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We narrowed to 839 results for: genome

Showing: 181 - 200 of 839 results

  1. Plasmids for Endogenous Gene Tagging in Human Cells

    Type
    Blog Post
    ...in the genome near either the beginning or end of the gene of interest —in our case in the genome of an...inserting large tags into a precise location in the genome is still inefficient, particularly in human cell...plasmids work and to discover more resources for your genomic tagging experiments. Browse the Allen Institute...an hiPS cell. While the majority of the time the genome will attempt to repair itself without outside influence...make your own, will make it easier for you to use genomic tagging in your experiments. Many thanks to our...

  2. CRISPR 101: Validating Your Genome Edit

    Type
    Blog Post
    ...quantitatively assess genome edits in your target sequence and other regions of the genome. The main advantage...with Cas9. Hooray! Now it’s time to make sure your genome edits went according to plan. In this blog post...insertions and deletions identified within a given genomic window, along with the estimated editing frequency...must generate a DNA molecule with homology to your genome edit to mimic what an edited sequence would look...sequencing, provided you have some idea of where in the genome you might expect off target editing to occur. Luckily...Bas van Steensel. Easy quantitative assessment of genome editing by sequence trace decomposition. (2014)...silico off-target site identification for CRISPR genome editing. (2019) Bioinformatics 36:2001–2008. https...

  3. Viral Vectors 101: An Introduction to AAV

    Type
    Blog Post
    ...the ssAAV genome has a mutation in the terminal resolution site (TRS) to form a vector genome with wild-type... non-pathogenic, do not integrate into the host genome, and can be specifically targeted to a number of... expression in a particular cell type to CRISPR genome editing, optogenetics, and chemogenetics experiments... of interest, AAVs used in research have their genomes “gutted”, meaning that all viral genes except ITRs...Remember that AAVs do not integrate into the host genome and therefore the transduced gene is episomal and...self-complementary AAV (scAAV) vector. Full-length ssAAV vector genome of both polarities are rescued from the vector ...individually packaged into the AAV capsids. As a genome conversion in the transduced cell nucleus, the ...

  4. Cre-ating New Methods for Site-specific Recombination in Drosophila

    Type
    Blog Post
    ...s004270100167. PubMed. Cryptic loxP sites in mammalian genomes: genome-wide distribution and relevance for the efficiency...system. Gerald Rubin’s lab sought to make complex genome modifications in Drosophila using multiple recombinases...recombinases. To make multiple, precise genome edits, the recombinases used must have high activity and ...recombinases. These tools should further enhance genome editing capabilities in Drosophila. References...site-specific recombinases for use in manipulating animal genomes. Nern A, Pfeiffer BD, Svoboda K, Rubin GM. Proc...

  5. Tag Your Favorite Yeast Genes with Ease

    Type
    Blog Post
    ... your experience with yeast genome modifications. In what ways have genome tagging systems enabled you...process by which nearly all domains of life repair genomic damage, specifically double strand breaks. Researchers...natural process to integrate protein tags into the genomes of S. cerevisiae and S. pombe. The protocol is ...have deposited a large collection of plasmids for genome modification in yeast developed by Dr. Pringle’...modular collection of plasmids for a wide variety of genome modifications in S. Pombe, including full and partial...

  6. The Advances Behind The World's First Personalized CRISPR Treatment

    Type
    Blog Post
    ...sites in the genome, they also have a higher risk of off-target editing and longer genome search times... a larger scale, too. The first paper reporting genome editing by CRISPR in mammalian cells appeared in...can fix any problematic C or A mutations in the genome. Off-target effects, editing efficiency, and target...Marraffini, L. A., & Zhang, F. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science (...2017). Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature, 551(7681), 464...2016). Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature... N., & Kleinstiver, B. P. (2020). Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9...

  7. CRISPR 101: Off-Target Effects

    Type
    Blog Post
    ...mechanisms. The RNA guide is typically 20 nts and the genomic locus must often be proximal to a PAM site for ...gRNA with low sequence similarity elsewhere in the genome. There are many predictive online tools which can...gRNA with low sequence similarity elsewhere in the genome to reduce off-targets, it is time to consider your...Even if there are similar sequences present in the genome, certain Cas enzymes are less compatible with the...several options to quantify these events. Whole genome sequencing The only way to quantify off-target ...off-target effects entirely is to perform whole genome sequencing. While this may be unnecessary for many applications...gRNA which doesn’t perfectly match any site in the genome. While this may effectively serve as a transfection...

