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We narrowed to 890 results for: genome

Showing: 161 - 180 of 890 results

  1. 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...

  2. Pairing CombiGEM and CRISPR for Combinatorial Genetic Screening

    Type
    Blog Post
    ...RNAs (gRNAs) for genome editing in large-scale has led to the rapid generation of genome-wide gRNA libraries...platforms CRISPR has revolutionized how we decode the genome by making it easy to create specific genetic perturbations... that can be used to combinatorially modify the genome, screen for a particular phenotype, and quickly...of perturbations and applications in functional genomics, cell reprogramming, and beyond. For further details...PMCID: PMC4744125. 3. Gilbert, Luke A., et al. "Genome-scale CRISPR-mediated control of gene repression... PMID: 26627737. 5. Koike-Yusa, Hiroko, et al. "Genome-wide recessive genetic screening in mammalian cells... PMID: 24535568. 6. Konermann, Silvana, et al. "Genome-scale transcriptional activation by an engineered...

  3. 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...

  4. 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...

  5. 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:...

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

    Type
    Blog Post
    ...expertise? “This is the next step in high-throughput, genome-wide screening,” Konermann said. “If you want to...helper protein. SAM can be combined with a human genome-wide library to activate all 23,430 known coding...for GeCKO, a lentiviral CRISPR library enabling genome-scale, knockout screening). As the Zhang lab's ... system is robust, specific, and can facilitate genome-scale gain-of-function screening when combined ...also enabled them to turn on genes anywhere in the genome for gene control over a 1,000-fold range. Weissman...: 10.1016/j.cell.2014.02.001. Epub 2014 Feb 13. Genome-scale transcriptional activation by an engineered...-8. doi: 10.1038/nature14136. Epub 2014 Dec 10. Genome-Scale CRISPR-Mediated Control of Gene Repression...

  7. Fluorescent Tagging of Endogenous Genes with SapTrap

    Type
    Blog Post
    ...replace the genomic copy of your gene of interest with a fluorescent protein fusion. CRISPR genome editing... create a DNA double stranded break (DSB) at a genomic site specified by a guide RNA (gRNA) sequence. ...design gRNAs to induce the break at a specific genomic site and, using the endogenous homology directed...assembly toolkit called SapTrap to improve CRISPR genomic tagging in C. elegans. SapTrap offers scientists...designed modular toolkits to assist with tagging genomic loci in other model systems, including mammalian...like SapTrap, scientists will be able to generate genome-wide libraries containing fluorescently-tagged ...Kunzelmann, Stefan, et al. “A Comprehensive Toolbox for Genome Editing in Cultured Drosophila melanogaster Cells...

  8. AAV Vector Quality Control: Going the Extra Mile with NGS

    Type
    Blog Post
    ...generation sequencing (NGS) of the viral genome to confirm viral genome identity and serotype. Additionally...common to find DNA from the packaging cell genome, bacterial genomes, cloning vectors, and helper plasmids ... This post will describe our workflow for viral genome sequencing (VGS). Why should you care about viral...fragments of DNA from the helper plasmids or the cell genome can be packaged inside the vectors during production... mishaps before distributing the vectors? Viral genome sequencing Thanks to the establishment of in-house... as 0.1% (Guerin et al., 2020).  In addition to genome identification, we developed custom open-access...

  9. CRISPR 101: Which Cas9 Do I Choose for My CRISPR Experiment?

    Type
    Blog Post
    ...verify your genome edit can be found in our blog post entitled “CRISPR 101: Validating Your Genome Edit”. ...made it easier than ever to make precise, targeted genome modifications. Cas9 has been modified to enable...frameshift mutations in the gene of interest. The genomic target for Cas9 and the introduction of this mutation... sequence is unique compared to the rest of the genome.  2) The target is present immediately upstream...sequence has little homology to other regions of the genome and consider using a Cas9 variant with higher specificity...most efficient option. If there is no NGG in your genomic region, then read on for your best options. There...using Cas9 Don’t want to permanently modify the genome but still want to affect gene expression? dCas9...

