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We narrowed to 698 results for: des.1

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  1. Cellosaurus: A Cell Line Information Database

    Type
    Blog Post
    ... if the name was the correct one!)    Fig. 1: HeLa cells. Image courtesy of Josef Reischig.  ...database describing nearly 145,000 cell lines. Cellosaurus Cellosaurus seeks to identify and describe all ...authors of the paper in which the cell line was described. Using Cellosaurus Cellosaurus is searchable by...Cellosaurus received a report that HT-55, which was described as a colon cancer cell line, is actually a rectal...

  2. Working 9-5: an Addgene Co-op

    Type
    Blog Post
    ... everyone was very approachable.     Fig. 1: Examples of DNA sequencing QC work    In addition...process When I first saw the comprehensive job description for this co-op, I was immediately interested ...had stood out to me because it gave me a full description of the tasks I would be responsible for, in comparison...it relates to other teams at the company. This provides new (and old) employees with information on how...

  3. IBEX Knowledge-Base: A Data Resource for Multiplex Tissue Imaging

    Type
    Blog Post
    ...that work for our experiments!)     Figure 1: The IBEX Imaging Community front page. That’s...spatial biology enthusiasts. This dataset currently includes 1049 community-validated reagents from 20 contributors... And the dataset is rich. Experimental data includes reagent type, target species, target name, host... inspired by the open-software community when designing the IBEX Knowledge-Base, seeking to create an ...

  4. The Open Repository of CRISPR Screens: CRISPR Screen Data in One Place

    Type
    Blog Post
    ...datasets by computational biologists. Figure 1: The BioGRID Open Repository of CRISPR Screens (ORCS...ve just discovered that your favorite gene was described in a CRISPR screen publication. You see this mentioned...This format is inherently flexible and allows the broadest possible scope of screens to be curated, for example...other than cell viability. The following video provides an in-depth walk through of how to use ORCS:   ...

  5. Custom CRISPR Screens & the Green Listed Software

    Type
    Blog Post
    ...in less than a minute (1). Green Listed is a new software tool used to design gRNAs for custom CRISPR...found through https://wermelinglab.com/.   References 1. Panda, Sudeepta Kumar, et al. "Green listed—a CRISPR... massive amount of descriptive transcriptomics data. Custom CRISPR screens designed to target differentially...Institutet, in Sweden. It can be very time consuming to design 5 guide RNAs (gRNAs) targeting each of the 1000...moment, 13 full genome SpCas9 knockout libraries designed by different academic labs, targeting mouse, human...drug targets  Another interesting approach is to design screens against known druggable targets, preferentially...library from Addgene, and then use Green Listed to design a smaller validation screen using selected gRNAs...

  6. 9 tips for a successful postdoctoral experience

    Type
    Blog Post
    ...briefly describe some tips for a successful postdoc fellowship. 1. Reverse engineer success On Day 1 of your...typically writes the grants that fund your research, guides the research directions of the lab, gives you constructive...Thesis committee members provide expertise in designing and interpreting experiments, as well as career... there a tractable question or are you simply describing a phenomenon? Exploration can be important, but...presentations benefit from practice. If you simply recycle slides from the last time you gave a presentation to a...story I can tell with my data?  Can I make better slides that more effectively tell a story? Generally,...or functional models or more helpful background slides. If you don't have much new data, speculate on ...

  7. Antibodies 101: Introduction to Antibodies

    Type
    Blog Post
    ... antibody recognizes and binds to.   Figure 1: Labeled diagram of an antibody including Fc, Fab,...45. https://doi.org/10.1016/B978-012198382-6/50026-1 Wang R, Xiang S, Feng Y, Srinivas S, Zhang Y, Lin ...been infected with a microbe, to trigger immune cascades that clear these infections. Anything that generates...immune response and initiates different immune cascades. In the research setting, antibodies of different...antibody, which recognizes the primary antibody and provides the method of detection. You’ll also want to use...used for. Addgene’s Antibody Plasmid Collection includes plasmids that express antibodies, nanobodies, ...

  8. Plasmids 101: What is a plasmid?

    Type
    Blog Post
    ...Figure 1: Map of a plasmid with its elements described below.   Vector Element Description Origin...molecular biology lab will undoubtedly be asked to design, modify, or construct a plasmid. A plasmid is a...why each is important. Our “Plasmids 101” series designed to educate all levels of scientists and plasmid...basics and spend more time developing cleverly designed experiments and innovative solutions necessary...utilized in the lab are usually artificial and designed to introduce foreign DNA into another cell. Minimally...the lab. Addgene’s Molecular Biology Reference includes information about molecular cloning, how to choose...