  8. What's New in CRISPR - December 2019

    Type
    Blog Post
    ...for the Application of Neuronal Genome Editing) mediates targeted genomic integration of fluorescent tags... editors, which decrease the rate of off-target genome edits compared to rat APOBEC1. Now, they’ve engineered... developed a CRISPR-based toolkit for targeted genomic integration of fluorescent tags in neurons. Their...

  9. CRISPR Antimicrobials

    Type
    Blog Post
    ...CRISPR-induced double-stranded break (DSB) in the genome is lethal. If this DSB occurs on a plasmid, the...encoded by a high-copy plasmid. In the case of the genomically encoded quinolone resistance, mediated by a single...vectors carry CRISPR RNAs (crRNAs) targeting either genomic (blue) or plasmid-based sequences (red). Treating..., specifically targets bacteria with the given genomic or plasmid sequence from a mixed population without...without affecting the other bacteria. Targeting a genomic sequence results in cell death. Plasmid targeting...introduced is lysogenic, integrating into the bacterial genome, and it carries CRISPR machinery targeting 1) the...CRISPR design for next-generation antimicrobials.” Genome Biol. 15(11):516. (2014). PubMed: PMID 25417800...

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

    Type
    Blog Post
    ...Cas9 technology has been a breakthrough for the genome-editing field. It has the possibility to treat ...Institute in The Netherlands used the CRISPR/Cas9 genome editing system to correct the cystic fibrosis transmembrane...difference with CRISPR/Cas9 in comparison to other genome editing techniques is its ease of use.  “I was ...They are the first direct demonstration of use of genome editing to correct point mutations in two diseases...adult stem cells has huge potential, because the genomes of adult stem cells in organoid cultures are stable.../jcp.30064 2. Barman et al. 2020. “A glance at genome editing with CRISPR-Cas9 technology.” Current genetics...s00294-019-01040-3 3. Khatibi et al. 2021.  “CRISPR Genome Editing Technology and its Application in Genetic...

  11. Plasmids 101: Mammalian Vectors

    Type
    Blog Post
    ...part of the genome. Because the foreign DNA becomes a permanent addition to the host genome, the cells ...incorporate the genetic material directly into the genome to form a stable transfection. Unlike bacterial...transfection process is not integrated into the nuclear genome, in the absence of plasmid replication, the foreign...incorporated foreign genetic material into their genomes. Unlike plasmids used for expression in yeast and...force cells to incorporate the plasmid DNA into the genome. For the purposes of this post, we will define ...gets targeted to a specific location within the genome. Positive selection in mammalian cells works similarly...

  12. Delivery Methods for Generating iPSCs

    Type
    Blog Post
    ...Retrovirus Integrating High Low Efficient and Stable Genome integration Insertional mutagenesis, transgene ...Lentivirus Integrating High Low Efficient and Stable Genome integration Insertional mutagenesis, residual expression...Generates transgene-free and vector-free cells Genome integration Need to sequence cells to verify excision...Generates transgene-free and vector-free cells No genomic integration Inefficient Sendai Virus Non-integrating...Generates transgene-free and vector-free cells No genomic integration Can be difficult to fully remove virus...Generates transgene-free and vector-free cells Limited genomic integration Multiple transfections required Need... Need to sequence to verify there’s no genomic integration Replicating EBNA1 episome Non-integrating...

  13. Pathways Over Time Plasmids Engage Students in Functional Genomics Research

    Type
    Blog Post
    ...ago. Over time, the two genomes have become very different due to a whole genome duplication and extensive...projects. In the O'Connor lab, we recognized that genome sequencing projects were generating huge amounts...basis for student projects in introductory labs. Genome projects use computational methods to identify ...characterization of the Saccharomyces cerevisiae genome by gene deletion and parallel analysis. Science...PMID: 10436161. 7. Dujon, B. Yeast evolutionary genomics. Nat Rev Genet 11, 512-524. (2010). PubMed PMID... O'Connor, C.M. Pathways over time: Functional genomics research in an introductory laboratory course.... functional genomics...

  14. Prime Editing: Adding Precision and Flexibility to CRISPR Editing

    Type
    Blog Post
    ...cataloged in the ClinVar database. Previously developed genome editing methods using nucleases and base editors... published in Nature, is a “search-and-replace” genome editing technique that mediates targeted insertions...also encodes the desired edit and homology to the genomic DNA locus. After nicking by Cas9, the homologous...location The prime editor extends the reach of CRISPR genome editing, as it can edit near to or far from PAM... Fyodor Urnov refers to as “PAM deserts” in the genome. More versatile and precise than base editing (...achieve the best efficiency. The type of edit, genomic context, delivery strategy, cell type, and goal...(though up to 45-fold) higher across different genomic sites compared to PE1 (Anzalone et al., 2019). ...

