We narrowed to 972 results for: REP

...a subset of the new plasmids and viral preps in the repository through our hot plasmids articles. These...to provide ready-to-use viral preps. Here are some of the new viral preps from recent months: Axon targeting...INTRSECT viral preps available! We are expanding our inventory of ready to use viral preps from the Deisseroth...pathways The CRISPR corner New ready-to-use viral preps Mapping antibody escape in SARS-CoV-2 by mutational...interest (Figure 3).   Figure 3: Schematic representation of the MPyV system. Image from Cheah et al....lineage tracing tool captures rare clones that represent 0.001% of the population.  Because indel generation...GCaMP8 vectors in serotypes AAV1 and AAV5. AAV9 preps and more AAV1 versions will be released soon. Visualize...

...through a repository, they remain accessible during these times. Centralized reagent repositories, also known...dedicated facilities and manpower that a repository provides. Repositories around the world facilitate the rapid...to be deposited into repositories, and financial support to maintain repositories’ capacity for storing... the scientific community can support repositories. Repositories are essential for the advancement of ...original sources. Figure 1: Biological repositories that distribute mouse strains, plasmids, cell...critical for pandemic research. Image from Reproducibility for Everyone. Case study 1: Cell lines Many...Culture Collection (ATCC) is a private, nonprofit repository for a variety of materials for life science research...

...brought issues in reproducible research to the forefront in the so-called “reproducibility crisis.” Results...after credible attempts to replicate major findings could not be replicated by other researchers.There...published research is difficult to replicate.  Why is replicating previous research findings so difficult...can be difficult to replicate. Unclear methods Until someone attempts to replicate the results of another...over the course of the Reproducibility Project: Cancer Biology, where reported methods may not include... registered reports, the gold standard for testing hypotheses Finally, Registered Reports combine all ...attention on the results instead of the methods. Unreported flexibility and questionable research practices...

...everyone who works in a lab struggles with reproducibility at some point. Usually it comes up when a researcher...decides on a new project and begins by trying to reproduce someone else’s result. Then, they hit trouble..... It won’t. When we hear about issues with reproducibility, time and time again, the problem comes down...students and postdocs sitting frustratedly in reproducibility jail and more effective collaboration to drive...Press journals, including Cell Metabolism, Cell Reports and Joule. In September 2017 she moved away from...blog Find more ways to make your research more reproducible Read all of our blog posts on scientific publishing...

...viral preps. Here are some of the new viral preps from recent months: New INTRSECT viral preps available...a subset of the new plasmids and viral preps in the repository through our hot plasmids articles. These...generate AID* tagged CRISPR knock-in repair constructs. These repair constructs can be used to integrate...available as a ready-to-use viral prep in AAV1!  New ready-to-use AAV prep from Hongkui Zeng's lab are available...recently contributed a set of plasmids to the repository that will help epigenetic researchers custom ...lab that enables simultaneous gene activation, repression, and editing with a single Cas9-VPR in Saccharomyces...cerevisiae. To control Cas9 activity and influence DNA repair pathways, Amit Choudhary's lab developed a chemogenetic...

...a subset of the new plasmids and viral preps in the repository through our hot plasmids articles. These...CRISPR–Cas9-based Dual-fluorescent DSB Repair) is a double-strand break repair assay for mammalian cells. It's...to provide ready-to-use viral preps. Here are some of the new viral preps from recent months: Expanded...INTRSECT viral preps from the Deisseroth Lab now available. Find all the Deisseroth viral preps here Coming...in a protein.    Cells expressing an RFP reporter plasmid for recombinase activity were exposed ...introduction & resolution of two DSBs in a fluorescent reporter. Find the plasmids here Yongsub Kim’s lab engineered.... Serotypes include AAV1, and AAV9. Find viral preps here pAAV-hSyn-Cre-P2A-dTomato is now available...

