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TypeBlog PostPublishedAug. 9, 2016, 2:30 p.m....of genome math. Figure 1: Genome math illustrated. Intersect (left) and set minus (right). ...embryonic stem cells (ESCs). Your ChIP-seq finds just over 13,000 significant binding peaks for NANOG ...explore. I hope that this brief guide can help you do just that. Good luck, and always keep going. Appendix...
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Tips from the Repository Trenches: Using Barcodes to Track Samples
TypeBlog PostPublishedOct. 6, 2015, 2:30 p.m.... is located in. Otherwise it could take us hours just to find one sample! Luckily, if a rack of tubes ...and in a way that can be easily traced. If you’re just starting a lab, or are looking for a way to organize...around or misread. 2. Track the container - It is just as important to track the location of the container... -
Negotiating Work and Life: How to Find the Joy
TypeBlog PostPublishedMarch 20, 2014, 3:04 p.m....matter how busy I am. Believe it or not, teenagers just go to bed and you’ll never know it so don’t miss...almost every morning. Of course, this is more than just fun, as your health needs to be a priority. Pick...friends – no spouses or kids. The bottom line We don’t just “do science” – we are scientists. We have to figure... -
Analyzing CRISPR Editing Results with ICE from Synthego
TypeBlog PostPublishedMay 8, 2018, 1 p.m....results from CRISPR edit data requires the help of robust software tools. As a consequence, a critical step...performed over multiple experiments and comparing the robustness, accuracy, and speed with existing tools. For... that a particular parameter was automatically adjusted to generate ICE results. If there are no results... -
Advancing Biology with Zebrafish: Genetic Tools for Developmental Studies and More
TypeBlog PostPublishedAug. 13, 2019, 12:58 p.m....ideal for studying vertebrate embryogenesis. To illustrate some of the reasons that zebrafish have been ...genes affecting diverse biological processes—not just development—are available from strain distribution...established (Felker and Mosimann, 2016). One common and robust strategy uses a transposon called Tol2 to randomly... -
Save Time with Transient Plant Leaf Transformations
TypeBlog PostPublishedJuly 25, 2019, 12:03 p.m.... or vacuum infiltration. Syringe infiltration (D'Aoust et al., 2009): Usually a syringe without a needle...MoClo system you can easily and quickly create customized vectors. For more information on MoClo for plants...his work in the Lee-Parsons Lab. References D'Aoust, Marc-André, et al. "Transient expression of antibodies... -
New Tools Enable CRISPRa for Neuroscience Applications
TypeBlog PostPublishedJuly 2, 2019, 12:51 p.m....the protein and RNA components, and several sgRNAs must be screened to identify effective ones. Simplified...sgRNAs targeting either transcript variant led to robust and specific upregulation of the targeted variants...neuron-optimized CRISPR/dCas9 activation system for robust and specific gene regulation." eNeuro 6.1 (2019... -
Designing Your Chalk Talk for the Academic Job Interview
TypeBlog PostPublishedMarch 12, 2019, 1:37 p.m....model is a standard scientific strategy. However, a robust research proposal will distinguish between competing...delivery. Design simple figures and diagrams to illustrate your vision. Practice drawing and writing everything...create a sculpture or print a 3D model to better illustrate your point. Practice the full chalk talk with... -
Bacterial Toxin-antitoxin Systems as Molecular Biology Tools
TypeBlog PostPublishedNov. 1, 2018, 12:35 p.m....the antitoxin is unstable, meaning that the cells must continually produce antitoxin to avoid cell death...RNA-regulated systems Toxin-antitoxin systems are not just restricted to the protein realm. Let’s take a look...-antitoxin system discovered. Unlike the systems just described, the hok/sok systems consist of three ... -
Rett Syndrome: A History of Research and Therapeutic Outlooks
TypeBlog PostPublishedNov. 19, 2020, 2:15 p.m....The Rett Syndrome Research Trust (RSRT) has an ambitious goal of curing Rett Syndrome and Addgene is ...Syndrome Rett Syndrome was first described in 1966 by Austrian physician, Andreas Rett, who tried to raise awareness...Meyer KC, Solano S, Nguyen K , Lang E, Kaspar AA, Foust KD, Thomsen G, Fugere M, Kaspar BK (2019) Rett syndrome... -
