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Results: 97
Mechanisms of stretch-mediated skin expansion at single-cell resolution.
Mariaceleste Aragona, Alejandro Sifrim, Milan Malfait, Yura Song, Jens Van Herck, Sophie Dekoninck, Souhir Gargouri, Gaëlle Lapouge, Benjamin Swedlund, Christine Dubois, Pieter Baatsen, Katlijn Vints, Seungmin Han, Fadel Tissir, Thierry Voet, Benjamin D Simons, Cédric Blanpain
Jun 09, 2020
Adaptor Proteins Signal Transducing Adherens Junctions Animals Base Sequence Cell Cycle Proteins Cell Differentiation Cell Self Renewal Chromatin Chromatin Assembly and Disassembly Clone Cells Disease Models Animal Extracellular Signal-Regulated MAP Kinases Gene Regulatory Networks Hydrogels Mechanotransduction Cellular Mice Mice Transgenic Mitogen-Activated Protein Kinase Kinases Mutation RNA Messenger RNA-seq Single-Cell Analysis Skin Stem Cells Trans-Activators Transcription Factor AP-1 Transcription Genetic YAP-Signaling Proteins
RNA proximity sequencing data and analysis pipeline from a human neuroblastoma nuclear transcriptome.
We have previously developed and described a method for measuring RNA co-locations within cells, called Proximity RNA-seq, which promises insights into RNA expression, processing, storage and translation. Here, we describe...
Souporcell
Haynes Heaton, Arthur M Talman, Andrew Knights, Maria Imaz, Daniel J Gaffney, Richard Durbin, Martin Hemberg, Mara Kn Lawniczak
Apr 01, 2020
Reprogramming of the wheat transcriptome in response to infection with Claviceps purpurea, the causal agent of ergot.
Eleni Tente, Nelzo Ereful, Anyela Camargo Rodriguez, Paul Grant, Donal M O'Sullivan, Lesley A Boyd, Anna Gordon
Aug 11, 2021
BACKGROUND: Ergot, caused by the fungal pathogen Claviceps purpurea, infects the female flowers of a range of cereal crops, including wheat. To understand the interaction between C. purpurea and hexaploid wheat we undertook an...
Analysis of genetic networks regulating refractive eye development in collaborative cross progenitor strain mice reveals new genes and pathways underlying human myopia.
BACKGROUND: Population studies suggest that genetic factors play an important role in refractive error development; however, the precise role of genetic background and the composition of the signaling pathways underlying...
Evolutionary conservation of pathways Gene-based genome-wide association analysis Genetic networks genetic variation Myopia RNA-seq Refractive eye development Signaling pathways Animals Chromosomes Human Collaborative Cross Mice Eye Gene Regulatory Networks Genetic Predisposition to Disease Humans Mice Myopia Refraction Ocular Retina Signal Transduction
SARS-CoV-2 within-host diversity and transmission.
Katrina A Lythgoe, Matthew Hall, Luca Ferretti, Mariateresa de Cesare, George MacIntyre-Cockett, Amy Trebes, Monique Andersson, Newton Otecko, Emma L Wise, Nathan Moore, Jessica Lynch, Stephen Kidd, Nicholas Cortes, Matilde Mori, Rebecca Williams, Gabrielle Vernet, Anita Justice, Angie Green, Samuel M Nicholls, M Azim Ansari, Lucie Abeler-Dörner, Catrin E Moore, Timothy EA Peto, David W Eyre, Robert Shaw, Peter Simmonds, David Buck, John A Todd, Oxford Virus Sequencing Analysis Group (OVSG), Thomas R Connor, Shirin Ashraf, Ana da Silva Filipe, James Shepherd, Emma C Thomson, COVID-19 Genomics UK (COG-UK) Consortium, David Bonsall, Christophe Fraser, Tanya Golubchik
Mar 10, 2021
A single cell characterisation of human embryogenesis identifies pluripotency transitions and putative anterior hypoblast centre.
Matteo A Molè, Tim HH Coorens, Marta N Shahbazi, Antonia Weberling, Bailey AT Weatherbee, Carlos W Gantner, Carmen Sancho-Serra, Lucy Richardson, Abbie Drinkwater, Najma Syed, Stephanie Engley, Philip Snell, Leila Christie, Kay Elder, Alison Campbell, Simon Fishel, Sam Behjati, Roser Vento-Tormo, Magdalena Zernicka-Goetz
May 13, 2021
Bone Morphogenetic Protein 1 Cell Lineage Cells Cultured Embryo Implantation Embryo Mammalian Embryonic Development Fibroblast Growth Factors Gastrulation Gene Expression Regulation Developmental Germ Layers Humans Image Processing Computer-Assisted Multigene Family Nodal Protein RNA-seq Single-Cell Analysis Spatio-Temporal Analysis Wnt Signaling Pathway
CITED2 coordinates key hematopoietic regulatory pathways to maintain the HSC pool in both steady-state hematopoiesis and transplantation.
