... It’s possible to associate the depositor’s ORCID ID with the deposit, and a DOI is added to the deposit...integration is described in this video and the Figshare integration in this video.  The ability to link from...making it searchable and shareable, but some ELNs provide better support for reproducibility than others....reproducibility is limited in two ways – only data inside the ELN is reproducible, and only the highly restricted...requirements that emerged from intensive engagement with a wide range of people at the University of Wisconsin in...principles in mind, and in response to further input provided by the research communities at the University ...online file storage tools, as illustrated in this video, and to data stored on institutional and lab servers...

...https://books.google.at/books/about/Arabidopsis.html?id=IfZAMNPWVk4C&redir_esc=y (Accessed: 21 September ...culture into a container that is wide enough to dunk your plant’s flowers inside. 50 mL falcon tubes or plastic...process right the first time. I’ll lay out some guidelines here. A detailed transformation protocol, as ... et al. (2006) ‘A rapid and robust method of identifying transformed Arabidopsis thaliana seedlings following...

...Short Tandem Repeat (STR) profiling can be used to ID the cell line. The same test is so good that it is...many journals strictly require evidence of cell line provenance and identity. The Nature Publishing Group...Resources ATCC Animal Cell Culture Guide Thermofisher Guidelines for Maintaining Cultured Cells Invitrogen...Invitrogen Cell Culture Basics Guide Abcam Cell Culture Guidelines Resources on the Addgene Blog Learn ...culture in the present day Cell culture is a widespread tool used in the fields of oncology, virology...this reason. Unreproducible results are rife. Misidentified or cross-contaminated cells have been known ...Invasion in Renal Cancer Cells, Marker-independent identification of glioma-initiating cells. The International...

...desired insert (e.g., mScarlet).   Plasmid ID Plasmid Name Tags 69090 pMJ915 MBP (N...differences in guide RNA efficiency. For example, in a two-guide floxed experiment, if one guide cleaves less...from the target exon on either side. They have successfully used guides targeting the same or complementary...on each side. For optimal repair, place the loxP sites precisely at the cut site for each guide. This design...RNP) complexes of Cas9 protein and the separated guide RNA components (crRNA and tracrRNA) for maximum ...given location, you’ll need to design only a single guide and your donor ssDNA. Here, we’ll use the example...homology-directed repair experiments, you’ll want the guide cut site to be as close as possible to your desired...

...Biology. New York: W. H. Freeman, 2000. Bookshelf ID: NBK21668. Matsuno-Yagi, Akemi, and Yasuo Mukohata...neuronal subpopulations, and this represents a major downside in optogenetics (Belzung et al., 2014). This could...genes. Strong cell-specific promoters, on the other side, are too long for rAAVs, which can only package ...Double-floxed Orientation)) is a powerful tool that provides precise temporal and spatial control of gene expression...produce behavioral and electroencephalography evidences of arousal in mice previously subjected to steady-state...., 2019). FLEx vectors represent, therefore, an ideal partner to optogenetics to understand the cellular...

.... (2024). A guide to selecting high-performing antibodies for Synaptotagmin-1 (Uniprot ID P21579) for ...antibodies when possible. If cost is prohibitive, consider an approach that prioritizes more reproducible... rate. If you need a more permanent knockdown, consider using shRNA vectors instead. With both siRNA and...this approach should also allow for the clear identification of the cell types of interest. By correlating...correlating your data sets, you can increase confidence that the labeling observed represents the expression ... at similar levels in your cell lines, you can consider a cell treatment approach. If there is a cell ...protein. A challenge to this approach is that the identity of the epitope is often not available to confirm...

...immunohistochemistry, and are summarized in the table below:   ID Cv (Capsid) FLAG Tag Terminus 79629 (N) and 79628... Neurosci 2016. PubMed PMID: 26950006 Plasmid ID Plasmid Name Plasmid Type 74309 pcDNA3.0-TRPV4-...DHS-seq, FAIRE-seq, and CHIP-seq), genome-wide identification and quantification of enhancer activity have...RNA-guided targeting mechanism. However, the laborious construction of repair templates and guide RNA ...: Targets of RNA-binding proteins identified by editing Identifying targets of RNA-binding proteins (RBPs...region sequencing) that tests enhancer sequences outside of their endogenous chromatin environment and relies...screen the entire genome for genes that regulate a wide variety of phenotypes, including but not limited...