Overcoming the AAV Size Limitation for CRISPR Delivery
TypeBlog PostPublishedSept. 16, 2020, 1 p.m....co-infection of two AAVs. Cas9 orthologs: shorter, but just as potent and specific? The two AAV strategies described...still fitting Cas9 and its gRNAs into one AAV, Cas9 must be made smaller. Previous attempts to “shrink” Cas9...published that deliver these Cas proteins with AAV, at just 1,108 and 986 amino acids, respectively, the size... -
Four Base Editing Reporters to Monitor and Enrich Editing in Real-time
TypeBlog PostPublishedJuly 7, 2020, 1:15 p.m....array of base editing reporters that can help you do just that. Monitoring APOBEC and Cas9-mediated editing...induce the translation of any detectable protein, not just fluorescent proteins. Figure 4: Reporters ...that contained the cytidine base editor exhibited robust induction of GFP fluorescence confirming the efficacy... -
An Inside Look into Addgene's Dev Team
TypeBlog PostPublishedJan. 23, 2020, 2:45 p.m....that works with Addgene in some way. For users, we just released a major redesign of how search works on...accountability on the part of each developer and creates trust amongst the team. Whether we are a highly collaborative...develop better software. Maintenance We’re not just about developing new features and fixing bugs: we... -
Using Video to Share Your Science: We Share Science
TypeBlog PostPublishedNov. 3, 2016, 2:30 p.m....less likely to read about our work. We therefore must discover new ways to reach our colleagues and other... in many disciplines has been a long brewing frustration for me. I read a variety of psychology, business...Scott Spicer at the University of Minnesota helps illustrate this: “In terms of total view count and videos... -
Twenty Years of Sharing: Expanding Accessibility
TypeBlog PostPublishedNov. 21, 2024, 10:47 p.m....countries, import and export regulations, differing customs processes, and the distances the packages needed...other things, could ensure our packages navigated customs and arrived at their destination in a timely manner...materials and information are truly accessible, not just available. Looking forward Over the past twenty... -
How to Be an Excellent Trainee
TypeBlog PostPublishedSept. 26, 2023, 1:15 p.m....prefer to review their notes, process what they’ve just learned, and ask questions later – maybe even the...your bench mentor’s training time is time set aside just for you – so do your best to show up as your most...with…now”. Ask for feedback so you can make adjustments. This could look like “What are some things I... -
Antibodies 101: Reading a Flow Plot
TypeBlog PostPublishedFeb. 6, 2024, 3:13 p.m....an X,Y axis to generate a dot plot (Figure 1). Clustered events are called a population. ..., like a box, ellipse, or circle, drawn around clusters to define populations. This shape is called a ...show frequency of events, instead of relying on clustered dots. In a contour plot, each line contains the... -
Plasmids 101: The Promoter Region – Let's Go!
TypeBlog PostPublishedApril 3, 2014, 8:05 p.m....that the promoter present in your plasmid backbone must to be compatible with the type of RNA that needs...differs between cell types or organisms, promoters must be similarly variable. Bacterial promoters only ...mammalian promoters. These lists is by no means exhaustive, but should be a good place to start when trying... -
Antibodies 101: Beyond Surface Labeling
TypeBlog PostPublishedJune 27, 2024, 1:15 p.m.... identifying lineage markers, like many of the cluster of differentiation (CD) proteins found on immune...labeling is through antibody host species reactivity. Just like for western blotting, a primary epitope-targeting...to a later day. Note that intracellular labeling must be performed only after viability staining and surface... -
Tips for Getting a Faculty Position
TypeBlog PostPublishedJuly 20, 2023, 1:15 p.m.... Erik Snapp just released version 3.4 of his eBook, How to Get a Faculty Position. This edition has ...then look at me quizzically and ask why I didn't just say that? Bottom line is to appreciate that your...the job search and interview process – these are just my top takeaways. My full eBook (available here ...