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

    Type
    Blog Post
    ...first discovered in bacteria, most CRISPR-based genome engineering has taken place in other organisms....bacteria. These quirks change the way CRISPR-mediated genome engineering functions in bacteria, but have no ...engineering One common way of accomplishing bacterial genome engineering is done with recombineering, a technique...multiple mutations simultaneously (Jiang et al. 2013). Genome editing tools for bacteria CRMAGE system combines... recombineering-based MAGE (Multiplex Automated Genome Engineering) technology (Ronda et al., 2016). pMA7CR...CRISPR to create a system for scarless, iterative genome engineering (Jiang et al., 2015). pCas contains...the early work of the Marraffini lab pioneering genome editing using CRISPR in bacteria, they also led...

  11. CRISPR Activation: A Practical Guide

    Type
    Blog Post
    ...required for Cas9-based activation. CRISPRa for genome-wide studies One of the best uses for Cas9 activators...screening. gRNAs targeting every gene in the human genome for example, can be made easily and cheaply using...Moosburner M, Church GM (2015) Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library...Bassik MC, Qi LS, Kampmann M, Weissman JS (2014) Genome-Scale CRISPR-Mediated Control of Gene Repression...Gootenberg JS, Nishimasu H, Nureki O, Zhang F (2014) Genome-scale transcriptional activation by an engineered...Complex Structure, Function, and Membership Using Genome-Scale Fitness Screens. Cell Systems 6:555-568.e7...functional guide RNAs for the CRISPR/Cas9 system. Genome Biol 16: . https://doi.org/10.1186/s13059-015-0784...

  12. Hot Plasmids June 2018 - Reverse transcriptase, nanobody, and protein-DNA interaction tools

    Type
    Blog Post
    ...transcribe the extremely long, highly structured HCV genome (~9.6 kb of highly structured template!). MarathonRT...method to identify proteins occupying a specific genomic locus: Caspex  Article contributed by Susanna Bachle...to detect proteins that associate with specific genomic loci. He made use of catalytically inactive dCas9... by a pre-defined sgRNA sequence to a specific genomic locus and labels the proteins in its vicinity with...method to identify proteins occupying a specific genomic locus: C-BERST Article contributed by Klaus Wanisch...they call C-BERST (dCas9–APEX2 biotinylation at genomic elements by restricted spatial tagging), to confirm...proteome localization in future studies of other genomic loci. Find the C-BERST plasmids here. Gao at ...

  13. Multiplex Genome Editing with CRISPR-Cpf1

    Type
    Blog Post
    ...Cas12a. There’s a new development for CRISPR-Cpf1 genome editing!  A recent paper from Feng Zhang's lab ...lab describes how to use Cpf1 for multiplex genome editing.  For a few reasons, Cpf1 is a simplified system...on the Addgene Blog Cpf1: A New Tool for CRISPR Genome Editing Which Cas9 Do I Choose for My CRISPR Experiment... multiplex genome editing...

  14. Advancing Biology with Zebrafish: Genetic Tools for Developmental Studies and More

    Type
    Blog Post
    ... the genome are powerful resources for investigating any biological process. High quality genome sequence...their roles in humans. The sequenced genome also permits “whole-genome/transcriptome” studies, in which, ...high-quality sequence assembly of the zebrafish genome was published in 2013, revealing that about 70%...committee). But as the field of genetics progresses and genome sequences become available, new hypotheses about...transgenic organisms by introducing foreign DNA into the genome is useful for a variety of applications. For example...Tol2 to randomly integrate foreign DNA into the genome. Non-random integration into specific pre-determined... Tol2, and the high-quality sequenced zebrafish genome. One study profiled 38,731 cells from 694 embryos...

  15. Hot Plasmids - September 2019 - CRISPR, Auxin Inducible Degradation, MerMAID Channelrhodopsins, and Genome Looping

    Type
    Blog Post
    ...contributed by Shreya Vedantam CRISPR/Cas9 is widely used genome editing tool. However, Cas9’s endonuclease activity... Article contributed by Eric Perkins Mammalian genomic DNA is not just a 2-D linear molecule snaking through...loops not only provide a 3-D structure for packing genomic DNA into nuclei, but are also thought to play a... or have attempted to engineer loops to create genomic interactions that wouldn’t normally occur. The ...gRNAs, they can then recruit these LADL Anchors to genomic targets, such as a distal promoter and an enhancer...to be a better model for the dynamic nature of genomic looping due to it’s briefer time scale and its ...marine microorganisms based on metagenomic data. MerMAIDs (Metagenomically discovered Marine, Anion-conducting...