...editing for precise genome modification. Plasmid ID Plasmid Name Cas9 Variant Speacial Features 85169...Cas9, been identified. In Rauch, et al. 2016 the Joseph Bondy-Denomy lab at UCSF identifes four proteins...our hot plasmids articles. These brief articles provide a synopsis of a plasmid or group of plasmids' functions...may be preferred for their intended uses, they provide a well-defined framework for the production of ...available at Addgene, and the Doyon lab has also provided a detailed protocol at Protocol Exchange. Plasmid...editors with editing windows as small as 1-2 nucleotides! To reduce off-target effects associated with... created HF-BE3, a base editor containing high fidelity Cas9 variant HF-Cas9. They subsequently tested...

...questions. Protocols Video protocol guides for standard laboratory procedures. How-To Videos Screencapture walk-throughs...Protocol How-To Videos (Link opens in a new window) Video Link Description Related Page MTA Guide - Requests... Educational Resources Addgene Videos Addgene Videos Browse Addgene's collection...collection of video content. Find video protocols, tips on using Addgene's resources, and career advice. For...walk-throughs to help guide you through Addgene's online resources. Career Videos Get career insight and...to Deposit Your guide to depositing plasmids with Addgene Depositing Page Career Videos (Link opens in ...A collection of Addgene's video content, including how-to screen captures, lab procedure protocols, and...

...(See section below.) For guide design, we decided to adapt the popular guide design tool Crispor by Max...which the guide binds. However, if the PAM resides in a coding region, the mutation may cause side-effects...optimal mutation in CrispyCrunch: If the guide PAM resides outside a coding region in a UTR, CrispyCrunch... experiments designed outside CrispyCrunch, or you can input pre-existing guides for primer design. The...return guides and primers in batch, optimized for HDR. Compared to wealth of resources for guide design... summary per batch. Ranking guides for HDR in-depth In other tools, guides are ranked by specificity of...specificity of a guide to the target. The CFD score ranges between 0 and 100 for each guide, with 100 being...

...genome-wide, unbiased identification of double-strand breaks (DSBs) evaluated by sequencing (GUIDE-seq) ... Not Provided 5% Inexpensive, simple Low-throughput, low sensitivity Sanger Sequencing Provided 20% ...PMC3782611. 8. Tsai, Shengdar Q., et al. "GUIDE-seq enables genome-wide profiling of off-target cleavage by ...gel electrophoresis. Surveyor™ and T7E1 have been widely adopted due to their relative simplicity and low... problem with these assays is that they do not provide sequence-level data. They also have a limit of ...sequencing. Used in concert, these approaches can provide the researcher with a reasonable level of certainly...off-targets. This is a valuable step toward enhancing confidence and reproducibility of a study’s findings. Table...

...Views Guides CRISPR Guide Lentiviral Guide AAV Guide Optogenetics Guide γ-Retrovirus Guide Protocols... popular videos are protocol videos, where showing exactly how to execute a step can provide needed clarity...accessible, due to a wide range of logistical barriers. Addgene worked to identify, reduce, and remove ...allowing people to access a wide catalog of plasmids from all over the world. This idea, that available and accessible...Addgene distributes to per year, 2005-2023. We identified and offered a number of solutions that increased...over half of our orders coming from researchers outside the USA, having some materials available to order...consistently accessible, wasn’t an option. So we identified countries that would benefit from a third-party...

...DNA guides NgAgo uses 5’ phosphorylated DNA guides (so called “gDNAs”) rather than the RNA guides employed...remains faithful to its guide DNA and cannot switch guides. While this fidelity would prevent other small...24 base DNA guides may be more user-friendly, since they can be ordered as oligonucleotides and should ...gDNA guides will also need to be transfected into the cells of interest. In contrast, RNA guides must ... tested if NgAgo preferred certain guide sequences - using 5 guides/gene for 10 genes, they did not observe... the DNA guide impaired NgAgo activity, with three mismatches abolishing activity. One-guide faithful...important role in RNA interference, binding RNA guides to cleave foreign RNA. Argonaute proteins are also...

