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We narrowed to 704 results for: des.1

Showing: 561 - 580 of 704 results

  1. Plasmids 101: NGS Quality Control for Pooled Libraries

    Type
    Blog Post
    ...can also rank the plasmids by abundance, scaled to 1, to create a “cumulative wealth distribution” curve...next-generation sequencing (NGS). For gRNA libraries, you’ll design primers to create 200-300 bp sequencing products...

  2. The Importance of High Titer for AAV Transductions

    Type
    Blog Post
    ...methods to improve AAV production.     References 1.Clark, K. Reed. "Recent advances in recombinant adeno-associated...if you end up concentrating your AAV above your desired titer and want to dilute it, err on the side of...less buffer than you would to achieve the exact desired concentration to avoid over-diluting, and make ...

  3. Visualizing Genomic Loci with CRISPR-Sirius

    Type
    Blog Post
    ...loci in the genome and the guides are relatively unstable.   Figure 1: CRISPRainbow labeling. Two... the gRNA tetraloop and went through subsequent design iterations to increase stability and minimize misfolding...

  4. DAP arrays for multiplex gene editing

    Type
    Blog Post
    ... genes with a single viral vector.   Fig. 1: Schematic of multiplex gene editing with DAP array...The natural CRISPR locus of a bacteria host encodes multiple guide RNAs (gRNAs) on a single array to ...applications, we provide detailed manual and online design examples of using Addgene plasmids hCtRNA_FT (#186715...

  5. Hot Plasmids - January 2023

    Type
    Blog Post
    ...as an endogenous RNA imaging tool.   Fig. 1: Csm, shRNA, and Cas13 were compared head-to-head ...effects, both of happen with Cas13. CRISPR-Csm degrades both nuclear and cytoplasmic mRNA with 90-99% ...crystalizing the hfYFP structure, the group rationally designed GFP variants with similar capabilities. If you...

  6. Four Factors that Differentiate the Stem Cell Field

    Type
    Blog Post
    ...regarding what makes this group of researchers special: 1. Stem cell scientists care deeply about ethics Ethics...speakers from top minds in the stem cell field have described the Yamanaka paper as "life changing". Dr. Yamanaka...affordable. 4. Stem cell scientists are generous Besides some of the scientists I've already mentioned, ...

  7. Antibodies 101: Flow Cytometry Controls

    Type
    Blog Post
    ...settings with experimental samples. Figure 1: Example flow plots for a single color control. A)...familiar with the basics of controls in experimental design, you’ll need a few controls specific to flow as...controls like FMO or isotype controls, which we’ll describe a bit later. Single Colors Single color controls...

  8. Will You Be My Mentor? Finding and Asking for Mentoring Support

    Type
    Blog Post
    ...Networking 101-Building Relationships for Success”. Choose 1-2 tactics to try. One of my favorites is making the...mentoring questions I set out to answer. First, I will describe some of the many ways you can approach finding...Watch for my upcoming mentoring post in which I describe how to organize a successful peer mentoring circle...

  9. CasPEDIA: A Functional Classification of Cas Enzymes

    Type
    Blog Post
    ...and CasPEDIA have got you covered!     Fig. 1 – CasPEDIA Cas ID display information for a given ... is also documented. Experimental design When you are in the design phase of your experimental planning...CasPEDIA is an online, searchable resource that provides summary information on Class 2 Cas enzymes. The...The information is organized in wiki format and includes biochemical properties, previously established...relevant resources The homepage displays a graphic describing CasIDs and relevant properties of Cas enzymes...What other RNA components are required? CasPEDIA provides information on crRNA and tracrRNA requirements... also show you how multiplexed arrays would be designed, if that’s your end goal. CasPEDIA also features...

  10. Fluorescent CRISPR Reporters: SRIRACCHA and GEmCherry2

    Type
    Blog Post
    ...into the genome of mammalian cells.  Figure 1: The SRIRACCHA reporter construct. Image from Wen ...created SRIRACCHA in 2017 to enrich and identify desired CRISPR mutants (Wen et al., 2018). SRIRACCHA uses...constructs for the reporter to work and to make the desired genome edit:  A donor plasmid that contains a ...OH-T and doxycycline. A gRNA that targets your desired gene (whose sequence is also found in the reporter...well. The ratio of RFP to GFP expressing cells provides a real-time read out of Cas9 activity.  By using...integrated GFP reporter leaving you with just your desired genomic edit.  Find SRIRACCHA plasmids at Addgene...DSB is repaired by NHEJ which depending on the nucleotides inserted or deleted, can result in an in-frame...

  11. Antibody Guide

    Type
    Guide
    ...and placed in a buffer. Antibody Structure Figure 1: Structure of an antibody A standard antibody is made... together to form a “Y” shape, as shown in Figure 1. The two arms of the Y structure are responsible for... is described in more detail in the Multiplex Assays section below. The following table describes the ... Science Guides Antibody Guide Antibody Guide View Addgene's Antibody...of B cells isolated from animals immunized as described above are used to create hybridomas, which produce...each antibody has two binding sites. Isotype Description Configuration and Valency Subclasses IgA Prevalent... used to quantify relative amounts of protein. Includes: Western blot ELISA Capture - used to isolate ...

