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Sequencing Options for CRISPR Genotyping

Posted by Guest Blogger on Oct 4, 2016 10:30:00 AM

This post was contributed by guest blogger Søren Hough, the Head Science Writer at Desktop Genetics.

One of the most important steps in the CRISPR experimental process is validating edits. Regardless of which CRISPR genome editing system you use, there remains a chance that the observed phenotype was caused by an off-target mutation and not an edit in the target gene.

The validation process, also known as CRISPR genotyping, is critical to demonstrating causal relationships between genotype and assayed phenotype. Verifying these connections can help alleviate the reproducibility crisis in biology. It is key to address these concerns as CRISPR use grows across the life sciences and to establish standardized validation techniques for academia, industry, and especially the clinic.

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Topics: CRISPR

CRISPR Kinome Libraries Available: Pooled and Individual Plasmid Formats

Posted by Guest Blogger on Sep 9, 2016 10:43:16 AM

This post was contributed by guest blogger, member of the Addgene Advisory Board, and Associate Director of the Genetic Perturbation Platform at the Broad Institute, John Doench.

A genetic screening project can be a tremendous undertaking, producing a wall of results that can only be described as bigly. But such a project should not be undertaken lightly. Whether executed in arrayed or pooled format there are of course materials costs, regardless of who is paying for them. More importantly, there’s the opportunity cost of your time; an investment of months of your life that may end with little more than an Excel spreadsheet of random numbers that’ll leave you, well, #sad.

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Topics: CRISPR

Cas9 Activators: A Practical Guide

Posted by Guest Blogger on Aug 18, 2016 10:30:00 AM

This post was contributed by guest bloggers Marcelle Tuttle and Alex Chavez, researchers at the Wyss Institute for Biologically Inspired Engineering.

Listen to Our Podcast Interview the Alex Chavez

Background on Cas9 Activators


CRISPR/Cas9
is an enormously plastic tool and has taken the scientific world by storm. While Cas9 has been most widely used to create specific edits in DNA, there has also been significant work on constructing Cas9 transcriptional activators. These constructs allow for the upregulation of essentially any gene by fusing mutants of Cas9 deficient in DNA cutting activity to a transcriptional activation domain (Fig 1).

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Topics: CRISPR

Single Base Editing with CRISPR

Posted by Mary Gearing on Aug 16, 2016 10:30:00 AM

This post was updated on Nov 27, 2017.

When we talk about CRISPR applications, one negative always comes up: the low editing efficiency of homology-directed repair (HDR). Compared to non-homologous end joining, HDR occurs at a relatively low frequency, and in nondividing cells, this pathway is further downregulated. Rather than try to improve HDR, Addgene depositor David Liu’s lab created new Cas9 fusion proteins that act as base editorsThese fusions contain dCas9 or Cas9 nickase and a cytidine deaminase, and they can convert cytosine to uracil without cutting DNA. Uracil is then subsequently converted to thymine through DNA replication or repair. Later work has improved base editor targeting flexibility and specificity. New adenine base editors also allow you to change adenine to inosine, which is then converted to guanine.

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Topics: Genome Engineering, CRISPR

CRISPR Between the Genes: How to Experiment with Enhancers and Epigenomics

Posted by Guest Blogger on Aug 9, 2016 10:30:00 AM

This post was contributed by guest blogger, Aneesh Karve, CTO at Qult Data. This post was originally published on the Quilt Genomics Blog and is republished here with permission.

Quilt is a collaborative database for genomics. In this article, Quilt CTO Aneesh Karve, shows how to design experiments that work anywhere in the genome. Aneesh's research interests include proteomics, machine learning, and visualization for big biology.
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Topics: CRISPR

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