Hannah Lawson, Louie N van de Lagemaat, Melania Barile, Andrea Tavosanis, Jozef Durko, Arnaud Villacreces, Aarushi Bellani, Christopher Mapperley, Elise Georges, Catarina Martins-Costa, Catarina Sepulveda, Lewis Allen, Joana Campos, Kirsteen J Campbell, Dónal O'Carroll, Berthold Göttgens, Suzanne Cory, Neil P Rodrigues, Amelie V Guitart, Kamil R Kranc
Oct 06, 2021
Hematopoietic stem cells (HSCs) reside at the apex of the hematopoietic differentiation hierarchy and sustain multilineage hematopoiesis. Here, we show that the transcriptional regulator CITED2 is essential for life-long HSC...
CITED2 MCL-1 PTEN Hematopoiesis Hematopoietic stem cell Animals Apoptosis Cell Proliferation Gene Expression Regulation Gene Regulatory Networks Hematopoiesis Hematopoietic Stem Cell Transplantation Hematopoietic Stem Cells Mice Inbred C57BL Mice Knockout RNA-seq Repressor Proteins Reverse Transcriptase Polymerase Chain Reaction Signal Transduction Time Factors Trans-Activators
Longitudinal RNA-Seq Analysis of Vertebrate Aging Identifies Mitochondrial Complex I as a Small-Molecule-Sensitive Modifier of Lifespan.
Mario Baumgart, Steffen Priebe, Marco Groth, Nils Hartmann, Uwe Menzel, Luca Pandolfini, Philipp Koch, Marius Felder, Michael Ristow, Christoph Englert, Reinhard Guthke, Matthias Platzer, Alessandro Cellerino
Mar 01, 2016
GAGE Nothobranchius furzeri RNA transport RNA-seq aging history trait hormesis hourglass life ribosome lifespan regulation longevity longitudinal study mitohormesis rejuvenation weighted gene coexpression network analysis (WGCNA) Zebrafish Animals Cyprinodontiformes Longitudinal Studies RNA Sequence Analysis RNA Vertebrates
Genome-wide analyses reveal the IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation.
Jhuma Pramanik, Xi Chen, Gozde Kar, Johan Henriksson, Tomás Gomes, Jong-Eun Park, Kedar Natarajan, Kerstin B Meyer, Zhichao Miao, Andrew NJ McKenzie, Bidesh Mahata, Sarah A Teichmann
May 14, 2019
BACKGROUND: The IRE1a-XBP1 pathway is a conserved adaptive mediator of the unfolded protein response. The pathway is indispensable for the development of secretory cells by facilitating protein folding and enhancing secretory...
Genome-wide XBP1 chromatin occupancy IRE1a IRE1a-XBP1 pathway RNA-seq T helper cell activation Th2 lymphocyte proliferation Th2 transcriptome xbp1 XBP1 ChIP-seq Animals Base Sequence Cell Cycle Cell Differentiation Cell Proliferation Cytokines Endoribonucleases Female Gene Expression Regulation Genome-Wide Association Study Lymphocyte Activation Mice Inbred C57BL Mice Transgenic Protein Serine-Threonine Kinases Signal Transduction Stress Physiological Th2 Cells Up-Regulation X-Box Binding Protein 1
geneBasis
Alsu Missarova, Jaison Jain, Andrew Butler, Shila Ghazanfar, Tim Stuart, Maigan Brusko, Clive Wasserfall, Harry Nick, Todd Brusko, Mark Atkinson, Rahul Satija, John C Marioni
Jan 28, 2022
scRNA-seq datasets are increasingly used to identify gene panels that can be probed using alternative technologies, such as spatial transcriptomics, where choosing the best subset of genes is vital. Existing methods are limited...
A high-resolution mRNA expression time course of embryonic development in zebrafish.
Richard J White, John E Collins, Ian M Sealy, Neha Wali, Christopher M Dooley, Zsofia Digby, Derek L Stemple, Daniel N Murphy, Konstantinos Billis, Thibaut Hourlier, Anja Füllgrabe, Matthew P Davis, Anton J Enright, Elisabeth M Busch-Nentwich
Feb 12, 2018
We have produced an mRNA expression time course of zebrafish development across 18 time points from 1 cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3'...
