Skip to main content
Addgene

Enter a sequence to perform a BLAST-based search of the Addgene plasmid sequence database.

Information

In Category

We narrowed to 648 results for: CHI

Showing: 81 - 100 of 648 results

  1. Water Bath Protocol

    Type
    Protocol
    ...can also be placed in walk-in refrigerators to achieve a temperature between 4°C and room temperature....

  2. Centrifugation

    Type
    Protocol
    ...separate different components in a liquid sample. It achieves this by using centrifugal force, which is generated...

  3. Pipetting Protocol

    Type
    Protocol
    ...submerge the pipette itself into the liquid and avoid touching the pipette to the inside of the tube. Only the...

  5. Kit Free RNA Extraction

    Type
    Protocol
    ... (Link opens in a new window) Chomczynski P and Sacchi N, 2006 and (Link opens in a new window) TRIzol...

  7. Choosing the B(right)est Fluorescent Protein: Photostability

    Type
    Blog Post
    ... 2-fold does not reduce photobleaching by half. How exactly the photobleaching rate depends on power is...thanks to our guest bloggers Joachim Goedhart and Marieke Mastop! Joachim Goedhart is an assistant professor...This post was contributed by guest bloggers Joachim Goedhart and Marieke Mastop from the Section of Molecular...to select a photostable fluorescent protein. Photobleaching is the irreversible destruction of a fluorophore...fluorescent proteins that are photostable. On top of photobleaching, fluorescent proteins may display reversible...Shaner et al, 2008; Bindels et al, 2017) and photoswitching (Kremers et al, 2009), which usually are undesired...destroyed. Factors that affect photostability The photobleaching rate of a fluorophore primarily depends on ...

  8. Tetbow: Bright Multicolor Labeling for Neuronal Tracing

    Type
    Blog Post
    ...This post was contributed by Richi Sakaguchi from Kyoto University, and Marcus N. Leiwe and Takeshi Imai...cells.   Many thanks to our guest bloggers Richi Sakaguchi from Kyoto University, and Marcus N. Leiwe ...Leiwe and Takeshi Imai from Kyushu University. Richi Sakaguchi is a graduate student at Kyoto University. ...25157152. PubMed Central PMCID: PMC4246963. Sakaguchi, Richi, Marcus N. Leiwe, and Takeshi Imai. "Bright...light microscopy-based neuronal reconstruction. To achieve stochastic multicolor labeling, Brainbow used the...Tetbow (Tetracycline trans-activator Brainbow) (Sakaguchi et al., 2018) (Figure 1). Once introduced, fluorescent...you use AAVs, it typically takes a few weeks to achieve optimal expression of XFPs. Any longer and the ...

  9. The Effect of COVID-19 on Liu Lab Plasmid Requests From Addgene Data

    Type
    Blog Post
    ...resulting in the following hierarchical model: Because the U.S., Europe, and China account for over 75% of...instabilities in the China data, so we recommend interpreting the model results for China with more uncertainty... dominated by the U.S. (42%), Europe (23%), and China (14%). Spikes in plasmid requests correspond to ...encountered COVID-19 at different times. Most notably, China was affected by COVID-19 earlier than the rest of...COVID-19 event windows as 01/15/20 -- 03/15/20 for China and 03/11/20 -- 05/19/20 (the last date in our dataset...day across regions, with Europe most impacted and China least impacted. The inferred weekend effect is, ...well. However, we observed one complication in the China data – there is a period of 1 month, from 1/22/20...

  10. CUT&RUN: An Improved Method for Studying Protein-DNA Interactions

    Type
    Blog Post
    ...limited biological materials. Problems with Chip-seq ChIP-seq typically requires a large amount of input...enough material for a ChIP-seq experiment can be a major technical hurdle.   ChIP-seq requires  cross-linking...immunoprecipitation followed by high-throughput sequencing, ChIP-Seq, is the go-to method for mapping where a protein...in many model organisms and cell lines. Although ChIP-seq is a relatively simple and robust protocol it...patterns that overcomes some of the limitations of ChIP-seq. CUT&RUN, which stands for ‘Cleavage Under Targets... using the Drosophila wing as a model. A typical ChIP-Seq experiment requires around 1,000 wings. Collecting...All in all, CUT&RUN offers a great alternative to ChIP-seq, especially in situations when it is technically...