...much more about cellular DNA repair pathways. An emphasis on cellular repair post-CRISPR cleavage When I...just how complicated DNA repair pathways are. I fully admit to being a DNA repair newbie - diagrams of resection...patterns with ssDNA repair templates. Their work demonstrates that different repair template strategies...Blugene and I represented Addgene at the recent Keystone meeting on Precision Genome Editing with Programmable... to CRISPR nucleases, but with a session on DNA repair. What stuck most in my mind from that session were... complexity and challenges of homology directed repair (HDR) are echoed in the amount of interest in base... to #KSgenome and seeing the intricacies of DNA repair has emphasized how essential these studies are ...

...scientific articles, only 46% could be reproduced. In a recent Nature report from researchers at Amgen, it was... literature was reproducible by their groups. Finally results from the Reproducibility Project: Cancer...have shown similarly disappointing rates of reproducibility. These alarming results are due, at least in...the table in terms of data traceability and reproducibility of research. Electronic lab notebooks (ELNs...ELNs) are here to make lab work much more reproducible, convenient and effective, in both academic circles...through all saved data and automated writing of reports. To be able to understand the situation in depth...keep paper records as well as digital, or for reporting on a project – printing your data out can be required...

...fluorescent executioner caspase reporters. Several apoptosis reporters have been developed, such as the...transfer (FRET)-based executioner caspase reporters. In these reporters, the FRET pair is linked by a caspase...FlipCherry: Red fluorescence protease reporter To add to the fluorogenic reporter toolkit, the Shu Lab also designed...novel fluorogenic reporter that has a large dynamic range and high brightness. This reporter achieves approximately...fluorescence emission. FRET and fluorescence based reporters however have several limitations. First, FRET ...study apoptosis in vivo scientists need a protease reporter that has a large dynamic range and high brightness...Shu Lab from UCSF designed an improved apoptosis reporter, ZipGFP, which utilized the self-assembling split...

...sharing, computational reproducibility, and tools to enable scientific reproducibility. This workshop was ...practice and teach reproducibility An early milestone for the group was the “reproducibility for everyone” ...Scientific Reproducibility Read a blog post on Unique and persistent IDs for improved reproducibility Other...Other resources: Reproducibility for Everyone website How-to-guide for Reproducibility workshops Levelling...protocols.io, organized a panel to discuss reproducibility issues in research. But he realized that it... enough to discuss the age-old problem of irreproducibility in science or even to discuss potential solutions...be an actionable way to tackle widespread irreproducibility. Luckily, there were other academics and like-minded...

...performed using the transfer plasmid, a plasmid encoding Rep and serotype-specific Cap genes, and a plasmid encoding...order to generate high quality preparations. After production, all virus preps are titered and subjected to... containing) AAV particles within representative vector preparations was quantified with electron microscopy...typically prepared using endotoxin-free plasmid purification kits. Resources Browse lentiviral preps available...encoding adenoviral helper sequences. AAV preparations are purified by iodixanol gradient ultracentrifugation...purity and titers adequate for in vivo studies. Preparations are then aliquoted and stored at -80 °C. Titer...on viral genomes isolated from the final AAV preparation. Sequencing results are analyzed to confirm the...

...real time, but each of these reporters has its drawbacks. Acoustic reporter genes (ARGs) overcome these...existing bacterial reporters Limited Depth of Signal/Imaging: Fluorescent reporters are not as well suited...fluorescent or bioluminescent reporters usually only detects the signal of the reporter and fail to pinpoint what...signal is coming from.   Acoustic reporter genes (ARGs) Acoustic Reporter Genes (ARGs) are engineered gene...imaging tools The luciferase reporter gene The green fluorescent protein reporter gene Resources on Addgene.org... researchers have developed in vivo bacterial reporters that use fluorophores and luciferases to track...these limitations by using gas vesicle reporters that are detectable by an inexpensive and widely available...

...demonstrated how CRISPR nickases improve homology directed repair rates, and share their design rules for your next...design.  Exploring nickases for homology directed repair The potential benefit of using nickases for HDR...targeting range: using an individual gRNA with WT Cas9, repair levels decrease rapidly 10 bp from the cut site...create a staggered cut - could this system mediate repair throughout the entire region between the nicks?...spots between the nick sites, they observed >20% repair (max 27%) across the 51 nt region using either ... sites tested by a wide margin, exhibiting >20% repair efficiency. Clearly, a nickase strategy can expand...the Addgene Blog Learn about Homology Directed Repair 3 Tips to Improve HDR Efficiency How to Design ...

