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...We perform over 100 transformations each week at Addgene, so we need to be cost and time efficient. We... stored at -80oC until we are ready to perform transformations. A typical 200mL bacterial culture produces...find the subsequent transformation protocols below: Untergasser Lab Transformation of chemically competent... easily transformed without a heat-shock step. Because of the large number of transformations being performed...that transforms well in other competent cells) to ensure that your cells can be readily transformed. Compare...Want even more tips for transforming your cells? Check out our transformation guide.   ...a little-known reagent for streamlining the transformation step. Read on to find protocols and tips that...

...libraries, chemical transformations can also be used. Efficiency for chemical transformations is less than that...for your transformation(s). The amount of competent cells you need total and per transformation may vary... DNA, you will likely need to perform several individual transformations, such as splitting 400 ng of ...the manufacturer’s protocol for transformation and expected transformation efficiency, or more specifically...library First, you’ll need to collect specific information about your library: the size of your library ...with a large backbone might be more difficult to transform.    Figure 1: Factors to consider when ... coverage, since this will help decide what transformation efficiency you need to achieve. Most pooled...

...research! Sequence information: Depositors may provide full or partial sequence information for their plasmids...successful cloning. Cloning information: This section provides useful information about how the vector was... NEB Stable cells. Resource information: This section contains information about the lineage of the plasmid... bamboozled by all of the different kinds of information on our plasmid pages? Well, to help make the ...through them and make the best use of all the information provided by your colleagues. Top of the plasmid...based off of the plasmid sequence and feature information given by our depositors. Many depositors also... pages, but these are found in the "Resource Information" section of the plasmid page (discussed below...

... but it’s really just formaldehyde. Formalin: You may also come across formalin, which refers to a saturated...cause some confusion. Paraformaldehyde: Many IF protocols call for paraformaldehyde (PFA) as the fixative...saturated solution of formaldehyde (saturated being 37%). Formalin solutions often contain methanol as ...order to slow the polymerization of formaldehyde.  Note: Formaldehyde in solution will naturally polymerize... maintaining cellular and tissue morphology. Formaldehyde is the most commonly used cross-linker for IF...fixative. PFA is a polymer of formaldehyde that, on its own, is not a fixative. However, when PFA is dissolved...solution and heated, it depolymerizes, producing formaldehyde. Often people will call the resulting solution...

...bridge helix, purple.   Apo Cas9 changes conformation frequently (Osuka et al., 2018), but it’s most...electron microscopy and FRET, can offer more information on these regions.   Cas9’s transition from weak...lobes move toward each other into the “closed” conformation shown in Figure 3. Though Cas9 is not a static...binding state, RNA loading stabilizes the closed conformation.   Fun Fact! Even though the Cas9:RNA complex...complex is well described in the closed conformation, recent electron microscopy studies have also found Cas9... Cas9:RNA complexes in the open conformation (Cofsky et al., 2022), indicating that there is more to learn...protein can switch between the closed and open conformations to bend the DNA, destabilizing the base pairs...

...distributed in digital or analog media formats. Cognitively demanding format. Equipment, expense and expertise...with is "how?" How are you going convey your information to your audience? There's so many ways options...incredibly varied in how they prefer to consume information. Personally, I would much rather read the instructions... science.                    Two of the platforms we use at Addgene: YouTube, for longer educational...octogenarians is going to be a hard sell!) Digital platforms often have demographic data of their users readily...geographic location. For example, not all social media platforms are available or used in all countries; not all...mitosis.   Consider also the amount and type of information you want to convey. Small tidbits and fast/fun...

...provides summary information on Class 2 Cas enzymes. The information is organized in wiki format and includes...display information for a given Cas (SpyCas9a) from CasPEDIA.   Helpful resources and information For ...could arise where you still need more information. If you are performing a viral delivery of Cas, the size...the features? CasPEDIA has collected relevant information on all the Cas enzymes you know and love, and... heard of. Each entry displays the following information for a Cas enzyme: Nuclease properties (CasID...properties of Cas enzymes. That’s a lot of helpful information! To get you started, we’ll give a quick overview... substrate (nick, bind, cleave, mixed). This information represents the ‘big picture’ features of the ...