  11. RANbodies: Reporter Nanobody Fusions

    Type
    Blog Post
    ...secondary antibody. Chicken IgY This RANbody reporter consists of two chicken IgY domains. Chicken IgY domains...antibodies. Chicken IgY RANbodies are easily detected with a labeled anti-chicken antibody. Chicken IgY RANbody..., H2A2B Myc Tagged RFP, H2A2B Chicken IgY (Y) Labeled Anti-Chicken IgY antibody Staining cultured cells...three varieties: HRP, Spaghetti Monster, and the Chicken IgY domain, which are discussed in more detail ...the Key Features of HRP, Spaghetti Monster, and Chicken IgY Domain RANbody Reporters. Reporter Detection... anti-rodent or -rabbit Detection with an anti-Chicken IgY antibody is approximately as sensitive as detecting...

  12. Fluorescent Proteins 101: Photoactivatable Fluorescent Proteins

    Type
    Blog Post
    ...FP-protein fusions (FP-chimeras) is that they undergo normal protein turnover. FP-chimeras are continuously ...degraded within the cell, so at any given time, an FP-chimeric protein may be at any one of many stages of synthesis...turnover or temporal expression using standard FP-chimeric proteins. Photoactivatable fluorescent proteins...bright state to a dark non-fluorescent state (“quenching”). The photoswitch can occur multiple times by...reversible PA-FPs also display this “negative” photoswitching. In 2008, scientists used mutagenesis screens...V157G / M159Y / F190S) (7). Padron’s “positive” switching behavior is the opposite of Dronpa; when exposed...monomeric PA-FPs, there is less chance that the chimeric protein will oligomerize, disrupting cellular ...

  13. Deep Dive: qPCR

    Type
    Blog Post
    ...and most machines have a protocol that automatically performs the normalization step.  Machines Most general-use...different brand of qPCR machine, especially if you’re using a rapid-cycle machine such as a LightCycler,... LUX fluorogenic primers Low Single self-quenching fluorescent molecule connected to a primer  ...previously-generated validation data, be aware that different machines, samples, and treatments may affect the assay....running a multiplex reaction or on a rapid cycle machine. Melt Curves An advantage of Sybr chemistry is ... by bubbles in wells, variations in volume, or machine surge errors and allow for well-to-well normalization... likely need to re-optimize protocols for that machine. (Teo, et al, 2002; see paper for more information...

  14. INTEGRATE: Bacterial Genome Engineering Using CRISPR-Transposons

    Type
    Blog Post
    ...Streamlined VchINT expression constructs. (B) High integration efficiencies achieved with VchINT, at two ...multiple distinct targets could be achieved (Vo et al., 2020). VchINT was also shown to be active in various...Vibrio cholerae (V. cholerae INTEGRATE - hereafter VchINT) and encodes a Type I-F CRISPR-Cas system. The ...Type I CRISPR-Cas systems, however, Cascade from VchINT does not recruit other nucleases (such as Cas3)...; although 5’-CC-3’ is one of the best PAMs for VchINT, many other PAMs are also efficiently recognized...engineering In the Sternberg group’s initial report of VchINT, three separate plasmids and multiple promoters... al., 2020. In E. coli, the new streamlined VchINT system was shown to catalyze insertion of mini-...

  15. Plasmids 101: Plasmid Incompatibility

    Type
    Blog Post
    ...origin of replication and the replication control machinery (Need a refresher on the Origin of Replication...they compete for the same replication control machinery within the cell. Most plasmids encode a negative...through inhibiting translation of replication machinery proteins, or directly inhibit replication by binding...origin of replication and blocking replication machinery (del Solar, 1998). As the copy number of the plasmid... structure that physically blocks replication machinery when plasmid copy number is high (del Solar et...replication of each plasmid using unique replication machinery. However, when plasmids have the same origin of...incompatibility due to having the same replication machinery. High copy plasmids with the same centromere-like...