  9. Antibodies 101: Fc Effector Functions

    Type
    Blog Post
    ...into three main effector functions.  Figure 1: Fc effector functions in an immune response to a ...know that the Fc domain provides structure, determines isotypes, and provides a place for secondary antibodies...yes, it does! While the Fc domain’s functions, besides structure and isotype determination, don’t generally... 2022). So the next time you see an antibody description with the Fc domain as only providing structure...

  10. Five Questions to Ask If You're Deciding Between a Master's or PhD Program

    Type
    Blog Post
    ...help you decide if a master’s might be for you. 1. Are you interested in master’s-level jobs? Ultimately...a job search website like Indeed. Do the job descriptions sound interesting? Is the work something you... types of jobs people with master's have Job descriptions often fail to capture all of the responsibilities...responsibilities of a role, so it helps to see how people describe their actual work. To do this, try looking at ...and industry, often means moving from the lab to a desk, although there’s often technical career tracks ...

  11. Choosing Your Perfect Empty Backbone

    Type
    Blog Post
    ...vectors (e.g. pBV-Luc) and gene silencing (e.g. pLKO.1 - TRC cloning vector). Check out our complete guide...vast collection of empty backbones that have been designed, tested, and published by academic scientists....find the vector that fits your experiments, I've described below some of the most frequently requested vectors...protein with a specific resin (e.g. 6xHis containing pDEST-HisMBP). After purification the protein can be released...vectors. Consider your applications and experimental design. You can create a new strain with a disrupted gene...

  13. What's New in CRISPR - March 2020

    Type
    Blog Post
    ...plasmids CRISPRi in Caulobacter crescentus Figure 1: Serial dilutions of CRISPRi in Caulobacter cells ... whose expression varies depending on transgene design and delivery. They generated hPSC lines with AAVS1...

  14. We're Updating Our Hold for Publication Policy

    Type
    Blog Post
    ... email in a busy inbox. Updated policy As of July 1, 2025, we are updating our Hold for Publication policy... release plasmids on hold if they are clearly described in a journal publication. Plasmids will be released...

  15. New Viral Vectors - Fall 2024

    Type
    Blog Post
    ... serotonin, and much more. Check them out! Table 1: New ready-to-use viral vectors in the Addgene repository...available in the Addgene viral vector repository! This includes the first Addgene prep packaged in the AAV9-X1.1...

  16. Fluorescent Proteins 101: Fluorescent Biosensors

    Type
    Blog Post
    ...of experiments they are commonly used for.  Table 1. Points to Keep in Mind When Performing Biosensor ...These sensors generally follow the same pattern described above - a sensing domain induces changes in a ...

  17. Sensing Neuronal Dopamine

    Type
    Blog Post
    ...region of the brain where DA quantitation is desired (Figure 1). The probe perfuses liquid, which causes ...et al., 2018). These sensors also exhibit high magnitudes of fluorescent responses. Studies on the kinetics...Ultrafast neuronal imaging of dopamine dynamics with designed genetically encoded sensors." Science 360.6396...

  18. Understanding GPCR Signaling Using TRUPATH

    Type
    Blog Post
    ...updated version of BRET called BRET2. Figure 1: TRUPATH measures heterotrimeric G protein dissociation...in the initiation of a vast number of signaling cascades, inducing different cellular responses. One of...localization of the Rluc8 insertion within the Gα. Despite exhaustive refinement, it was not possible to generate...protein signal transducers. The TRUPATH collection provides scientists with a toolkit to gain an understanding...

  19. Why Add Sucrose? Improved Yields for Adeno-associated Virus Preparation

    Type
    Blog Post
    ...materials to the research community. References 1. Coroadinha, A. S., et al. "Effect of osmotic pressure... to improve viral vector production. Whether redesigning viral packaging plasmids, investigating different...untreated and sucrose treated viral preparations.    Despite observing a positive effect on our overall yield...due to impaired endocytosis. In parallel assays designed to test the endocytosis of a fluorescent dye and...

  20. Addgene Begins Distribution of Recombinant Antibodies

    Type
    Blog Post
    ...ScFvs, based on community demand. Figure 1: Antibody against PSD-95 from the Trimmer Lab. Information...Addgene is building our antibody resource, which includes recombinant antibodies, educational materials,...California Davis School of Medicine. This deposit includes frequently cited antibodies for use in brain imaging...supporting hybridoma sharing within the community for decades. Educational Resources The Basics of Western Blotting...