...similar to TIDE known as TIDER (Tracking of insertions, deletions, and recombination events). TIDER can screen...both trace files to the TIDE tool online along with your sgRNA sequence. The TIDE software will generate...off-target effects with Sanger sequencing, provided you have some idea of where in the genome you might expect...knockouts is Tracking of Indels by Decomposition (TIDE) (Brinkman et al., NAR). This technique uses the... deletion frequency. Fig. 1: Overview of TIDE. The input is sequencing trace files of WT and edited...input population or clone.   How to perform a TIDE First, use PCR to amplify the target region of interest...graph representing all insertions and deletions identified within a given genomic window, along with the...

...with peptide/protein analyses using ELISA. Peptides 72:4–15 . https://doi.org/10.1016/j.peptides.2015.04.012...vary the acrylamide content of the gel. For small proteins, use a higher percentage of acrylamide to increase...usually composed of a nitrocellulose or polyvinylidene difluoride (PVDF) in a step called protein transfer...they provide qualitative measurements. If you require precise quantification of a protein, consider using...immunoprecipitation and pull-down assays.  Westerns are divided into two categories, native and denaturing. In ... protein mix by size Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) is the first...agent, typically containing thiols, to cleave disulfide bonds. Load the samples, one sample per lane, ...

...Having answer slides ready after your formal conclusion slide will also help with your confidence. It is best...suspense. Notice the simplicity of their slides and how the slides complement the spoken message. Learn from...speak to start creating slides or thinking about content. Create a Google.slides or Powerpoint file right...this might sound condescending, consider explaining the term on a slide but not reading the explanation...everything I allow 1 slide for every 1 minute of talk length, and then I cut a few more slides. Do not run over...always be a future boss in the room, so it is a good idea to start thinking about public speaking early and...talks for non-academic settings. Many of these guidelines will apply to any type of science presentation...

...overhangs with the same three nucleotides in a row; (4) no more than two nucleotides in the same position; (...that high-fidelity reactions could be done using overhang sets that broke rules 3—5. Fidelity, it turns... design high-fidelity Golden Gate Assemblies and overhang sets: NEBridge Ligase Fidelity Viewer™; NEBridge...reactions. NEBridge Ligase Fidelity Viewer This tool allows a user to check fidelity of an overhang set by ...remarkably high 71% fidelity, while the 52-piece assembly of a lac operon dropped to 49% fidelity, with significant...be strictly followed in order to generate high-fidelity reactions. (Need a refresher? The five rules are... a single tube. Their assembly had a predicted fidelity of 71% (Pryor et al., 2020). And in 2022, using...

... requires that you provide two out of six forms of documentary evidence: Evidence of receipt of major...obtain permanent residence. The recently established case Matter of Dhanasar provides the three-prong ...field Evidence of original scientific or scholarly research contributions in the field Evidence of authorship... to convey general information only and not to provide legal advice or opinions. The contents of this ...advice on specific legal issues.  The permanent residence “green card” process is a necessary and often ...uncertainty associated with filing a permanent residence case with United States Citizenship and Immigration...national researchers who require visas, permanent residence or citizenship to continue their work in the US...

...defined peptides. Munro and Pelham’s first published peptide tagging experiment involved a peptide from ...with unrelated peptides that already had high quality antibodies available - aka peptide tagging.  Key ...bound to the mid-protein peptide, while three bound to the C-terminal peptide. One of these C-terminal... of these new antibodies and identified Myc1-9E10 and its target peptide as a suitable pair for protein...from the neuropeptide substance P. This protein had a highly specific antibody to the C-terminal five amino...could be quite small. However, substance P has an amide group added to its C-terminus post-translationally...critical for antibody recognition. As such, the peptide could only be added to the C-terminus of proteins...

...for protein-peptide locking, Mark Howarth’s lab has developed a new tool for peptide-peptide locking. The...One 2013 Oct 7;8(10):e76117. Irreversible peptide-peptide ligation using SpyLigase Building off their...that promotes the formation of an isopeptide bond between 2 peptide tags, SpyTag and KTag. The group demonstrated... demonstrated the use of the SpyLigase peptide-peptide interaction to link affibodies or antibodies against...scientists to use CRISPR-Cas technology to perform genome-wide knockout screens. These vectors and sgRNA libraries... to browse CRISPR plasmids, watch informational videos, download protocols, and more! Looking for background... CRISPR technology? See our improved CRISPR-Cas Guide. Wang et al., Science. 2014. Jan 3;343(6166):80...