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Results: 36
Quantitative Proteomics Analysis of Lytic KSHV Infection in Human Endothelial Cells Reveals Targets of Viral Immune Modulation.
HHV-8 KSHV NK cell receptor ligands herpesvirus host cell restriction factors lytic reactivation Proteomics Viral immune evasion Antigens Differentiation T-Lymphocyte Cell Line DNA-Directed DNA Polymerase Down-Regulation Endothelial Cells Gene Library Gene Ontology Genes Viral Genetic Testing Herpesvirus 8 Human Humans immunomodulation Kinetics Ligands Mutation Proteome Proteomics Sarcoma Kaposi Up-Regulation Viral Proteins Virus Activation eIF-2 Kinase
Strategies for sample labelling and library preparation in DNA metabarcoding studies.
Kristine Bohmann, Vasco Elbrecht, Christian Carøe, Iliana Bista, Florian Leese, Michael Bunce, Douglas W Yu, Mathew Seymour, Alex J Dumbrell, Simon Creer
Oct 13, 2021
Metabarcoding of DNA extracted from environmental or bulk specimen samples is increasingly used to profile biota in basic and applied biodiversity research because of its targeted nature that allows sequencing of genetic markers...
Genome-wide high-throughput screening to investigate essential genes involved in methicillin-resistant Staphylococcus aureus Sequence Type 398 survival.
Mette T Christiansen, Rolf S Kaas, Roy R Chaudhuri, Mark A Holmes, Henrik Hasman, Frank M Aarestrup
Jul 15, 2014
Animals Anti-Bacterial Agents DNA Transposable Elements Gene Library Genes Essential Genome Genotype High-Throughput Screening Assays Humans Hydrogen-Ion Concentration Methicillin-Resistant Staphylococcus aureus Mutation Plasmids Sequence Analysis DNA Staphylococcal Infections Swine Virulence Factors
TobEA
Kieron D Edwards, Aureliano Bombarely, Geraint W Story, Fraser Allen, Lukas A Mueller, Steve A Coates, Louise Jones
Jun 16, 2011
Enhanced Methylation Analysis by Recovery of Unsequenceable Fragments.
Gordon R McInroy, Dario Beraldi, Eun-Ang Raiber, Katarzyna Modrzynska, Pieter van Delft, Oliver Billker, Shankar Balasubramanian
Apr 07, 2016
A simple method for directional transcriptome sequencing using Illumina technology.
Nicholas J Croucher, Maria C Fookes, Timothy T Perkins, Daniel J Turner, Samuel B Marguerat, Thomas Keane, Michael A Quail, Miao He, Sammey Assefa, Jürg Bähler, Robert A Kingsley, Julian Parkhill, Stephen D Bentley, Gordon Dougan, Nicholas R Thomson
Sep 06, 2019
High-throughput sequencing of cDNA has been used to study eukaryotic transcription on a genome-wide scale to single base pair resolution. In order to compensate for the high ribonuclease activity in bacterial cells, we have...
Small RNA Sequencing
Identifying microRNA (miRNA) signatures in animal tissues is an essential first step in studies assessing post-transcriptional regulation of gene expression in health or disease. Small RNA sequencing (sRNA-Seq) is a...
Ultrasensitive amplicon barcoding for next-generation sequencing facilitating sequence error and amplification-bias correction.
Ibrahim Ahmed, Felicia A Tucci, Aure Aflalo, Kenneth GC Smith, Rachael JM Bashford-Rogers
Aug 17, 2020
The ability to accurately characterize DNA variant proportions using PCR amplification is key to many genetic studies, including studying tumor heterogeneity, 16S microbiome, viral and immune receptor sequencing. We develop a...
High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease.
Alan W Walker, Jeremy D Sanderson, Carol Churcher, Gareth C Parkes, Barry N Hudspith, Neil Rayment, Jonathan Brostoff, Julian Parkhill, Gordon Dougan, Liljana Petrovska
Sep 06, 2019
BACKGROUND: The gut microbiota is thought to play a key role in the development of the inflammatory bowel diseases Crohn's disease (CD) and ulcerative colitis (UC). Shifts in the composition of resident bacteria have been...
Nuclear RNA sequencing of the mouse erythroid cell transcriptome.
Jennifer A Mitchell, Ieuan Clay, David Umlauf, Chih-Yu Chen, Catherine A Moir, Christopher H Eskiw, Stefan Schoenfelder, Lyubomira Chakalova, Takashi Nagano, Peter Fraser
Jul 15, 2019
In addition to protein coding genes a substantial proportion of mammalian genomes are transcribed. However, most transcriptome studies investigate steady-state mRNA levels, ignoring a considerable fraction of the transcribed...
Animals Chromatin Immunoprecipitation Erythroid Cells Gene Expression Regulation Gene Library High-Throughput Nucleotide Sequencing Mice Protein Binding RNA Polymerase II RNA Long Noncoding RNA Nuclear Regulatory Sequences Nucleic Acid Reproducibility of Results Sequence Analysis RNA Transcription Genetic Transcriptome
Transcriptomic analysis of polyketide synthases in a highly ciguatoxic dinoflagellate, Gambierdiscus polynesiensis and low toxicity Gambierdiscus pacificus, from French Polynesia.