  15. 10 Great Guest Posts We're Thankful For

    Type
    Blog Post
    ... virulent components behind. Minigenomes are stripped down viral genomes containing only the sequences...publication. Optimizing Donor DNA for Enhanced CRISPR Genome Editing CRISPR has revolutionized how researchers...researchers make knockouts and other types of genome edits, but, even with CRISPR, it isn’t always easy to insert...insert a section of DNA into the genome of your target organism. In this post, Chris Richardson, a postdoctoral...your donor DNA template to achieve more efficient genome editing - all influenced by an understanding of...and Mark Wanner from the Jackson Laboratory for Genomic Medicine described Casilio, a system that uses ... virus infection. Microbiology and virology Minigenomes - A Safe Way to Study Dangerous Viruses Contributed...

  16. Addgene's Top 10 Blog Posts of 2015

    Type
    Blog Post
    ...Validating Your Genome Edit Once you’ve used CRISPR/Cas9 to make a change to the genome, you need to check...directed repair (HDR) and how it’s used in CRISPR genome editing.   2. Plasmids 101: Cre-lox Cre recombinase...potential solution. 5. Cpf1: A New Tool for CRISPR Genome Engineering While the vast majority of CRISPR plasmids..., may make it easier to make gene edits at new genomic locations. 6. CRISPR 101: Non-homologous End Joining...basics of the validation process for CRISPR mediated genome engineering. 10. Plasmids 101: Control Plasmids...

  17. Nanoblades: Tiny CRISPR Ninjas for Genome Editing Difficult Cells

    Type
    Blog Post
    ...and accessible genome editing tool.   References Mangeot, Philippe E., et al. "Genome editing in primary...CRISPR is a simple and versatile tool for genome engineering, but its utility is dependent on its ability...) virus-like particles (VLPs). VLPs lack viral genomes which means they are non-infectious and non-replicative...Nanoblades? Plasmids are available from Addgene. Genome editing primary cells with Nanoblades Primary cells...

  18. Viral Vectors 101: Gamma-Retroviral Packaging Systems

    Type
    Blog Post
    ...of the transfer plasmid sequences into the host genome. Typically, it is the sequences between and including...including the LTRs that are integrated into the host genome upon viral transduction. Most transfer plasmids...flexibility in pseudotyping.   Figure 1: Genome of a prototypical gamma-retrovirus.    Frequently...First, these viruses were derived from different genomes (MoMLV and MSCV for γ-retrovirus; HIV for lentivirus...: U3; Unique 3'; region at the 3' end of viral genomic RNA (but found at both the 5' and 3' ends of the...Contains sequences necessary for activation of viral genomic RNA transcription. R; Repeat region found within...; Unique 5'; region at the 5' end of the viral genomic RNA (but found at both the 5' and 3' ends of the...

  19. Viral Vectors 101: Types of viruses

    Type
    Blog Post
    ...to synthesize complementary DNA copies of their genome upon infecting a host cell. This viral DNA (also... proviral DNA) is then inserted into the host's genome and is used to make more virus. The most studied...common features with gamma-retrovirus including genome architecture, host integration, and its association... remaining an extrachromosomal part of the host genome that can replicate and divide along with the endogenous...Adenovirus Adenovirus has a linear, double stranded DNA genome which is non-enveloped. It can infect humans, many...dividing and non-dividing cells and doesn’t require genomic integration to express its cargo, in fact its viral... viral life cycle does not include genomic integration. While the expression of adenovirus cargo is high...

  20. CRISPR 101: Non-Homologous End Joining

    Type
    Blog Post
    ...Protocol for Genomic Deletions in Mammalian Cell Lines [Video] Pooled CRISPR Libraries Offer Genome-Wide Control...One advantage to using the CRISPR/Cas system for genome engineering is the fact that Cas9 can be easily... to make a DNA double strand break (DSB) in the genome wherever the user chooses. After the initial cut...impacts what happens to Cas9-mediated DSBs in the genome. Non-homologous end joining steps Unlike HDR,... Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity. Cell 154:1380–1389 . https...Nonhomologous End-Joining Strategy for Efficient Genome Editing in Mycobacterium tuberculosis. mBio 11:...
Showing: 181 - 200 of 839 results