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Showing: 301 - 320 of 756 results

  1. A Guide to Starting Your Own Journal Club

    Type
    Blog Post
    Published
    Feb. 6, 2020, 3 p.m.
    ... by polling and informal communications we made a decision to try out a Bioinformatics/HTS a journal club...popular, including those based on Twitter. At my former academic department, we had two recurring journal...teams had various levels of experience with bioinformatics and HTS, we all had much to learn. And, many...supplemental data, software repositories, or other information needed by someone to critically discuss the paper...Discussing next-generation sequencing at the Addgene bioinformatics journal club! What happens during journal...diving deep into the individual data points. All formats should be an open forum where people feel welcome...These questions should be tailored to the group and format but should almost universally include the questions...

  2. Plasmids 101: Colony PCR

    Type
    Blog Post
    Published
    May 12, 2016, 2:30 p.m.
    ...Molecular Cloning Technique Learn to Perform a Bacterial Transformation Deposit Your Positive Clones with...discusses some of the key things to consider when performing colony PCR.   Designing colony PCR primers ...downside: this type of primer does not provide information about the orientation of the insert. Orientation-specific...Orientation-specific primers: If you need information about insert orientation, then you might consider designing...each insert Backbone-Specific Provides information about the size of the insert and if it's in the...primers are plasmid dependent Doesn't provide information about the orientation of the insert Orientation-Specific...control. A good positive control is bacteria transformed with the same backbone plasmid. If this control...

  3. Viral Vectors 101: Preparing Pooled Libraries

    Type
    Blog Post
    Published
    July 13, 2023, 1:15 p.m.
    ... the pooled library is transformed into E. coli for amplification. Transformed E. coli are allowed to ...used to determine functional titer with a colony formation titering assay or similar protocol. After functional...library. This is similar to amplifying a plasmid: transform E. coli with the pooled library DNA, allow the...red.    Unlike a standard single plasmid transformation, though, a pooled library has hundreds to millions...diversity of the library sample, and any other information or scripts provided by the depositing lab for... be skipped or whether selecting colonies and performing Sanger sequencing will suffice…and the answer...mostlibrary requests specifically to allow scientists to perform functional titering and optimize transduction efficiency...

  4. CRISPR 101: Off-Target Effects

    Type
    Blog Post
    Published
    Feb. 8, 2024, 2:15 p.m.
    ... line to perform downstream characterization of, isolating 2 or 3 distinct clones to perform key experiments...CRISPR-Cas system localizes to unintended sites and performs its programmed function there, this is an off-...associated with an elevated mutation burden. The CRISPR platform must be optimized to reduce off-targets and patient...Hopefully you can understand that depending on your platform, off-target effects should impact your experimental...would confound your experimental results and 2) perform targeted off-target measurements at those sites... to quantify off-target effects entirely is to perform whole genome sequencing. While this may be unnecessary... The con to these approaches is that NHEJ must perform the repair to allow for detection, not Homologous...

  5. A Guide to Designing a Scientific Poster: Content, Layout, and More

    Type
    Blog Post
    Published
    Oct. 22, 2019, 12:20 p.m.
    ... understand that presenting your work in poster format differs in many ways from writing a manuscript....to include are a references section, contact information, and potentially a photograph of yourself. A ...where you can insert your references and contact information, and it is generally acceptable for the font ...accomplish this by employing a neat and organized format.  Columns. You can choose from either a two, three...than horizontally. Instead of displaying your information as columns, you may choose to display it as rows...barcode is included that links readers to more information if they desire it. Shapes. In this type of poster...poster, written and graphical information are inserted into larger circles or ovals, that are arranged...

  6. Adapting Toehold Switches to Detect Zika Virus

    Type
    Blog Post
    Published
    Aug. 30, 2016, 2:30 p.m.
    ... on advancing the paper-based platform toward a more field-ready format when the Zika virus outbreak was... 2014). The second was an in vitro paper-based platform that allowed gene circuits to be deployed out ...out of the laboratory in a cell-free and biosafe format that was stable for up to a year at room temperature...we say the timeline to develop our paper-based platform into clinically relevant diagnostics for the Zika...prototyping pipeline that can take pathogen sequence information from public databases to the production of validated...regions of the genome, we have deposited the best performing sensors and constructs encoding corresponding...and electronic companion technologies that has transformed the assay’s capabilities. Specifically this includes...

  7. AAV Vector Quality Control: Going the Extra Mile with NGS

    Type
    Blog Post
    Published
    Sept. 12, 2017, 1:44 p.m.
    ...are suitable for in vivo studies, our scientists perform all the standard quality control assays for AAVs... and Seqwell’s plexWell technology, we can now perform NGS at Addgene to sequence all the DNA packaged...should align to this reference sequence. Second, we perform a megaBLAST search on all the reads that did not...assembly of the unmapped reads, employing our bioinformatics software to assemble the reads into longer ...developed custom open-access Python scripts that can perform a deeper analysis of the data. Our serotype detection...contaminants in AAV preparations and provide information on these DNA species with exquisite detail (Lecomte...clinical-grade materials, and is not commonly performed for research-grade materials. Addgene is going...

