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Tips for Using BLAST to Verify Plasmids

Posted by Jason Niehaus on May 29, 2014 9:29:00 AM

This post was updated on Dec 4, 2017.

At Addgene, we continually use the Basic Local Alignment Search Tool (BLAST) provided by NCBI. BLAST helps us compare the sequencing results of the plasmids in our repository with known reference sequences, such as full plasmid sequences provided by the laboratories that deposit their plasmids with us or other entries in NCBI’s numerous databases.

As our repository has grown over the years (we now have over 60,000 plasmids!), the number of sequencing results we analyze as part of our quality control process has steadily grown. On a busy week, we may need to analyze more than 200 plasmids as part of our quality control process. Consequently our team has refined our use of the BLAST web browser interface to be as efficient as possible.

If you find yourself frequently on the BLAST website to verify plasmids or validating your new clones, try these tips to make the most of your time and sequence! You might also enjoy seeing how our quality control process has changed with the introduction of next generation sequencing! 

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Topics: Plasmid How To, Lab Tips

Dos & Don'ts When Publishing a Scientific Manuscript

Posted by Guest Blogger on May 22, 2014 12:02:55 PM

This post was contributed by Maaike Pols, PhD, a Developmental Editor at F1000Research. 

With many changes taking place in the world of science publishing, and an ever increasing number of journals and publishers to choose from, it gets very confusing for scientists writing research articles. What should you take into account when writing up your research?

What type of journal should I choose?

Writing a research paper for publication in a scientific journal requires several considerations. First, it is important to establish the type of audience you want to reach with your paper. Is it the wider scientific community, or are you writing for a specific subgroup of researchers in your area of expertise? Sometimes, the funders of your research may stipulate that your article must be published in an open access journal or by using the open access option in a conventional journal. Publishing via open access means that your manuscript will be available to anyone who wishes to read it, without them needing a subscription to the journal. An increasing number of funding bodies insist that the research data resulting from their funding should also be published. All these factors will influence your choice of journals to submit your work to.

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Topics: Career, Lab Tips

Your Lentiviral Plasmid FAQs Answered

Posted by Kendall Morgan on Apr 23, 2014 9:08:00 AM

Lentiviruses are useful and efficient tools to introduce your gene of interest into cells. Unlike gamma-retroviruses that can only infect dividing cells, lentiviruses can infect dividing and non-dividing cells. 

Addgene has an extensive collection of lentiviral plasmids created for a variety of applications including cDNA expression, shRNA-mediated knockdown, Tet and Cre-regulated expression, CRISPR genome editing, and more. Not surprisingly, we receive many questions from scientists all over the world looking for some additional information or clarification on these vectors. Read on to find the answers to our most frequently asked lentiviral questions.

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Topics: Plasmid How To, Plasmid Elements, Lab Tips, Viral Vectors

The Stingy Scientist: How the Baby Gel Box Was Born

Posted by Joanne Kamens on Apr 15, 2014 11:11:00 AM

It is probably good news for our environment that more people are paying attention to living a “green” life and creating less waste.  Most communities seem to have recycling programs and it seems to me that most Addgenies make an effort to avoid plastic bags and to conserve resources where possible.  At the lunch table, for instance, we have a plastic container problem…reusable containers pile up by the sink after lunch as fewer and fewer people use plastic bags.  We also try to recycle our discards according to the Cambridge, Massachusetts guidelines and wear an extra sweater so we don’t have to turn up the heat when there is a bad Northeastern chill.

Check out Joanne's Reddit AMA 

Few of us spend much time thinking about conserving resources in the labs. Disposable plastic materials are fairly inexpensive in this country and we are quick to throw out chipped or imperfect equipment.  We can’t safely recycle these materials either. 

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Topics: Fun, Lab Tips

CRISPR-Cas9 FAQs Answered!

Posted by Caroline LaManna on Mar 13, 2014 12:08:00 PM

As Kendall mentioned in Tuesday's blog post, keeping up with the newest CRISPR technologies and their applications can be exhausting. A quick search for "CRISPR", short-hand for Clustered Regularly Interspaced Short Palindromic Repeats, in Pubmed returned 728 articles (3/12/2014). With so many options for CRISPR plasmid tools and numerous experimental design decisions to make, it makes sense that scientists, many of whom are venturing into genome editing for the first time, have lots of questions.

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Topics: Plasmid Technology, Genome Engineering, Lab Tips, CRISPR

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