Frances M Van Dolah, Jeanine S Morey, Shard Milne, André Ung, Paul E Anderson, Mireille Chinain
Apr 15, 2020
Marine dinoflagellates produce a diversity of polyketide toxins that are accumulated in marine food webs and are responsible for a variety of seafood poisonings. Reef-associated dinoflagellates of the genus Gambierdiscus produce...
Split & mix assembly of DNA libraries for ultrahigh throughput on-bead screening of functional proteins.
Laurens Lindenburg, Tuomas Huovinen, Kayleigh van de Wiel, Michael Herger, Michael R Snaith, Florian Hollfelder
Apr 21, 2020
Enhancing the genome editing toolbox
Emmanouil Metzakopian, Alex Strong, Vivek Iyer, Alex Hodgkins, Konstantinos Tzelepis, Liliana Antunes, Mathias J Friedrich, Qiaohua Kang, Teresa Davidson, Jacob Lamberth, Christina Hoffmann, Gregory D Davis, George S Vassiliou, William C Skarnes, Allan Bradley
Oct 14, 2020
CRISPR-Cas9 technology has accelerated biological research becoming routine for many laboratories. It is rapidly replacing conventional gene editing techniques and has high utility for both genome-wide and gene-focussed...
Towards complete and error-free genome assemblies of all vertebrate species.
Arang Rhie, Shane A McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano-Silva, William Chow, Arkarachai Fungtammasan, Juwan Kim, Chul Lee, Byung June Ko, Mark Chaisson, Gregory L Gedman, Lindsey J Cantin, Francoise Thibaud-Nissen, Leanne Haggerty, Iliana Bista, Michelle Smith, Bettina Haase, Jacquelyn Mountcastle, Sylke Winkler, Sadye Paez, Jason Howard, Sonja C Vernes, Tanya M Lama, Frank Grutzner, Wesley C Warren, Christopher N Balakrishnan, Dave Burt, Julia M George, Matthew T Biegler, David Iorns, Andrew Digby, Daryl Eason, Bruce Robertson, Taylor Edwards, Mark Wilkinson, George Turner, Axel Meyer, Andreas F Kautt, Paolo Franchini, H William Detrich, Hannes Svardal, Maximilian Wagner, Gavin JP Naylor, Martin Pippel, Milan Malinsky, Mark Mooney, Maria Simbirsky, Brett T Hannigan, Trevor Pesout, Marlys Houck, Ann Misuraca, Sarah B Kingan, Richard Hall, Zev Kronenberg, Ivan Sović, Christopher Dunn, Zemin Ning, Alex Hastie, Joyce Lee, Siddarth Selvaraj, Richard E Green, Nicholas H Putnam, Ivo Gut, Jay Ghurye, Erik Garrison, Ying Sims, Joanna Collins, Sarah Pelan, James Torrance, Alan Tracey, Jonathan Wood, Robel E Dagnew, Dengfeng Guan, Sarah E London, David F Clayton, Claudio V Mello, Samantha R Friedrich, Peter V Lovell, Ekaterina Osipova, Farooq O Al-Ajli, Simona Secomandi, Heebal Kim, Constantina Theofanopoulou, Michael Hiller, Yang Zhou, Robert S Harris, Kateryna D Makova, Paul Medvedev, Jinna Hoffman, Patrick Masterson, Karen Clark, Fergal Martin, Kevin Howe, Paul Flicek, Brian P Walenz, Woori Kwak, Hiram Clawson, Mark Diekhans, Luis Nassar, Benedict Paten, Robert HS Kraus, Andrew J Crawford, M Thomas P Gilbert, Guojie Zhang, Byrappa Venkatesh, Robert W Murphy, Klaus-Peter Koepfli, Beth Shapiro, Warren E Johnson, Federica Di Palma, Tomas Marques-Bonet, Emma C Teeling, Tandy Warnow, Jennifer Marshall Graves, Oliver A Ryder, David Haussler, Stephen J O'Brien, Jonas Korlach, Harris A Lewin, Kerstin Howe, Eugene W Myers, Richard Durbin, Adam M Phillippy, Erich D Jarvis
Jul 05, 2021
High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial...
Paired rRNA-depleted and polyA-selected RNA sequencing data and supporting multi-omics data from human T cells.
Li Chen, Ruirui Yang, Tony Kwan, Chao Tang, Stephen Watt, Yiming Zhang, Guillaume Bourque, Bing Ge, Kate Downes, Mattia Frontini, Willem H Ouwehand, Jing-Wen Lin, Nicole Soranzo, Tomi Pastinen, Lu Chen
Nov 09, 2020
Defining multiplicity of vector uptake in transfected Plasmodium parasites.