  12. Choosing a CRISPR Nuclease: Site Accessibility, Specificity, and Sensitivity

    Type
    Blog Post
    ...sites that were previously unavailable. Figure 1: The PAM sequence that the Cas nuclease recognizes...Requirement and Expanding CRISPR Beyond SpCas9 described the PAM specificity of Cas9s isolated from different..., and NGCG). Since then, the Osamu Nureki Lab described a rationally engineered Cas9, SpCas9-NG, which...Nishimasu et al., 2018). The David Liu Lab similarly described xCas9, which displayed the ability to target multiple... also high off-target activity, which may be undesirable in many applications. At the time of our first...post on choosing a Cas9, the Feng Zhang Lab had described eSpCas9, while the Keith Joung Lab had developed...

  13. Sharing is Caring: But How to Distribute Open Hardware?

    Type
    Blog Post
    ...accessible to practically everyone.     Fig. 1: Open source hardware builds   Since I started...provide the construction plans or CAD (computer aided design) drawings of their devices, which makes it very...has allowed the community to regularly replicate designs worldwide. Distributing hardware via globally established...similar way to the biological protocol, and assembly designs based around the use of commercially available ...users outside the project to modify the raw and design files, allowing the device to take on a community-driven...of work from universities and research centers provides a potential conflict between traditional IP-based...

  14. How to Keep a Lab Notebook for Bioinformatic Analyses

    Type
    Blog Post
    ...the output of the analysis performed in experiment 1. Use camelCase: In camelCase, each subsequent word...instance, your Desktop directory contains the folders and files that you see on your desktop. The location...immediately write a text document with a brief description of the directory contents, at a minimum. This...for a single use, save the script as originalName_descriptionOfEdit in the same directory where it was ...Your Next Experiment Find Our List of CRISPR gRNA Design Tools ...

  15. Pooled CRISPR Libraries Offer Genome-Wide Control for Large-Scale Functional Screens

    Type
    Blog Post
    ...endogenous genes and it consists of three components: 1. A nucleolytically inactive Cas9-VP64 fusion; 2. A...first generation of CRISPR-Cas9 plasmids were not designed with gene activation in mind. “We had not managed...Konermann and her colleagues in Feng Zhang’s lab describe just such a system, which they call CRISPR/Cas9...from the structure to guide and improve activator design,” she said. “Before it was a little like tapping...instead of at the protein’s C terminus. With that new design in place, Konermann immediately saw an order of...consistency and validation with >80% effectively enriched guides per gene hit, and 100% validation of the top 10...

  16. Summer SciComm: Preprints

    Type
    Blog Post
    ...medRxiv.org) in the past few years.   Figure 1: Stand aside, CERN — it's a new age of accelerating...been common in fields like math and physics for decades (see: arXiv.org), but have been only adopted by...course, preprints don’t replace journals and other modes of scientific communication. Researchers often post...to receive deposits of plasmids that have been described in a preprint. In fact, over 1,500 plasmids in...Depositing plasmids that were used in a preprint provides all the same benefits as sharing those plasmids...resources on the Addgene blog Summer SciComm Series: Modes of Communication Intro to Our Summer SciComm Series...

  17. Cas13d: Small RNA-targeting CRISPR enzymes for transcriptome engineering

    Type
    Blog Post
    ... Effectors.” Cell (2018) pii: S0092-8674(18)30207-1. PubMed PMID: 29551272 Plasmids from this paper ...New work from Konermann et al. and Yan et al. describes new Cas13d enzymes that average only 2.8 kb in...Like other Cas13 enzymes, the Cas13d orthologs described in these papers can independently process their... high targeting efficiency, both of which are described below. Yan et al.: WYL-domain-containing accessory...produced very similar cleavage products even when guides were tiled across a target RNA, indicating that...

  18. CRISPR Methods for Bacteria: Genome Engineering, CRISPRa, CRISPRi, Base Editing, and More

    Type
    Blog Post
    ...Streptomyces (Cobb et al., 2015). pCRISPomyces-1 includes Cas9, a tracrRNA, and a CRISPR array, while pCRISPomyces...INTEGRATE consists of four major components including (1) a CRISPR RNA, (2) four proteins forming the QCascade...Marraffini’s lab took advantage of this lethality to design the first synthetic bacterial CRISPR system in ...gRNA cassette for plasmid curing through "self-destruction" after induction with L-rhamnose and aTet. CRMAGE...citrea scarless editing plasmids Sheng Yang’s lab describes a two-plasmid system that combines recombineering...editing efficiency, perhaps due to its condensed design. For both systems, custom spacers/gRNAs are easily...et al., 2013), the Qi lab employed a gRNA-based design more familiar to those using CRISPR in eukaryotes...

  19. Improving Transduction Efficiency with Exosome AAVs

    Type
    Blog Post
    ...vector-exosomes), exosome AAVs, or exo-AAVs (Figure 1). The researchers discovered that these particles ...producer cells and purification protocols often describe a process that begins with cell lysis to release...

  20. Using CRISPR/Cas9 to Edit Disease Out of the Genome

    Type
    Blog Post
    ...through the use of nanoparticles. [6].    References 1. Zhang B. 2021. “CRISPR/Cas gene therapy.” Journal...ability to influence editing efficiency. In 2022, despite the increasing effectiveness of CRISPR/Cas9, scientists...
Showing: 561 - 580 of 704 results