...Not all plasmid preps are the same. Before purifying a plasmid from a bacterial culture, it is important... on these premises we can classify a plasmid preparation in 3 different ways: Transformation grade DNA...and flawless cloning it is important that the preparation is pure from other nucleic acids (genomic DNA...DNA for each reaction. As a consequence, the preparations for this technique must be larger scale, to ...decide what will be the optimal type of plasmid preparation in terms of quantity and purity.  Additional...

...sending the phages to the clinicians. Creating a repository of phage data and information Since the inception... their role in the phage community by being a repository of phage data and information. “We want to be...particular phage researcher may only know how to prepare phage for one application but not another or they...Directory have the resources or know what it takes to prepare phages for clinical use. There are also different...

...What are Acoustic Reporter Genes (ARGs)? Fluorescent and bioluminescent reporter genes are widely used... to study gene expression in cells. But these reporters have limited use in vivo because they are based...expression in vivo.  But what ultrasound lacked was reporter genes that could produce ultrasound contrast. ...our lab - the Shapiro Lab - developed Acoustic Reporter Genes (ARGs), which are sets of genes that, when...promoter pBAD and a low-copy number origin of replication (p15A) worked best under a wide range of inducer...5202–5209 (2017). Bourdeau, R. W. et al. Acoustic reporter genes for noninvasive imaging of microorganisms... Hurt, R. C. et al. Genomically mined acoustic reporter genes for real-time in vivo monitoring of tumors...

...lab team takes over and prepares the sample for entry into Addgene’s repository. For long-term storage ...The lab prepares bacterial glycerol stocks on Fridays. From each overnight culture, we prepare three sets...sent from depositors, bacterial glycerol stocks, prepped DNA ready for our quality control processes - all...missing so that we can make a new tube from a replicate sample. The transformation After the DNA has ...plasmid can grow. As the bacteria divide, they replicate and retain the plasmid. This allows us to make...is contaminated. We use filtered pipet tips and prepare fresh media with antibiotics at each stage. The...Addgene Get help with plasmid transformation, preparation, and analysis from our protocols and molecular...

...following sucrose treatment. Moreover, several reports have shown that cells treated with sucrose or other...downstream applications scientists rely on our AAV preparations for, we wanted to be certain that this supplementation...the purity or infectivity of the final viral preparation. Through sugar detection assays, in vitro transduction...between the untreated and sucrose treated viral preparations.    Despite observing a positive effect on our...

... Figure 4: Reporters in Gene On include a mScarlet reporter, luciferase reporter, and neomycin resistance... editing. eGFP reporters for single base editing by APOBEC-Cas9 Though the ACE reporter quantifies APOBEC-Cas9...DSB in their previous reporter, the Harris Lab created a panel of eGFP reporters to quantify the on-target...editing reporters. Image from St. Martin et al., 2019. The Harris lab used these eGFP reporters to analyze...Transient reporter for editing enrichment (TREE) The Wang and Brafman lab developed a transient reporter for...cells segregated solely by a reporter of transfection, which only report the efficiency of plasmid delivery... functional reporter system to identify and enrich for base-editing activity The reporters mentioned above...

...you out. What is the Open Repository of CRISPR Screens? The Open Repository of CRISPR Screens (ORCS) database...This post was contributed by the Open Repository of CRISPR Screens. Imagine you’ve just discovered that...research. Fortunately, there’s a growing open repository of CRISPR screen data that might be able to help... resource developed by the Biological General Repository for Interaction Datasets (BioGRID) in order to...biologists. Figure 1: The BioGRID Open Repository of CRISPR Screens (ORCS) homepage. Screenshot...Screenshot updated 2024.   Using the Open Repository of CRISPR Screens BioGRID ORCS currently houses over ...also captured as metadata.   Screen results are reported as the original quantitative gene-level scores...