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We narrowed to 522 results for: des.2

Showing: 181 - 200 of 522 results

  1. Design Tips for Prime Editing

    Type
    Blog Post
    Published
    Jan. 23, 2025, 2:15 p.m.
    ...inhibit editing (Anzalone et al., 2019). Figure 2: Starting lengths for optimizing your pegRNA primer...great tips to guide your experimental design, especially the design of the RNA sequences you’ll use in prime...principles pegRNA design If you’re just starting out with prime editing, you’ll need to design and optimize...reverse transcriptase (RT) template including the desired edit. Figure 1: Prime Editing schematic.... be edited and the sequence of the edit, so its design changes for every new prime editing application...transcriptase template, starting with about 10–16 nucleotides. For longer templates, it is even more important...and PE5b: In this approach, the nicking sgRNA is designed to bind only after the edit is installed. This...

  2. Hot Plasmids: Summer 2025

    Type
    Blog Post
    Published
    Aug. 28, 2025, 1:15 p.m.
    ...RNA guide (known as an omega RNA, or ωRNA) (Figure 2), but TnpB is small enough to be carried by viral ...than a third of the size of Cas9). Figure 2: Comparison of TnpB (A) and Cas9 (B) genome editors...Figure 5: Mechanism of ATLASCre. VAMP2 = synaptobrevin 2; At = ALFA-tag; BACE = β-secretase; AF = AMPA.FingR...., 2025). By co-delivering TRV1 with TRV2 that encodes ISYmu1 and an ωRNA under the same promoter, they...different applications require careful selection or design to ensure reliable readout and avoid biases. The...ex vivo HSC expansion cultures. A) Experimental design. B) UMAP of cell states in ex vivo expansion cultures...only at excitatory synapses; however, its modular design allows components to be swapped out, potentially...

  3. Deep Dive: qPCR

    Type
    Blog Post
    Published
    Sept. 29, 2022, 1:15 p.m.
    ...indicating primer dimers. (c) A double peak indicating 2 amplicons. Image credits (respectively): Zuzanna K...details for reproducibility’s sake!   Fig. 2: Setting up triplicates in multiple configurations...used method is the Standard Curve method. See Table 2, (adapted from Wong, 2018) for a comparison of different...Statistically defined log-linear phase   Table 2: A comparison of different qPCR analysis methods. ... for RNA quantitation. Biotechniques. 2000 Aug;29(2):332-7. doi: 10.2144/00292rv02. PMID: 10948434.Taylor...from Wong, 2018   Primers Design of primers and probes Primer design, of course, could easily be its...useful primer design resources in the References and Resource section. Validation Once designed, your primer...

  4. The AAVantages of AAV in CRISPR Screens

    Type
    Blog Post
    Published
    Feb. 4, 2025, 2:15 p.m.
    ...handled at BSL-1, while lentivirus requires a BSL-2 setup. This requires a less involved setup when working...infection rates in your experiment. Figure 2: Visual representation of common AAV serotypes used..., 10(1). https://doi.org/10.1038/s41467-019-12449-2 Pupo, A., Fernández, A., Low, S. H., François, A.,... This vastly increases the possibilities when designing screens. Each serotype has its own tropism, or...experiment. Additional considerations One of the downsides to using AAV is the limited packaging capacity...Adames, A. C., Saur, D., & Rad, R. (2022). Tutorial: design and execution of CRISPR in vivo screens. Nature...

  5. Plasmids 101: Protein tags

    Type
    Blog Post
    Published
    Dec. 11, 2014, 4:26 p.m.
    ...(you generally don’t want more tag than protein), 2-3 tags is increasingly common. Tandem affinity purification...TEV cleavage site (more on that in a moment), and 2 ProtA IgG-binding domains. TAP has since come to encompass...found in this paper (available at Addgene).   Table 2: Protease recognition sites commonly used with tags... Protein tags are usually smallish peptides incorporated into a translated protein. As depicted in the...depending on their protein of interest. After several decades of trying to address these challenges, researchers...examples. The tables list more common tags than are described in the post, but have been categorized to help...

  6. Comparing Cas9 to NgAgo: Can the Argonautes Best CRISPR?

    Type
    Blog Post
    Published
    June 9, 2016, 2:30 p.m.
    ...Epub 2016 May 2. PubMed PMID: 27136078. Find plasmids from this publication at Addgene. 2. Swarts, Daan...DNA guides NgAgo uses 5’ phosphorylated DNA guides (so called “gDNAs”) rather than the RNA guides employed...24 base DNA guides may be more user-friendly, since they can be ordered as oligonucleotides and should ...gDNA guides will also need to be transfected into the cells of interest. In contrast, RNA guides must ...important role in RNA interference, binding RNA guides to cleave foreign RNA. Argonaute proteins are also...cleave DNA in vitro, directed by phosphorylated DNA guides. Unfortunately, Swarts et al. were unable to show...NgAgo preferred certain guide sequences - using 5 guides/gene for 10 genes, they did not observe differences...