  16. Viral Vectors 101: Optogenetic Tools

    Type
    Blog Post
    ...Vierock et al., 2021). Step-function opsins are chimeric ion channels that turn on with a light-pulse at...with greater spatial and temporal control than is achieved by traditional pharmacologic methods. A number...Abreu & Levitz, 2020), including light-sensitive chimeric GPCRS (OptoXRs) (Tichy et al., 2019), photoswitchable...remotely-tethered ligands (PORTLs). OptoXRs are chimeras of the extracellular domain of endogenous light-sensitive...signaling pathway is unknown.      Figure 3: Chimeric OptoXR incorporating rhodopsin undergoes a conformational...secondary signaling pathways with light. This is achieved by coupling endogenous signaling molecules with...Protein-Coupled Receptor Signaling. In D. Niopek (Ed.), Photoswitching Proteins (Vol. 2173, pp. 21–51). Springer US...

  17. dTAG - You're it!

    Type
    Blog Post
    ...previously developed small molecule degraders that achieve selective degradation of endogenous proteins (notably...Hippel-Lindau (VHL) to bring the endogenous degradation machinery into close proximity with the target protein, ...to co-opt the endogenous ubiquitin proteasome machinery to degrade any protein. We are particularly excited...FKBP12F36V-fusion and the ubiquitin proteasome machinery through binding with cereblon, leading to rapid...of N- or C-terminally FKBP12F36V-tagged fusion chimeras or locus-specific knock-in of FKBP12F36V. Detailed...your lab Confirm the functionality of your fusion chimeras For each protein-of-interest, it is important ... evaluate degradation of the FKBP12F36V-fusion chimera of interest. In the cell lines we have evaluated...

  18. CRISPR Between the Genes: How to Experiment with Enhancers and Epigenomics

    Type
    Blog Post
    ...Technique What It Locates ChIP-seq Proteins (for our example later, histones) ChiRP-seq RNA Hi-C DNA (genome-to-genome...Aneesh's research interests include proteomics, machine learning, and visualization for big biology. GPS...detect modified histones with “GPS for proteins,” ChIP-seq from Table 1. Because of DNA’s 3D geometry and...formula to a real-world experiment. We’ll start with ChIP-seq data from the ENCODE project, find enhancers...enhancers. A real-world experiment Suppose you run a ChIP-seq experiment (think “GPS for proteins”) for NANOG...transcription factor in embryonic stem cells (ESCs). Your ChIP-seq finds just over 13,000 significant binding peaks... (loops) and tertiary structures (globules) to achieve exquisite compaction—on the order of 700 terabytes...

  19. Illuminating Choices: A Guide to Selecting Fluorescent Dyes and Ligands

    Type
    Blog Post
    ...conditions. Common issues include photobleaching, non-specific binding, and quenching, which can be mitigated through...photostability, and most importantly, a photoswitching ability. This photoswitching refers to the ability to ‘toggle... must be taken to assess if proper staining is achieved. Fluorescent ligands have more flexibility due...peak wavelength can also decrease the rate of photobleaching. Interaction with receptors: Understanding ... technical manuals. Specific applications and matching dye/ligand choices For effective live-cell imaging.../doi.org/10.1007/s41048-017-0037-8 Lucidi, M., Capecchi, G., Visaggio, D., Gasperi, T., Parisi, M., Cincotti..., M., & Ghods, R. (n.d.). Comparison of the Photobleaching and Photostability Traits of Alexa Fluor 568...

  20. Tips for Using FRET in Your Experiments

    Type
    Blog Post
    ...microscopy (FLIM) method. Acceptor photobleaching method The acceptor photobleaching method is simple but limited...when FRET occurs. By photobleaching the acceptor, you release the donor's quenching and the fluorescence...An EAMNET Teaching Module http://www.embl.de/eamnet/downloads/modules/FRET_teaching_module.pdf Day RN, ...brightness of a fluorophore pair, donor:acceptor stoichiometry, and cross-talk between the two fluorophore ...has five-fold less brightness than YFP. The stoichiometry of donor:acceptor is difficult to address especially...commonly used to measure FRET: the acceptor photobleaching method and the fluorescence lifetime imaging...
Showing: 81 - 100 of 648 results