  8. Antibodies 101: Flow Cytometry

    Type
    Blog Post
    Published
    July 20, 2021, 1:15 p.m.
    ...these types of experiments easier and faster to perform. Introduction to flow cytometry Flow cytometry ... path of a laser and the instrument collects information about the cell’s size, complexity and fluorescence...is captured by detectors and provides useful information about the cell. Light that continues in the same...is called forward scatter (FSC) and provides information about the relative size of the cell; larger cells...traveling is called side scatter (SSC) and provides information about the cell’s complexity. A cell with a high...antibodies to pass through the cell membrane. Formaldehyde fixation creates cross-links between lysine ...Sometimes, users will combine methods and fix with formaldehyde first to freeze everything in place followed...

  9. The Addgene Antibody Data Hub

    Type
    Blog Post
    Published
    Sept. 12, 2024, 1:15 p.m.
    ... for accuracy and completeness. The information is then formatted and published as a report with a DOI...user-deposited data detailing how an antibody performed in an experiment.   Figure 1: The front page ...contains experimental data showing how the antibody performed in the submitted application, along with a brief... included in a publication, you'll find that information in the report as well.    Figure 3: An antibody... results of an immunocytochemistry experiment performed with the anti-Lhx6.1 antibody.    For a more detailed..., and a short description of how the antibody performed.  Figure 5: Results for the data report shown...

  10. Tips for Screening with Yeast Two Hybrid Systems

    Type
    Blog Post
    Published
    Oct. 22, 2015, 2:30 p.m.
    ...activities (1). Researchers also discovered the modular format of some transcriptional activators: that the DNA...interactions. In later years, improvements to yeast transformation protocols also helped establish the yeast two-hybrid...  from Yu-Zhu Zhang’s lab) is an example of the former. In this system, histidine-auxotrophic host strains...applied to the bait in a single population (e.g. transforming both fusion plasmids, or mating two single haploid... haploid yeast fusion plasmid transformants into a diploid strain for screening), or arrayed on a 96 well... each well contains a defined prey fusion.  The former allows for screening greater numbers, but the latter...conducted and analysed with care to get reliable information. Although two-hybrid systems are a powerful tool...

  11. Tag Your Favorite Yeast Genes with Ease

    Type
    Blog Post
    Published
    Nov. 19, 2013, 2:37 p.m.
    ...product is introduced into the cell by direct transformation. A given insert will typically contain both...selectable gene product for isolation of successful transformants. Addgene distributes several ready-to-use, modular...fluorescent tags in S. cerevisiae, looking at their performance in categories such as brightness, stability, ...associated with plasmid-based overexpression. Tim Formosa, at the University of Utah, has built a complete...from this collection will yield an insert with the format (protease site)-6xGly linker-(epitope tag)-ADH1...terminator-(selection marker). Additionally, Dr. Formosa has deposited six plasmids with a multiple cloning...modification in yeast developed by Dr. Pringle’s former lab at UNC Chapel Hill. Bähler et al.(2) describe...

  12. An Integrin Antibody Toolkit from IPI

    Type
    Blog Post
    Published
    March 28, 2024, 1:15 p.m.
    ...and drug development. Integrin structure and conformational complexity There are 24 known mammalian integrins...the cytoskeleton. Most integrins have three conformational states: bent-closed, extended-closed, and extended-open...further stabilizes the extended open integrin conformation. During embryonic development, extended-open...extracellular matrix. During immune responses, this same conformation encourages immune cell adhesion and migration...migration into inflamed tissues. Integrins' conformational flexibility is crucial for their function. With the...research reagents, researchers can measure this conformational change to investigate the role of specific ... Figure 1: Integrins can shape into three conformations: (A) bent-closed, (B) extended-closed, and (...

  13. CRISPR 101: Engineering the Plant Genome Using CRISPR/Cas9

    Type
    Blog Post
    Published
    Oct. 11, 2016, 2:30 p.m.
    ...Presented in figure 1). More information on Agrobacterium-mediated transformation can be found in this blog...modify several genomic loci at once (get more information on multiplexing gRNAs here). Cas9 is commonly...Simplified schematic of agrobacterium-mediated transformation in plant cells. Agrobacterium tumefaciens can...plant genome. B) The Ti plasmid and helper are transformed into agrobacterium tumefaciens and exposed to...methods do not involve double strand break (DSB) formation and do not require donor DNA, . These precise ...plant cytorhabdovirus as versatile expression platforms for planthopper and cereal genomic studies. New...Gelvin SB (2003) Agrobacterium-Mediated Plant Transformation: the Biology behind the “Gene-Jockeying” Tool...