...More concretely, scientists gather information about reality informing people and their governments on what...article are those of the author do not represent a formal stance taken by Addgene or its staff. In Washington...reality and science is how we learn about reality. Formally, a government can be defined as a social contract...into in order to protect their rights (2). Less formally, governments are the organizations that make and...other citizens. Thus civilization proceeds in an informed fashion. For science to be useful to governments... of the bargain and do the research required to inform the public (8–13). Facing the possibility that ...march include: General inclusion of science to inform policy (17). The facts surrounding a matter or ...

...Arabidopsis seed following floral dip transformation next to an untransformed seed from the same plant beginning...Selectable transgene markers for plant transformation fall into two main categories: antibiotic/herbicide...resistance genes usually involves killing the untransformed seedlings or callus (undifferentiated plant ...For example, with CRISPR-Cas9 gene editing, transformation may be identified by resistance to an antibiotic...antibiotic. Successful editing of transformants then typically occurs in T0 plants (from callus) or T1 plants...contaminate it. I have used it for selecting transformation events and am currently planning to use it ...beginning to germinate. (Top right, second panel) Transformed seedlings can be selected without antibiotics...

...procedure to be performed using a simple two-step, 2 hr protocol prior to transformation (Figure 1). As...false positive colonies. Transformation - the linear fragments are transformed into E. coli and plasmid...important is the transformation efficiency of the strain: when asking the cell to perform multiple recombination...assembly of a circular plasmid in vitro, before transforming it into E. coli for propagation. However, while...adopted by any laboratory. All procedures are performed using the same three step protocol:  Fragment... encode homology arms to allow immediate co-transformation with linearized vector backbone. DpnI digestion...competent cells of 107 CFU/μg are perfectly fine, yet performing multiple modifications will require ultracompetent...

...’s time to think big and perform your assemblies in a high-throughput format. If your lab owns a liquid... after each transformation and/or use different E. coli strains with higher transformation efficiency....in silico cloning tools When available, always perform your MoClo assemblies in silico before you start...original Addgene kit plate for fresh bacteria. Performing your Assemblies Calculate your volumes As you...Save time, go high throughput You are ready to perform your assemblies, but you have a high number to ...restriction–ligation reactions in a 96-well (or higher!) format. Liquid handling robots are not only faster and...lowers experimental costs. If you are planning to perform a high number of assemblies, you will also likely...

...bacterial transformation One protocol that has been automated is high throughput transformation. With our...a couple of platforms that fit 48 well q- trays allowing us to do up to 96 transformations in one run ...easier and more efficient. Here, I’ll discuss transformation, DNA purification, and filling vials with agar...deposits (over 100 deposits per month!), manual transformations were taking a lot of time. Enter the Biomek... We wanted a machine that would improve our transformation protocol and, after looking at a few options...run compared to doing about 50 transformations in the same amount of time by hand! Setting up a basic ... fine piece of machinery we have been able to transform 96 samples in about 4 hours with a greater than...

...anyone who has ever worked to sequence DNA on NGS platforms will tell you, while the process has become much...sequencing. This process is completed in a plate format yielding anywhere from two to six plates of 96 ...donated MiSeq.  For Complete Plasmid Sequencing we perform a 2x251 run on our MiSeq that takes about two days...involves a significant amount of QC. First, we perform Picogreen quantification on each and every isolated...samples for Viral Genome Sequencing (VGS). QC is performed throughout the library preparation process and...Aligning the sequence The first step we take when performing quality control of newly deposited plasmids is...detecting common features using Snapgene. If we find information that differs from what we would expect given ...