  21. Antibodies 101: Epitope Availability

    Type
    Blog Post
    ... to just that particular assay.      Fig. 1: A native protein (left) is denatured, allowing the...available for binding change as well. If this change hides the epitope that the antibodies used to recognize...conditions. In those cases, pay special attention to designing your controls in validation, as you may need to...help you avoid a great deal of frustration when designing and troubleshooting immunoimaging assays. It can...

  22. Addgene's Top 10 Blog Posts of 2015

    Type
    Blog Post
    ...year and happy reading! Top 10 blog posts of 2015 1. CRISPR 101: Homology Directed Repair Addgenie Chari...inversions, deletions, and translocations. It also provides researchers with many different ways to control...the right one. In this post, Addgenie Melina Fan guides us through the basics of the validation process...experiment? In this post, Addgenie Chari Cortez guides us through some common controls and why you might...

  23. Fluorescent Proteins 101: Monitoring Cell Mobility Using Fluorescent Proteins

    Type
    Blog Post
    ...do researchers track fluorescently labeled cells? 1. Epifluorescence microscopy This technique uses a ...of the immune system and its dynamics. References 1. Peters, Nathan C., et al. "In vivo imaging reveals...their specificity or from the thymus to the lymph nodes. These methods gave researchers much more information...expressing cells. For example, by harvesting lymph nodes at different times after antigen challenge, scientists... cellular dynamics in lymphoid organs. In lymph nodes, for example, two-photon microscopy allowed scientists...extravasate from the bloodstream to invade lymph nodes and scan antigen presenting cells, but two-photon...interactions in diverse tissues, including lymph nodes, brain, liver, gut and skin. Two-photon intravital...

  24. Antibody Guide

    Type
    Guide
    ...and placed in a buffer. Antibody Structure Figure 1: Structure of an antibody A standard antibody is made... together to form a “Y” shape, as shown in Figure 1. The two arms of the Y structure are responsible for... is described in more detail in the Multiplex Assays section below. The following table describes the ... Science Guides Antibody Guide Antibody Guide View Addgene's Antibody...of B cells isolated from animals immunized as described above are used to create hybridomas, which produce...each antibody has two binding sites. Isotype Description Configuration and Valency Subclasses IgA Prevalent... used to quantify relative amounts of protein. Includes: Western blot ELISA Capture - used to isolate ...

  27. Rewiring Metabolic Circuitry with CRISPR RNA Scaffolds [Video]

    Type
    Blog Post
    ... 160(1), 339-350 (2015). PubMed. Find the Plasmids @Addgene: Plasmids for CRISPRi are described here...stepwise protocol on designing and using RNA scaffolds: Delebecque, C. J. et al. Designing and using RNA scaffolds...regulators allows a greater degree of control of desired expression levels dependent upon the type of transcriptional...transcriptional regulator or the number of designed scaffold binding sites. With hundreds of characterized...tunability of transcription is possible. From a design perspective, this is appealing since the RNA scaffold...pairing, allowing for rational, straightforward design. Since the technique relies on base pairing, it...and multidirectional multiplex control via scRNA design is readily apparent in metabolic engineering. The...

  28. Hot Plasmids - June 2020 - Barcoded CRISPR Library, Sparse Cell Labeling, Calcineurin Reporter, and DNA Staining Dye Alternative

    Type
    Blog Post
    ...Article contributed by Susanna Bachle Figure 1: Initial steps in the CRISPR-pooled screening using...assign four different barcodes to each of the gRNAs and to embed these barcodes within the gRNA sequences...lab designed a calcineurin transcriptional reporter consisting of a quickly-degraded destabilized GFP ...method that makes use of guide RNAs with internal barcodes (iBARs) in their loop region. After infecting ...bioRxiv 2019. https://doi.org/10.1101/788679 A destabilized GFP reporter for calcineurin activity in yeast...intracellular Ca2+ (bottom panels) equipped with destabilized GFP calcineurin reporter (blue) and stained ...

  29. Viral Genome Sequencing - A One Stop Shop for AAV Identity and Serotype Confirmation

    Type
    Blog Post
    ...and cost for AAV genome sequencing.  Figure 1: The viral genome sequencing workflow. Using this...our AAV preparations. We recently published a description of the VGS process and use cases in Human Gene...ligation and tagmentation preparation approaches described previously require a preliminary double stranding... the expression cassette that we want, it also includes a small amount of spurious DNA from the packaging...plasmids. We decided to use this to our advantage by designing a Python script that looks for pre-defined serotype...signature sequences in the data. Unlike previously described thermodynamics-based methods of serotype confirmation...