  14. Technique: Probe Phage Genomes for Host Binding Proteins

    Type
    Blog Post
    Published
    Sept. 29, 2016, 2:30 p.m.
    ...plates) (see box below). This initial transformation should be performed using a highly competent strain that...polymerase is a phage-derived polymerase that can perform whole genome amplification (by a mechanism known...certain modifications to DNA bases.  Ligate and transform your resultant plasmid libraries into chemically...chemically competent E. coli and analyze transformants for appropriately sized inserts. We consider a library...culture, dilute and plate the complete library of transformants for single colonies (this usually requires 10...extract plasmid DNA directly from the colonies. Transform the resultant plasmid DNA into E. coli BL21 (DE3... protein production), then dilute and plate transformants for isolated colonies (150-200 per plate) across...

  15. Multiplexed Overexpression of Regulatory Factors (MORF) collection

    Type
    Blog Post
    Published
    March 30, 2023, 1:15 p.m.
    ...expression atlas, including over 3,500 human TF isoforms, to help researchers understand this regulatory...encodes approximately 1,800 TFs, with >3,500 unique isoforms transcribed from these sites. The Zhang lab generated...cultured following a differentiation protocol before performing single-cell RNA sequencing. The sequencing results...were differentiated and single cell RNA-seq was performed to map TFs to cell fates. (Adapted from Joung ...MORF to work Screens and selections In its current format, the MORF library is most immediately useful for...on cellular processes. For help with library transformation and amplification, refer to the Zhang lab’s...library to further investigate specific genes and TF isoforms. Due to the size of the collection, we’re releasing...

  16. How Addgene Creates Content

    Type
    Blog Post
    Published
    Nov. 17, 2022, 2:15 p.m.
    ... them. That’s where our content - the useful information on scientific literature, technical skills, and...e-books – comes into play. Our goal is to provide informative content to help researchers in creating and sharing...spring of 2022. The first step was to understand information our guide needed to have. Through a series of...applications should be included and what basic information someone new to antibodies might need to successfully...primary literature search to collect up to date information on the scientific topic. If that’s not enough...from papers or image sharing repositories. Then we format, do a final review to catch those pesky typos, ...research community! We work to provide engaging and informative resources that answer questions our depositors...

  17. A History of Genome Engineering in Popular Culture

    Type
    Blog Post
    Published
    Feb. 25, 2020, 2:15 p.m.
    ...writers have been curious about the capability of transforming the genetic code of living organisms and its...that Streptococcus pneumoniae bacteria could be transformed from one organism to the other. This is now famed... myth that protein is the carrier of genetic information and led to the coronation of DNA as the molecule...scientists established that DNA encoded all the information necessary for regulating and propagating life...machinery, which can lead to high frequency of indel formation in the genome and are inefficient at introducing...Together, CBE and ABE have obviated the indel formation rates that are typically associated with the DSBs...advertisement of the technology on various non-scientific platforms, CRISPR has also transcended into the world of...

  18. RNA Extraction Without A Kit

    Type
    Blog Post
    Published
    March 24, 2020, 1:15 p.m.
    ... to avoid contamination, take extra care when performing RNA extraction. RNA is inherently not as stable... protocol with guanidinium thiocyanate-phenol-chloroform. In this method, samples are still homogenized..., water-saturated phenol, sodium acetate, and chloroform are added to the homogenate and shaken. After...ultracentrifugation!), the layers of phenol and chloroform separate, and RNA is retained in the top, aqueous...centrifugation and the supernatant is extracted with chloroform as in the above no-kit method.  Researchers have...Isolation by Acid Guanidinium Thiocyanate–Phenol–Chloroform Extraction. Analytical Biochemistry 162:156–159...isolation by acid guanidinium thiocyanate–phenol–chloroform extraction: twenty-something years on. Nature...

  19. Quickest Way to Deposit Plasmids: The Deposit Spreadsheet

    Type
    Blog Post
    Published
    March 8, 2017, 3:15 p.m.
    ...broken down into four simple steps: Send plasmid information to Addgene Material Transfer Agreement (MTA) ..., we’ve made it easy to send us your plasmid information in a deposit spreadsheet. The data entry process...require that you send your samples to Addgene pre-transformed in this strain. Hazardous If the plasmid...finished filling out the spreadsheet, save it in the format: labname_addgene_batch_upload.xls Replace ‘labname...spreadsheet to [email protected] with the following information: Addgene account username. In order for the ...Yachie, 2021) but can accept sequence files in any format. Distribution status for your plasmids: Hold for...were first created. From there, we’ll use the information in the spreadsheet to generate plasmid pages....

  20. Pathways Over Time Plasmids Engage Students in Functional Genomics Research

    Type
    Blog Post
    Published
    May 22, 2018, 1:38 p.m.
    ...students first transform the S. cerevisiae met deletion strains and then isolate transformed strains on media...organism into overexpression plasmids. Students next transform deletion strains from the reference organisms ... (7). In our class research project, students transform S. cerevisiae met deletion strains with overexpression...expression of the plasmid-encoded MET gene allows the transformed strain to grow in the absence of methionine (... to select yeast that have been successfully transformed with the plasmids, because the S. cerevisiae ...of MET/Met genes from the plasmids allows the transformed strains to grow in the absence of methionine....
Showing: 301 - 320 of 756 results