Manuela Carrasquilla, Sophie Adjalley, Theo Sanderson, Alejandro Marin-Menendez, Rachael Coyle, Ruddy Montandon, Julian C Rayner, Alena Pance, Marcus CS Lee
Sep 09, 2020
The recurrent emergence of drug resistance in Plasmodium falciparum increases the urgency to genetically validate drug resistance mechanisms and identify new targets. Reverse genetics have facilitated genome-scale knockout...
An efficient method to assemble linear DNA templates for in vitro screening and selection systems.
A method is presented to assemble a gene of interest into a linear DNA template with all the components necessary for in vitro transcription and translation in approximately 90 min. Assembly is achieved using a coupled uracil...
The small RNA locus map for Chlamydomonas reinhardtii.
Small (s)RNAs play crucial roles in the regulation of gene expression and genome stability across eukaryotes where they direct epigenetic modifications, post-transcriptional gene silencing, and defense against both endogenous...
Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH).
Roy R Chaudhuri, Andrew G Allen, Paul J Owen, Gil Shalom, Karl Stone, Marcus Harrison, Timothy A Burgis, Michael Lockyer, Jorge Garcia-Lara, Simon J Foster, Stephen J Pleasance, Sarah E Peters, Duncan J Maskell, Ian G Charles
Jun 13, 2011
Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags.
Jan Gorodkin, Susanna Cirera, Jakob Hedegaard, Michael J Gilchrist, Frank Panitz, Claus Jørgensen, Karsten Scheibye-Knudsen, Troels Arvin, Steen Lumholdt, Milena Sawera, Trine Green, Bente J Nielsen, Jakob H Havgaard, Carina Rosenkilde, Jun Wang, Heng Li, Ruiqiang Li, Bin Liu, Songnian Hu, Wei Dong, Wei Li, Jun Yu, Jian Wang, Hans-Henrik Staefeldt, Rasmus Wernersson, Lone B Madsen, Bo Thomsen, Henrik Hornshøj, Zhan Bujie, Xuegang Wang, Xuefei Wang, Lars Bolund, Søren Brunak, Huanming Yang, Christian Bendixen, Merete Fredholm
Jun 17, 2011
ncRNAseq
Despite their abundance, mid-sized RNAs (30-300 nt) have not been extensively studied by high-throughput sequencing, mostly due to selective loss in library preparation. The authors propose simple and inexpensive modifications...
UMI-linked consensus sequencing enables phylogenetic analysis of directed evolution.
Paul Jannis Zurek, Philipp Knyphausen, Katharina Neufeld, Ahir Pushpanath, Florian Hollfelder
Oct 15, 2020
Biocatalysis Cloning Molecular Computational Biology Consensus Sequence Datasets as Topic Directed Molecular Evolution Enzyme Assays Epistasis Genetic Gene Library High-Throughput Nucleotide Sequencing High-Throughput Screening Assays Mutagenesis Mutation Oxidoreductases Acting on CH-NH Group Donors Phylogeny Protein Engineering Recombinant Proteins Software
The pharmaceutical solvent N-methyl-2-pyrollidone (NMP) attenuates inflammation through Krüppel-like factor 2 activation to reduce atherogenesis.
Marta Roche-Molina, Bryn Hardwick, Cristina Sanchez-Ramos, David Sanz-Rosa, Dirk Gewert, Francisco M Cruz, Andres Gonzalez-Guerra, Vicente Andres, Joaquin A Palma, Borja Ibanez, Grahame McKenzie, Juan A Bernal
Jul 28, 2021
N-methyl-2-pyrrolidone (NMP) is a versatile water-miscible polar aprotic solvent. It is used as a drug solubilizer and penetration enhancer in human and animal, yet its bioactivity properties remain elusive. Here, we report that...
Animals Anti-Inflammatory Agents Aorta Apoptosis Atherosclerosis Cell Adhesion Cell Line DNA Complementary Endothelial Cells Gene Expression Profiling Gene Library Human Umbilical Vein Endothelial Cells Humans Inflammation Kruppel-Like Transcription Factors Mice Mice Knockout ApoE Monocytes Pyrrolidinones RNA Small Interfering Solvents Tumor Necrosis Factor-alpha
The pig X and Y Chromosomes
Benjamin M Skinner, Carole A Sargent, Carol Churcher, Toby Hunt, Javier Herrero, Jane E Loveland, Matt Dunn, Sandra Louzada, Beiyuan Fu, William Chow, James Gilbert, Siobhan Austin-Guest, Kathryn Beal, Denise Carvalho-Silva, William Cheng, Daria Gordon, Darren Grafham, Matt Hardy, Jo Harley, Heidi Hauser, Philip Howden, Kerstin Howe, Kim Lachani, Peter JI Ellis, Daniel Kelly, Giselle Kerry, James Kerwin, Bee Ling Ng, Glen Threadgold, Thomas Wileman, Jonathan MD Wood, Fengtang Yang, Jen Harrow, Nabeel A Affara, Chris Tyler-Smith
Feb 09, 2016
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