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

    Type
    Blog Post
    ...heterodimerizes with CIBN upon blue light exposure (see Fig 1*). When the group targeted the enhancer region of ...almost complete desensitization when exposed to continuous bright light. Desensitization is mediated by...discovered Marine, Anion-conducting and Intensely Desensitizing ChRs) differ from currently used ChRs in that...regulation of many genes. A number of groups have designed means of studying the effects of endogenous looping... they call the LADL Anchor. Using specifically designed gRNAs, they can then recruit these LADL Anchors...

  31. Antibodies 101: Epitope Tags

    Type
    Blog Post
    ...net negative charge with 4 negatively charged and 1 positively charged amino acids. Myc tags are frequently... What are epitope tags? Epitope tags are short peptides introduced at the N or C terminus of a protein...purification or detection of the tagged protein. These peptides consist of as little as 8 or as many as several...need monoclonal GFP antibodies or guidance on designing a GFP tag Addgene has you covered!   Potential...Protein folding issues, steric hindrances, and destabilization can be brought about by the tag so it’s important...

  32. Creating accessible biology activities in schools with BioBits

    Type
    Blog Post
    .... You can email her at [email protected].   References 1. Huang, Ally, et al. "BioBits™ Explorer: A modular...resources to provide them to their students. My desire to create a set of low-cost, easy-to-use educational...protein – you first need the DNA sequence that encodes it. That DNA sequence then needs to be incorporated...one is as cheap as 10 cents, making activities designed with FD-CF reactions affordable to many schools...students. In our BioBits kit for example, we’ve designed FD-CF experiments that result in outputs that ...

  33. CRISPR 101: Multiplex Expression of gRNAs

    Type
    Blog Post
    ...post about multiplexing with Cpf1.   Figure 1: Multiplexing allows researchers to express multiple...be used in a wide range of bacteria. References 1. Maddalo, Danilo, et al. “In vivo engineering of oncogenic...ligated into Cas9 or dCas9-containing destination vectors. Destination vector options include humanized wt...cell that gets the plasmid contains all of the desired gRNAs. This increases the chance that all the edits...promoters. To use this plasmid, you simply order oligonucleotides for your chosen gRNA target sequences and ...ordered assembly of multiple components into a destination vector. The first step in CRISPR/Cas9 Golden ...Golden Gate multiplexing is to clone the oligonucleotides specifying each gRNA target sequence into distinct...

  34. Tips for Improving Your Next Manuscript

    Type
    Blog Post
    ...class.   Four ways to improve your next manuscript 1. Be consistent with your figures The figures of a ...should also be easily understood and consistent in design and layout. 2. Be concise in your writing  When...

  35. 10 Ways to Share Your Science!

    Type
    Blog Post
    ...them you can do today! 10 ways to share your science 1)   If you don’t already make it a habit to talk – ...research, SciFund is really motivated more by the desire to help close the widening gap between science ...

  36. An Addgene Summer Internship

    Type
    Blog Post
    ...intern to complete and present on.    Figure 1: Addgene's summer interns presenting their capstone...instrument. They are the oldest sibling in a Guatemalan family of Mayan descent.   ...teaching me the basics of physics and sustainable design while allowing me to do my internship in the daytime...

  37. Viral Vectors 101: Transductions

    Type
    Blog Post
    ...depending on the virus, cell type, and/or desired event.   Figure 1: Transduction to expression process...retrovirus, lentivirus, adenovirus, or AAV. Then, your desired DNA to be integrated can be cloned into the vector...packaged, when the vector is expressed. Once the design and construction steps are complete, it’s time ...

  39. Plasmids 101: Gram Negative and Positive Bacteria

    Type
    Blog Post
    ...heat-fixed smear with the crystal violet stain for 1 minute. Rinse the slide briefly with tap water. Flood...phrase gram negative or positive being used to describe a species of bacteria, but what does it actually...bacteria. In a gram negative bacteria, the alcohol destroys the outer lipid membrane, and the thin inner peptidoglycan... is also useful in a laboratory setting. When designing a plasmid to be inserted into a specific bacterium...

  40. Hot Plasmids and Viral Preps - September 2021

    Type
    Blog Post
    ... difficult to modify in the past.   Figure 1: Identification and enrichment use of XMAS-TREE. a...without end-point sequencing assays.  This tool was designed by putting together the coding sequence of a mCherry...MYC-CRISPR library targets E-boxes genome-wide. It was designed based on MYC-ChIP-seq data from several MYC-dependent...

  41. What Do I Do Now? Academic v. Non-Academic Career Decisions

    Type
    Blog Post
    ...occur, but good performers move around easily  Table 1: Taking it a Step Further - Big Company v. Small Company...one list can ever encompass them all. We can’t designate non-academic jobs as “alternative” anymore. ...Develop expertise areas quickly Jack/Jane of all trades More sources of training and resources within...