  16. Tips for a 1st Time CRISPR User (by a 1st Time CRISPR User)

    Type
    Blog Post
    ...Verifying genomic edits with the surveyor assay Overview: I used the Surveyor assay to look for genomic edits...designing primers flanking my edits in genomic DNA and doing PCR on genomic DNA. The surveyor assay itself was...limited by the sequence of the human genome. I used the UCSC genome browser and Primer3 to design primers...Primer3: for Designing Primers UCSC Genome Browser: For eploring genomic DNA ImageJ: Free Software for Analyzing...easy. Figure 4: Detection of edited BRAF genomic loci in Cas9-expressing A549 cells transduced with... shown). Pro-Tips: 1.Designing primers against genomic DNA to amplify the gRNA targets was challenging... straightforward, and is a testament to how far genome engineering has come. For comparison, in 2007 it...

  17. 27 Hot Plasmids from 2016

    Type
    Blog Post
    ...harness this powerful genome engineering tool. Bassett, et al. J Genet Genomics. 2015. PubMed PMID: 26165496...bacterial genome engineering across multiple species Recent discoveries in the fields of genome engineering...automated, and high-throughput genome editing is multiplex automated genome engineering (MAGE) (1). MAGE...combinations and combinatorial genomic libraries. MAGE has allowed genome-engineering endeavours of unparalleled...binding (e.g. DHS-seq, FAIRE-seq, and CHIP-seq), genome-wide identification and quantification of enhancer...transcription start site. In STARR-seq, randomly sheared genomic libraries are cloned downstream of a minimal promoter...libraries enable researchers to screen the entire genome for genes that regulate a wide variety of phenotypes...

  18. Enabling Precision Functional Genomics with the Target Accelerator Plasmid Collection

    Type
    Blog Post
    ...Take a patient’s tumor sample, use cutting edge genomic technologies to map the mutations that are present...clones corresponding to cancer variants found in genome sequencing studies (as well as reference cDNA clones...variants derived from analysis of lung adenocarcinoma genomes (Lung Cancer Mutant Collection) or “pan-cancer”...exciting new field we call “precision functional genomics.” The goal of this field is to functionally map...it out: Progress towards precision functional genomics in cancer. Johannessen, CM and Boehm JS. Curr.... realize the potential of precision functional genomics and propel the future of cancer precision medicine... and is focused on making precision functional genomics a reality for future cancer patients. You can ...

  19. Degrading DNA with Cascade-Cas3

    Type
    Blog Post
    ...2022). Genome editing technology and applications with the type I CRISPR system. Gene and Genome Editing...chance in the spotlight — Cas3. Cas3 can induce genomic alterations on a scale that other Cas effectors...it requires multiple Cas effectors to carry out genomic editing. Specifically, these types of CRISPR systems...naturally bound to the DNA. Cas3 or Cas9? Large genomic deletions can be achieved using Cas9, but Cas3 ...). CRISPR-Cas3 induces broad and unidirectional genome editing in human cells. Nature Communications, ...2019). Harnessing type I CRISPR–Cas systems for genome engineering in human cells. Nature Biotechnology...Switch Off CRISPR-Cas Systems INTEGRATE: Bacterial Genome Engineering Using CRISPR-Transposons Additional...

  20. Design Tips for Prime Editing

    Type
    Blog Post
    ...scaffold sequence into the genome, ensure it is not homologous to the target genomic sequence (Chen et al.,...refresher: prime editing is a “search and replace” genome editing technique that relies on a fusion enzyme... primer binding site (PBS) complementary to the genome and a reverse transcriptase (RT) template including...BioRender.com. The pegRNA specifies both the genomic location to be edited and the sequence of the edit...editing efficiency is affected by the type of edit, genomic context, delivery strategy, cell type, and goal... the pegRNA scaffold sequence (orange) and the genomic target can increase the odds of incorrect editing...Raguram, A., & Liu, D. R. (2019). Search-and-replace genome editing without double-strand breaks or donor DNA...
Showing: 161 - 180 of 890 results