Spatiotemporal immune zonation of the human kidney.
Benjamin J Stewart, John R Ferdinand, Matthew D Young, Thomas J Mitchell, Kevin W Loudon, Alexandra M Riding, Nathan Richoz, Gordon L Frazer, Joy UL Staniforth, Felipe A Vieira Braga, Rachel A Botting, Dorin-Mirel Popescu, Roser Vento-Tormo, Emily Stephenson, Alex Cagan, Sarah J Farndon, Krzysztof Polanski, Mirjana Efremova, Kile Green, Martin Del Castillo Velasco-Herrera, Charlotte Guzzo, Grace Collord, Lira Mamanova, Tevita Aho, James N Armitage, Antony CP Riddick, Imran Mushtaq, Stephen Farrell, Dyanne Rampling, James Nicholson, Andrew Filby, Johanna Burge, Steven Lisgo, Susan Lindsay, Marc Bajenoff, Anne Y Warren, Grant D Stewart, Neil Sebire, Nicholas Coleman, Muzlifah Haniffa, Sarah A Teichmann, Sam Behjati, Menna R Clatworthy
Oct 07, 2019
DSCAM-AS1-Driven Proliferation of Breast Cancer Cells Involves Regulation of Alternative Exon Splicing and 3'-End Usage.
Jamal Elhasnaoui, Valentina Miano, Giulio Ferrero, Elena Doria, Antonette E Leon, Aline SC Fabricio, Laura Annaratone, Isabella Castellano, Anna Sapino, Michele De Bortoli
Aug 21, 2020
DSCAM-AS1 is a cancer-related long noncoding RNA with higher expression levels in Luminal A, B, and HER2-positive Breast Carcinoma (BC), where its expression is strongly dependent on Estrogen Receptor Alpha (ERα). DSCAM-AS1...
Single cell derived mRNA signals across human kidney tumors.
Matthew D Young, Thomas J Mitchell, Lars Custers, Thanasis Margaritis, Francisco Morales-Rodriguez, Kwasi Kwakwa, Eleonora Khabirova, Gerda Kildisiute, Thomas RW Oliver, Ronald R de Krijger, Marry M van den Heuvel-Eibrink, Federico Comitani, Alice Piapi, Eva Bugallo-Blanco, Christine Thevanesan, Christina Burke, Elena Prigmore, Kirsty Ambridge, Kenny Roberts, Felipe A Vieira Braga, Tim HH Coorens, Ignacio Del Valle, Anna Wilbrey-Clark, Lira Mamanova, Grant D Stewart, Vincent J Gnanapragasam, Dyanne Rampling, Neil Sebire, Nicholas Coleman, Liz Hook, Anne Warren, Muzlifah Haniffa, Marcel Kool, Stefan M Pfister, John C Achermann, Xiaoling He, Roger A Barker, Adam Shlien, Omer A Bayraktar, Sarah A Teichmann, Frank C Holstege, Kerstin B Meyer, Jarno Drost, Karin Straathof, Sam Behjati
Mar 03, 2021
Tumor cells may share some patterns of gene expression with their cell of origin, providing clues into the differentiation state and origin of cancer. Here, we study the differentiation state and cellular origin of 1300...
Liver organoids reproduce alpha-1 antitrypsin deficiency-related liver disease.
Gema Gómez-Mariano, Nerea Matamala, Selene Martínez, Iago Justo, Alberto Marcacuzco, Carlos Jimenez, Sara Monzón, Isabel Cuesta, Cristina Garfia, María Teresa Martínez, Meritxell Huch, Ignacio Pérez de Castro, Manuel Posada, Sabina Janciauskiene, Beatriz Martínez-Delgado
Dec 12, 2020
BACKGROUND AND AIMS: Alpha-1 antitrypsin (AAT) is a product of SERPINA1 gene mainly expressed by hepatocytes. Clinically relevant mutations in the SERPINA1 gene, such as Z (Glu342Lys), results in an expression of misfolded AAT...
Chaperone-like protein DAY plays critical roles in photomorphogenesis.
Ho-Seok Lee, Ilyeong Choi, Young Jeon, Hee-Kyung Ahn, Huikyong Cho, JiWoo Kim, Jae-Hee Kim, Jung-Min Lee, SungHee Lee, Julian Bünting, Dong Hye Seo, Tak Lee, Du-Hwa Lee, Insuk Lee, Man-Ho Oh, Tae-Wuk Kim, Youssef Belkhadir, Hyun-Sook Pai
Sep 05, 2021
Photomorphogenesis, light-mediated development, is an essential feature of all terrestrial plants. While chloroplast development and brassinosteroid (BR) signaling are known players in photomorphogenesis, proteins that regulate...