  42. Another Pathway into Cells: iTOP

    Type
    Blog Post
    ...vesicles. Okada CY, Rechsteiner M. Cell. 1982 May;29(1):33-41. PubMed. Protein transduction: unrestricted...transduced using only protein. Read on for a description of the lab’s iTOP protein-only transduction method...transduction by osmocytosis and propanebetaine) to describe this method of protein transduction. Later studies...

  43. Visualizing Translation at the Single Molecule Level

    Type
    Blog Post
    ... cell types and physiological states. References 1. Ingolia, Nicholas T., et al. “Genome-wide analysis... determine if proteins are targeted to their destination co- or post-translationally. TRICK: Visualizing... usually translated in a specific compartment. Despite these limitations, these techniques represent powerful...

  44. Components of CRISPR/Cas9

    Type
    Blog Post
    ...components necessary to: 1. Bind to a guide RNA The guide RNA, which will be described in more detail below...express a gRNA designed to direct Cas9 to their target sequence of choice (see tips for designing a gRNA) and... of the major CRISPR lingo and will be able to describe the functions of the various CRISPR/Cas9 components...responsible for processing foreign DNA as well as the RNA guides required for endonuclease function, when used for...DNA damage is a DSB within the target DNA ~3-4 nucleotides upstream of the PAM sequence. Cas9 Species/Variants...with the appropriate PAM sequence) to modify the desired genomic locus.   Some historical notes CRISPR ... combined with its adjacent spacer, ultimately encodes a single crRNA. The direct repeat regions contain...

  45. How Addgene Creates Content

    Type
    Blog Post
    ...to do that than in the Addgene blog?  Fig. 1: One of our favorite content collections is our Help...up walls of text. Since our guides are heavily used, our graphic designer made most of the Antibody Guide... quickly." Final design (right). Immediate and immense regret of the graphic designer not shown.   ...blog, website, social media, videos, newsletters, guides, and e-books – comes into play. Our goal is to ...communication between our content team and our graphic designer to make sure things are clear, accurate, and in...Reference image (left) provided to our graphic designer upon request that the science communicator "just...

  46. Behind the scenes: Addgene’s new search engine and more

    Type
    Blog Post
    ...present in the data such as synapsin, hsyn synapsin-1, human synapsin, hSynap. Matching We capture multiple...educational resources — including blog posts, protocols, guides, and collections — is a lot of material to sift... launched earlier in the year, as well as our redesigned homepage and our new search tool, are the results...a few of the strategies we used in our software design. In each case, we leveraged the team’s knowledge...per resource category to expose as filters and designed the search engine to return only the filters that... bits of information for a given resource, and designed the search engine to weight search results differently...'s new search Read to learn more about why we redesigned our homepage and mascot ...

  47. Plasmids 101: Methylation and Restriction Enzymes

    Type
    Blog Post
    ...into account, the digest pattern depicted in Lane 1 would be expected for a XbaI/NotI digest. The program... NEB's Resource describing Dam and Dcm Methylases Discovery of DpnI Review describing dam-/dcm- E. coli...mutagenesis. During this process, incorporation of a desired mutation into your plasmid of interest by PCR generates...only the non-mutated and methylated template is destroyed leaving behind a pool of mutated plasmids which...

  48. Scientists Map the SARS-CoV-2-Human Interaction Network

    Type
    Blog Post
    ...faster. Years of science, done in weeks Figure 1: Sending out 80 FedEx envelopes in a single day --...s time, we’ve published an article on BioRxiv describing a comprehensive SARS-CoV-2 virus-human interaction... viral proteins except for Nsp3 and Nsp16, and includes an additional catalytically dead version of the...the viral protease, Nsp5. Our set also includes a GFP construct as a control. For easier portability, ...

  49. Communicating Your Science With Help From ComSciCon

    Type
    Blog Post
    ... will be a positive asset throughout your career? 1. Make scicomm practice a priority The good news for... craft sentences for abstracts and presentation slides, learn from audiences as they do science outreach...about whether the same principle applies to other slides in your deck.  If someone asks a question about...of a new science communication initiative that provides yet more scientists with opportunities to practice...

  50. Plasmids 101: Blue-white Screening

    Type
    Blog Post
    ...and also by a lactose analogue, IPTG (isopropyl β-D-1-thiogalactopyranoside). (To be completely accurate...bacterial lac operon contains a gene called lacZ that encodes for the enzyme β-galactosidase. Expression of the...process is called α-complementation. The system described above was put to practical use in the following...Although blue-white screening is probably the most widespread way to select for plasmids containing an insert...
Showing: 501 - 550 of 698 results