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TypeBlog Post...for Designing Primers UCSC Genome Browser: For eploring genomic DNA ImageJ: Free Software for Analyzing...
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Deep Dive: Statistical Tests (Comparisons)
TypeBlog Post...SMJ.0b013e3182498ad5 Curran-Everett, Douglas. Explorations in statistics: statistical facets of reproducibility... -
An “elegans” Approach to Better CRISPR/Cas9 Editing Efficiency
TypeBlog Post...the haystack” type of problem and led to me to explore alternate approaches. Being a “lazy” geneticist... -
Fluorescent Proteins 101: Monitoring Cell Mobility Using Fluorescent Proteins
TypeBlog Post... by 750 nm to 760 nm laser light, enabling dual color imaging studies with blue or cyan proteins without... -
Plasmids 101: Modular Cloning Applications and Kits
TypeBlog Post...https://doi.org/10.1021/acssynbio.3c00167. Hahn, Florian, et al. “A Modular Cloning Toolkit for Genome Editing... -
Special Delivery: Fluorophore Targeting for FRET Studies
TypeBlog Post... Degorce, François, et al. "HTRF: a technology tailored for drug discovery–a review of theoretical aspects... -
CRISPR 101: Multiplex Expression of gRNAs
TypeBlog Post...below. Figure 2: gRNA target sequences (colored rectangles) are cloned into various plasmids using... -
Selecting Your Plasmid Purification Kit
TypeBlog Post...kits are quick, easy, and don’t involve phenol-chloroform. The default option is to use the kit that ... -
CRISPR 101: Cytosine Transversion Editors
TypeBlog Post...apyrimidinic sites and abbreviated as AP sites. To explore this further, the team started engineering a CBE... -
Optogenetics Guide
TypeGuide...Channelrhodospin plasmids . Halorhodopsins Halorhodopsins are light-gated inward chloride pumps isolated from ...species include: CsChR (from Chloromonas subdivisa ), CoChR (from Chloromonas oogama ), and SdChR (from ...Jaws Browse Halorhodopsin plasmids . Archaerhodopsins Archaerhodopsin-3 (Arch) from Halorubrum sodomense...Channelrhodopsin from Chloromonas oogama CsChR Channelrhodopsin from Chloromonas subdivisa CheRiff Channelrhodopsin... mutations 540 Channelrhodopsins: chloride channels iChloC Chloride-conducting channel, CrChR2 with mutations... ReaChR variant 517 Halorhodopsins Jaws Red-shifted, light-driven inward chloride pump from Haloarcula...identified in other species - by acting as light-gated chloride channels, these variants result in the hyperpolarization... -
Troubleshooting and Optimizing a Western Blot
TypeBlog Post...need such precise measurements, you can use a colorimetric ladder, visible to the naked eye; a fluorescent... -
Antibody Guide
TypeGuide... Here, HRP is used as a colorimetric, in which the reaction produces a colored product that accumulates...well. In colorimetric assays, protein amount can be determined by correlating the amount of color in a well...small multiplex experiments 4-color flow panel: BV421, FITC, PE, and APC 4-color microscopy panel: DAPI for...molecules , proteins that emit a measurable light or color in response to a specific stimulus, can be conjugated...than HRP, fluorophores are available in a range of colors activated by different wavelengths, allowing for...indirect or direct method. Since IF uses fluorophore color to differentiate between the targets of interest...theoretically allow for roughly fifty different fluorophore colors in flow cytometry, but the largest panels used ... -
Chemogenetics Guide
TypeGuide... Compound 21, Deschloroclozapine (DCZ), Perlapine, and Olanzapine have all been explored as alternative...pair a PSAM domain with a Glycine-receptor (GlyR) chloride-selective IPD. Binding of the cognate PSEM allows...Higuchi M, Jin J, Roth BL, Minamimoto T (2020). Deschloroclozapine, a potent and selective chemogenetic actuator...a new window) Strader CD, Gaffney T, Sugg EE, Candelore MR, Keys R, et al. (1991). Allele-specific activation... -
CRISPR Guide
TypeGuide...fluorescently-tagged RNA-binding proteins (RBPs). Multicolor CRISPR imaging can be achieved by using orthogonal... L., Jung, K., McCool, R. S., Johnson, K. A., & Taylor, D. W. (2022). Structural basis for mismatch surveillance...Petris, G., Montagna, C., Reginato, G., Maule, G., Lorenzin, F., Prandi, D., Romanel, A., Demichelis, F., ...Zhang, H., Finkelstein, I. J., Johnson, K. A., & Taylor, D. W. (2024). Unraveling the mechanisms of PAMless...Wolfe, S. A., Zhang, S., & Pederson, T. (2015). Multicolor CRISPR labeling of chromosomal loci in human ...., Ramos, D., Hibshman, G. N., Wright, J. T., & Taylor, D. W. (2023). Structural snapshots of R-loop formation... -
Molecular Biology Reference
TypeGuide...100 µg/mL Carbenicillin* 100 mg/mL 100 µg/mL Chloramphenicol 25 mg/mL (dissolve in EtOH) 25 µg/mL Hygromycin...as a sequencing chromatogram which provides the color and intensity of each fluorescent signal. Sanger...bases and a microscope captures the fluorescent color that is emitted each time a base is added. Again...base (A,C,T, or G) is labelled with a different color making it easy to identify the order of the DNA ... -
Viral Vectors 101: Systemic Capsids
TypeBlog Post...intravenous delivery by directed evolution of underexplored sites on the AAV capsid. Molecular Therapy -... -
Sequencing Primers
TypeGuide...primer CAT-R GCAACTGACTGAAATGCCTC 5' end of chloramphenicol resistance gene, reverse primer CMV Forward... -
Adenovirus Guide
TypeGuide... (Link opens in a new window) Mendonça, S. A., Lorincz, R., Boucher, P., & Curiel, D. T. (2021). Adenoviral... -
Adeno-associated virus (AAV) Guide
TypeGuide...short coding sequences of channelrhodopsins, halorhodopsins, and other optogenetic genes makes them suitable...