Arabidopsis Arabidopsis Proteins Brassinosteroids Chlorophyll Chloroplasts Etiolation Gene Expression Regulation Plant Gene Knockdown Techniques HSP40 Heat-Shock Proteins LIGHT Membrane Proteins Microtubule-Associated Proteins Morphogenesis Mutation Plants Genetically Modified Protein Kinases RNA-seq Recombinant Proteins Seedlings Signal Transduction
Identification of Subtypes of Barrett's Esophagus and Esophageal Adenocarcinoma Based on DNA Methylation Profiles and Integration of Transcriptome and Genome Data.
Sriganesh Jammula, Annalise C Katz-Summercorn, Xiaodun Li, Constanza Linossi, Elizabeth Smyth, Sarah Killcoyne, Daniele Biasci, Vinod V Subash, Sujath Abbas, Adrienn Blasko, Ginny Devonshire, Amber Grantham, Filip Wronowski, Maria O'Donovan, Nicola Grehan, Matthew D Eldridge, Simon Tavaré, Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium, Rebecca C Fitzgerald
Jun 05, 2020
BACKGROUND & AIMS: Esophageal adenocarcinomas (EACs) are heterogeneous and often preceded by Barrett's esophagus (BE). Many genomic changes have been associated with development of BE and EAC, but little is known about...
antitumor immune response gene repression prognostic factor response to treatment Adenocarcinoma Aged Antineoplastic Agents Barrett Esophagus Cyclin E DNA Methylation Disease Progression Epigenesis Genetic Esophageal Mucosa Esophageal Neoplasms Female Gene Amplification Gene Expression Regulation Neoplastic Humans Male Middle Aged Oncogene Proteins Promoter Regions Genetic RNA-seq Retrospective Studies Temozolomide whole genome sequencing
Transcriptome of pleuropodia from locust embryos supports that these organs produce enzymes enabling the larva to hatch
Abstract: Background: Pleuropodia are limb-derived glandular organs that transiently appear on the first abdominal segment in embryos of insects from majority of “orders”. They are missing in the genetic model Drosophila and...
Novel Insights Into Rheumatoid Arthritis Through Characterization of Concordant Changes in DNA Methylation and Gene Expression in Synovial Biopsies of Patients With Differing Numbers of Swollen Joints.
Andrew YF Li Yim, Enrico Ferrero, Klio Maratou, Huw D Lewis, George Royal, David F Tough, Chris Larminie, Marcel MAM Mannens, Peter Henneman, Wouter J de Jonge, Marleen GH van de Sande, Danielle M Gerlag, Rab K Prinjha, Paul P Tak
May 06, 2021
In this study, we sought to characterize synovial tissue obtained from individuals with arthralgia and disease-specific auto-antibodies and patients with established rheumatoid arthritis (RA), by applying an integrative...
DNA Methylation Arthralgia multi-omics analyses rheumatoid arthritis synovial biopsies target identification transcriptomics Adult Aged Aged 80 and over Arthralgia Arthritis Rheumatoid Arthroscopy Biopsy DNA Methylation Epigenesis Genetic Female Humans Male Middle Aged RNA-seq Severity of Illness Index Synovial Membrane whole genome sequencing Young Adult
Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids.
Susanne C van den Brink, Anna Alemany, Vincent van Batenburg, Naomi Moris, Marloes Blotenburg, Judith Vivié, Peter Baillie-Johnson, Jennifer Nichols, Katharina F Sonnen, Alfonso Martinez Arias, Alexander van Oudenaarden
Oct 28, 2019
Using single-cell technologies to map the human immune system - implications for nephrology.
Advances in single-cell technologies are transforming our understanding of cellular identity. For instance, the application of single-cell RNA sequencing and mass cytometry technologies to the study of immune cell populations in...
Liver organoids reproduce alpha-1 antitrypsin deficiency-related liver disease
Gema Gómez-Mariano, Nerea Matamala, Selene Martínez, Iago Justo, Alberto Marcacuzco, Carlos Jimenez, Sara Monzón, Isabel Cuesta, Cristina Garfia, María Teresa Martínez, Meritxell Huch, Ignacio Pérez de Castro, Manuel Posada, Sabina Janciauskiene, Beatriz Martínez-Delgado
Jun 06, 2020
Abstract: Background and aims: Alpha-1 antitrypsin (AAT) is a product of SERPINA1 gene mainly expressed by hepatocytes. Clinically relevant mutations in the SERPINA1 gene, such as Z (Glu342Lys), results in an expression of...
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