...purification before transformation. After transforming cells, you should perform colony PCR with vector..., ligation, and transformation. While restriction cloning is still routinely performed by many labs, a...products are then transformed directly into chemically competent E. coli and transformants selected with ...+ + Gel Purification + - Ligation + - Transformation + + The FastCloning process in brief In ...for this procedure to work properly. Directly transform chemically competent cells with the digested mixture...-cycle PCR leads to the most colonies after transformation. When a 1:1 vector:insert ratio is used in ... and 2 µL of digest product are used in the transformation, >70% of the colonies are correct. Good luck...

...AMA   Guidelines for giving feedback Use formal and informal mechanisms for feedback (more on this below...her management style. Formalizing the feedback session Giving regular, informal feedback is a very effective...Using this standard format not only enables you to discuss a person's performance or what has been learned...scientists seem to find it easier to give feedback in formal sessions using a specific list of questions after... it helps to plan effective next steps. For a formalized feedback session, answer the questions below ...discuss openly. Both parties get used to using this format and it becomes even more effective over time if...of indirect language You must be honest about performance problems. While giving corrective feedback isn...

...organizational performance and often have to be able to quickly synthesize information from a variety ... their visual format is quite appealing to many audiences. While all of these platforms were developing...not hosted on the platform, they can be hosted on YouTube, Vimeo, and other platforms (such as university...quickly. Taking what I loved from each of these platforms (such as social networking, visual appeal, instant... across multiple other sites), I created a new platform for sharing video abstracts about research: www.WeShareScience.org...www.WeShareScience.org. WeShareScience is a free platform for sharing short, 3 to 5 minute videos about ...university websites). WeShareScience is a social platform that provides links to the videos, keeping the copyright...

...The ability of our users to discover all this information, however, did not improve at the same pace as...as the quantity and quality of the information. As a result, resources on the website were hard to find... than that: the general “findability” of the information on the site. Different users have different strategies...paths, the organization and completeness of our information, and the accuracy and relevance of our search...the advantage of a very specialized domain of information so we were able to fine tune our approach much...than if we were dealing with general purpose information. Below are a few of the strategies we used in...Categories We created a categorization of our information in order to more granularly customize the search...

...optimization as each antibody performs differently and some antibodies impact the performance of other antibodies...beautiful results. Performing an immunofluorescence experiment The process to perform IF can be broadly...important considerations to make when planning and performing an IF experiment. What is immunofluorescence... different species and colors makes it easy to perform multiplexed IF. By using multiple primary antibodies...in IF experiments. Precisely which controls you perform will depend on your experimental context.  Choosing... to use, then the primary antibody will likely perform as expected in both.  How do you find validated...may be, it is always important to verify their performance in your hands and in your specific experiment...

...80) are transformed to 100. This transformation (illustrated in the graph below) is performed because ...order reagents Perform your wet lab experiment Analyze the data For more detailed information on using CrispyCrunch...even more.) However, none of the tools we found performed batch guide design, batch primer design or batch... burden of having to manage all the standard information that goes into a 96-well plate and comes out ... reports. With CrispyCrunch, you get the all information from Crispresso plus a summary per batch. Ranking... at a genome by eye. We came up with a ranking formula that does just this: Rank = (compressed CFD score...the DNA target. CFD scores are then modified (“transformed”) such that weak interactions (e.g., scores <...

... base editing platforms for plant systems.  Figure 2: Plant base editor platforms and their molecular...72 hours post-transformation/transfection in a transient assay. For stable transformation, regenerated ... reducing the likelihood of detrimental indel formation. After binding with DNA, the CBE deaminates a ...G)? You may wonder if a CRISPR-base editor can perform this change. However, there are no naturally known...deaminases (ecTadA), fused it with dCas9, and transformed it into E. coli harboring the defective CamR ...genome edited plants via Agrobacterium-mediated transformation. We also constructed smaller vectors suitable...suitable for transient assays using protoplast transformation. Cytosine base editors for plant There are several...