Hematopoietic Stem Cells Hibernation Mice Mice Inbred C57BL Multiprotein Complexes Signaling Lymphocytic Activation Molecule Family Member 1 Single-Cell Analysis Stem Cell Niche Suppressor of Cytokine Signaling Proteins Transcription Factor AP-1 Transcriptome
Notch Signaling Mediates Secondary Senescence.
Yee Voan Teo, Nattaphong Rattanavirotkul, Nelly Olova, Angela Salzano, Andrea Quintanilla, Nuria Tarrats, Christos Kiourtis, Miryam Müller, Anthony R Green, Peter D Adams, Juan-Carlos Acosta, Thomas G Bird, Kristina Kirschner, Nicola Neretti, Tamir Chandra
Apr 17, 2019
CEBPB Notch TGFB bystander senescence oncogene induced senescence paracrine senescence secondary senescence Senescence senescence associated secretory phenotype single-cell RNA sequencing Animals Cells Cultured Cellular Senescence Humans Mice Inbred C57BL Oncogenes Receptors Notch Signal Transduction Single-Cell Analysis Transcriptome
Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn's Disease.
Rasa Elmentaite, Alexander DB Ross, Kenny Roberts, Kylie R James, Daniel Ortmann, Tomás Gomes, Komal Nayak, Liz Tuck, Sophie Pritchard, Omer Ali Bayraktar, Robert Heuschkel, Ludovic Vallier, Sarah A Teichmann, Matthias Zilbauer
Dec 10, 2020
Human gut development requires the orchestrated interaction of differentiating cell types. Here, we generate an in-depth single-cell map of the developing human intestine at 6-10 weeks post-conception. Our analysis reveals the...
human fetal gut development inflammatory bowel disease intestinal organoids intestinal stem cells pediatric Crohn's disease single-cell RNA sequencing villus formation Adolescent Cells Cultured Child Crohn Disease Humans Intestinal Mucosa RNA-seq Receptors G-Protein-Coupled Single-Cell Analysis Transcription Factors Transcriptome
Single-Cell RNA-Seq of Mouse Dopaminergic Neurons Informs Candidate Gene Selection for Sporadic Parkinson Disease.
Paul W Hook, Sarah A McClymont, Gabrielle H Cannon, William D Law, A Jennifer Morton, Loyal A Goff, Andrew S McCallion
Apr 19, 2018
Genetic variation modulating risk of sporadic Parkinson disease (PD) has been primarily explored through genome-wide association studies (GWASs). However, like many other common genetic diseases, the impacted genes remain...
Complexin 1 Parkinson Disease Dopaminergic Neurons Gene Regulatory Networks genome-wide association studies MOUSE single-cell RNA sequencing Substantia Nigra Animals Cell Separation Dopaminergic Neurons Gene Regulatory Networks Genetic Association Studies Genetic Loci Genetic Markers Genome-Wide Association Study Mice Knockout Parkinson Disease Sequence Analysis RNA Single-Cell Analysis Substantia Nigra
The Human Lung Cell Atlas
Herbert B Schiller, Daniel T Montoro, Lukas M Simon, Emma L Rawlins, Kerstin B Meyer, Maximilian Strunz, Felipe A Vieira Braga, Wim Timens, Gerard H Koppelman, GR Scott Budinger, Janette K Burgess, Avinash Waghray, Maarten van den Berge, Fabian J Theis, Aviv Regev, Naftali Kaminski, Jayaraj Rajagopal, Sarah A Teichmann, Alexander V Misharin, Martijn C Nawijn
Dec 12, 2019
Differential IRF8 Transcription Factor Requirement Defines Two Pathways of Dendritic Cell Development in Humans
Urszula Cytlak, Anastasia Resteu, Sarah Pagan, Kile Green, Paul Milne, Sheetal Maisuria, David McDonald, Gillian Hulme, Andrew Filby, Benjamin Carpenter, Rachel Queen, Sophie Hambleton, Rosie Hague, Hana Lango Allen, James ED Thaventhiran, Gina Doody, Matthew Collin, Venetia Bigley
Aug 05, 2020
The formation of mammalian dendritic cells (DCs) is controlled by multiple hematopoietic transcription factors, including IRF8. Loss of IRF8 exerts a differential effect on DC subsets, including plasmacytoid DCs (pDCs) and the...
CyTOF IRF8 dendritic cell Hematopoiesis Immunity primary immunodeficiency single-cell RNA sequencing Transcription factor Animals Antigens CD1 Antigens CD34 Cell Line Cell Lineage Dendritic Cells Glycoproteins Hematopoiesis Hematopoietic Stem Cells Humans Interferon Regulatory Factors Interleukin-3 Receptor alpha Subunit Lipopolysaccharide Receptors Mice Receptors Immunologic
Diversity of Reactive Astrogliosis in CNS Pathology
Astrocytes are essential for the development and homeostatic maintenance of the central nervous system (CNS). They are also critical players in the CNS injury response during which they undergo a process referred to as "reactive...
Microglia Diversity in Health and Multiple Sclerosis.
Sameera Zia, Khalil S Rawji, Nathan J Michaels, Mena Burr, Bradley J Kerr, Luke M Healy, Jason R Plemel
Nov 20, 2020
Multiple Sclerosis (MS) is a neurodegenerative disease characterized by multiple focal lesions, ongoing demyelination and, for most people, a lack of remyelination. MS lesions are enriched with monocyte-derived macrophages and...
Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis.
Ross Dobie, John R Wilson-Kanamori, Beth EP Henderson, James R Smith, Kylie P Matchett, Jordan R Portman, Karolina Wallenborg, Simone Picelli, Anna Zagorska, Swetha V Pendem, Thomas E Hudson, Minnie M Wu, Grant R Budas, David G Breckenridge, Ewen M Harrison, Damian J Mole, Stephen J Wigmore, Prakash Ramachandran, Chris P Ponting, Sarah A Teichmann, John C Marioni, Neil C Henderson
Dec 19, 2019
Iterative liver injury results in progressive fibrosis disrupting hepatic architecture, regeneration potential, and liver function. Hepatic stellate cells (HSCs) are a major source of pathological matrix during fibrosis and are...
Single-cell RNAseq reveals seven classes of colonic sensory neuron.
James RF Hockley, Toni S Taylor, Gerard Callejo, Anna L Wilbrey, Alex Gutteridge, Karsten Bach, Wendy J Winchester, David C Bulmer, Gordon McMurray, Ewan St John Smith
Apr 27, 2018
OBJECTIVE: Integration of nutritional, microbial and inflammatory events along the gut-brain axis can alter bowel physiology and organism behaviour. Colonic sensory neurons activate reflex pathways and give rise to conscious...
Diversity of Reactive Astrogliosis in CNS Pathology
Aaron J. Moulson, Jordan W. Squair, Robin J. M. Franklin, Wolfram Tetzlaff, Peggy Assinck
Aug 11, 2021
Astrocytes are essential for the development and homeostatic maintenance of the central nervous system (CNS). They are also critical players in the CNS injury response during which they undergo a process referred to as “reactive...
Single-cell molecular profiling provides a high-resolution map of basophil and mast cell development.
Fiona K Hamey, Winnie WY Lau, Iwo Kucinski, Xiaonan Wang, Evangelia Diamanti, Nicola K Wilson, Berthold Göttgens, Joakim S Dahlin
Oct 06, 2020