  7. CRISPR 101: Anti-CRISPR Proteins Switch Off CRISPR-Cas Systems

    Type
    Blog Post
    Published
    July 23, 2020, 1:20 p.m.
    ...base pair to another base pair at a specific site. 2. Temporal, spatial, or conditional control of CRISPR...difficult-to-engineer Sulfolobus islandicus rod-shaped virus 2 (Mayo-Muñoz et al., 2018). Only viral particles that...Editing of Sulfolobus islandicus Rod-Shaped Virus 2. Viruses 10:695 . https://doi.org/10.3390/v10120695.../35++ Adenovirus Vector Expressing Anti-CRISPR Peptides Decreases CRISPR/Cas9 Toxicity in Human Hematopoietic...

  8. Cloning Mammalian Cells with the Agarose Method

    Type
    Blog Post
    Published
    Sept. 7, 2017, 12:17 p.m.
    ...3 plates at different densities for selection). A 2% agarose solution is then melted (and thereby sterilized...96-well assay plate. We generally freeze at least 2 ampules each of 4 clones with different levels of ...of agarose, which is then overlaid with the firmer 2% agarose gel solution discussed above for picking....investigators to identify specific clones with desirable properties, either initially, or using secondary...

  9. Antibodies 101: Flow Compensation

    Type
    Blog Post
    Published
    May 16, 2024, 1:15 p.m.
    .... Let's look at an experimental example in Figure 2. Figure 2A shows the sample prior to compensation.... line with the other populations.   Figure 2: Compensation example based on experimental sample..., you will see the populations move, as in Figure 2, following compensation. Figure 3: Flow plot...This will make it difficult to properly gate your desired cell population. By compensating between fluorescent...

  10. Neuronal labeling with Spaghetti Monster

    Type
    Blog Post
    Published
    Aug. 14, 2018, 12:42 p.m.
    ...experiment using smFPs and standard neuronal tracers. 2. Visualization of neuronal sub-cellular structures...similar proteins. For example, N-cadherin (cadherin-2) is a postsynaptic cell adhesion protein that plays...PMID: 25915120. PubMed Central PMCID: PMC4573404. 2. Shepherd, G.M. (2004). In "The synaptic organization...map these neuronal networks. For almost three decades, recombinant Adeno-associated virus (AAV) has been...symbol of opposition to the teaching of intelligent design in public schools and was started in 2005 in Kansas...

  11. Avoiding the Dark Side of Fluorescent Protein Fusions with mOX FPs

    Type
    Blog Post
    Published
    Oct. 27, 2015, 3 p.m.
    ...properly exiting the ER and fluorescing (see Figure 2) [5].  When using FPs containing two cysteine residues...compartments including the secretory pathway (Figure 2), the inner membrane space of mitochondria and chloroplasts...PMID: 18228466. Pubmed Central PMCID: PMC2875081. 2. Snapp, Erik Lee. "Fluorescent proteins: a cell biologist's... live cells in real time. Previously, we have described a number of practical considerations that should... herpesvirus.       References 1. Snapp, Erik. "Design and use of fluorescent fusion proteins in cell ...

  12. Tips from the Repository Trenches: Using Barcodes to Track Samples

    Type
    Blog Post
    Published
    Oct. 6, 2015, 2:30 p.m.
    ...that numbers are not switched around or misread.  2. Track the container - It is just as important to ...all of these samples have the 2D barcodes mentioned above. These barcodes identify what type of sample is...tubes. 1D barcodes are better for tubes that are meant to be read one at a time. 1D barcodes can be purchased...the tubes’ physical location in the lab. These barcodes additionally allow us to store multiple types ...fresh media with antibiotics at each stage. The barcodes and LIMS help us track each sample, but we also... a petri dish plate that is also barcoded. The barcodes on both of these are scanned into our LIMS system...samples within your lab, we highly recommend using barcodes! Barcoded tubes are easily accessible and can ...

  13. Mapping the 4D nucleome with CRISPR/Cas9

    Type
    Blog Post
    Published
    Aug. 11, 2015, 2:30 p.m.
    ...resolved loci with physical map distances of 75 and 2 Mbp, with the calculated fluorescent distances correlating...established physical map. In comparing pairs of targets ~2 Mbp apart, they noticed that they could evaluate the...PAM sequences required by each ortholog, a gRNA designed for one dCas9 should be specific to that ortholog...

  14. Selecting Your Plasmid Purification Kit

    Type
    Blog Post
    Published
    May 27, 2025, 1:15 p.m.
    ...all specifically designed with environmental sustainability in mind (Table 2). Table 2: Sustainability ..., or beads) are designed to work together — no mixing and matching!   Figure 2: Plasmid isolation...debris”; and then clean-up the plasmid DNA (Figure 2). For most kits, the steps for lysing cells and removing...high quality DNA. Figure 1 illustrates the three grades of DNA you may need based on their relative quality...bacterial culture. Plasmid purification kits are designed to accommodate specific volume ranges of culture...column-based miniprep kit for example. These kits are designed to handle ~1–5 mL of liquid culture. Using a higher.... To help combat this, some manufacturers have designed eco-friendly DNA purification kits by reducing...

  15. Twenty Years of Sharing: Expanding Accessibility

    Type
    Blog Post
    Published
    Nov. 21, 2024, 10:47 p.m.
    ...China, Korea, Japan, Brazil, India, and Mexico. Table 2: Addgene distributors Distributor Partnership...distribution after we partnered with them (Figure 2). In others, the distributor helped solve an issue...temperature for the duration of their journey. Figure 2: Annual distribution of items to countries with a ...shipping. However, there were issues that persisted despite our best efforts. With a little over half of our...packages navigated customs and arrived at their destination in a timely manner and at the correct temperature...for their experiment.     Table 1: Most popular guides, protocols, and collections of 2023. Educational...Educational Resource Top Five by Views Guides CRISPR Guide Lentiviral Guide AAV Guide Optogenetics...

  16. Filming Science Videos in the Age of Social Distancing

    Type
    Blog Post
    Published
    May 20, 2021, 1:15 p.m.
    ... Figure 2: Ironing boards. Good as a WFH desk, and as a video control center.   Cycle 2: Zooming ...ironing board, giving it the perfect height (Fig. 2). We recorded video using a simple, external video... So, much like SynBio, it was time to start our Design-Build-Test-Learn cycles. If you’re not familiar...again. Here’s that process!   Figure 1: The Design-Build-Test-Learn cycle adapted for video making...through. I know cameras, but we needed someone else. Design: Jennifer thankfully volunteered, and we decided...Zooming Forward Design: We produced a video celebrating Massachusetts Nonprofit Day, which was the perfect opportunity...here, the operator is in a different room.   Design: The previous cycle made me realize we needed to...

  17. Hot Plasmids: Winter 2025

    Type
    Blog Post
    Published
    March 11, 2025, 1:15 p.m.
    ...resistance to the herbicide chlorsulfuron (Homo line 2) or wild type (WT), two weeks after herbicide was ... CLIPf tag and a C-terminal SNAPf tag; see Figure 2), the authors developed a cost-effective expression... when associated with microtubules. Figure 2: CLIP-SNAP fusion proteins for single-molecule FRET...Optimized dicot prime editing enables heritable desired edits in tomato and Arabidopsis. Nature Plants,...

  18. Production of Virus in Insect Versus Mammalian Cells

    Type
    Blog Post
    Published
    Nov. 5, 2024, 8:32 p.m.
    ...) 38 kb Cells HEK-293T Sf9 Time to collection 2–4 days 5–10 days Purification Ultracentrifugation...Centrifugation Titration time ~1 day (AAV); ~1 week (lenti) 2–10 days Initial titers Higher Lower Resources... a factory to produce adeno-associated virus type 2 vectors. Human Gene Therapy, 13(16), 1935–43. https... (about three to four days), this second round provides the added benefit of producing a stock P1 virus...

  19. Droplet Digital PCR for AAV Quantitation

    Type
    Blog Post
    Published
    Jan. 16, 2020, 2:18 p.m.
    ... qPCR is that the results can vary by a factor of 2. This means that if you set up two identical assays...amplitude measured for each droplet in each well (Figure 2). A clean ddPCR should have a clear separation between...as low as 1C/s. Increasing the elongation time to 2 minutes and the denaturation time to 1 minute has ... to a new plate containing the mastermix which includes primers and a ddPCR supermix. Note that the supermix...

  20. Tips for CRISPR Gene Editing in Mice

    Type
    Blog Post
    Published
    June 28, 2016, 10:59 a.m.
    ... than control, 3; same as control (Cetn1/sgRNA1), 2; darker than control, 1; very dark). Brighter fluorescence...you can hold off on genotyping until the pups are 2-4 weeks old and use the ear tag method (creating different...PMID: 24253446. PubMed Central PMCID: PMC3875854. 2. Mashiko, Daisuke, et al. "Generation of mutant mice... screen them for your desired edit. Good news! Remember the primers you designed to generate your pCAG-EGXXFP...CRISPR/Cas9 system floating around, and many pre-designed plasmids containing these variants ready for purchase...that do it for you. One such option is the CRISPR Design tool supplied by the Zhang lab. This simple website... and cons of using many different types of gRNA design software. When you are happy with your selection...
Showing: 181 - 200 of 522 results