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Showing: 241 - 260 of 648 results
  1. CrispyCrunch: High-throughput Design and Analysis of CRISPR+HDR Experiments

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    Blog Post
    ...designing primers, and running analyses. New team members have taken up to a month to design a single 96-...began building CrispyCrunch in July 2018 and in November, we began using it internally. Guiding principles...biopython, bwa, samtools, bowtie, UCSC genome browser, Ensembl, and others. It builds on existing popular web ...
  2. Tips for Using BLAST to Verify Plasmids

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    Blog Post
    ... (nr/nt)” as it contains a composite of GenBank, EMBL, DDBJ, and PDB sequences and may be the most comprehensive...regions by default, meaning that you do not have to remember to adjust any blastp algorithm parameters. We ...http://www.expasy.org/genomics/sequence_alignment EMBL-EBI - http://www.ebi.ac.uk/services http://www....
  3. CRISPR 101: Ribonucleoprotein (RNP) Delivery

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    Blog Post
    ...figure above), which generates pores in the cell membrane, allowing for entry of the RNP into the cytoplasm...nucleofection, which forms pores in the nuclear membrane, allowing for entry of a DNA template. Other techniques...protoplasts and biolistic bombardment of immature embryos (Liang et al. 2017).  PEG-mediated methods, while...
  4. Negative Can Be Positive: Open AAV Data with Addgene

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    Blog Post
    ...notebooks and computer files. If you asked your team members or colleagues: How much unpublished AAV data do...Therapy - Methods and Clinical Development, 18(September), 98–118. https://doi.org/10.1016/j.omtm.2020.05.018...Stimulation. Frontiers in Human Neuroscience, 14(December), 1–12. https://doi.org/10.3389/fnhum.2020.578687...
  5. Better Dyeing Through Chemistry & Small Molecule Fluorophores

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    Blog Post
    ...compromising the photon budget. Likewise, the switch from ensemble imaging to single-molecule imaging places a greater...recently discovered that incorporation of four-membered azetidine rings could substantially enhance the...analogs without sacrificing their small size and membrane permeability (Figure 2c). These cell-permeable...
  6. CRISPR Between the Genes: How to Experiment with Enhancers and Epigenomics

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    Blog Post
    ...data from the ENCODE project, find enhancers in embryonic stem cells, and conclude with a targeted CRISPR...for NANOG, an essential transcription factor in embryonic stem cells (ESCs). Your ChIP-seq finds just over...CRISPR screen. We start by infecting millions of embryonic stem cells (ESCs) with a lentiviral vector, an...
  7. Plasmids 101: Codon usage bias

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    Blog Post
    ...structures in RNA transcripts Effects on transcription (remember, it’s not all about translation - e.g. codon choice... isoacceptors induced by amino‐acid starvation." EMBO reports 6.2 (2005): 151-157. PubMed PMID: 15678157...transfer RNA abundance in Escherichia coli." The EMBO journal 9.13 (1990): 4359-4366. PubMed PMID: 2265611...
  8. New Tools Enable CRISPRa for Neuroscience Applications

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    Blog Post
    ...development, complex genetic programs specify and assemble diverse arrays of neurons, forming the neuronal...subgenome-scale CRISPRa screening approach in embryonic stem (ES) cells to determine which transcription...gene-function relationships in the CNS using CRISPRa as a member of the Gelbard Laboratory at URMC.     References...
  9. To Codon Optimize or Not: That is the Question

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    Blog Post
    ... The G·U wobble base pair. EMBO Rep 1:18–23 . https://doi.org/10.1093/embo-reports/kvd001 Additional resources...mammalian cells. This was the first codon optimized membrane protein expressed in mammalian cells. In this ...
  10. Binning Singletons: Tackling Conference Networking When You Don’t Know Anyone

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    Blog Post
    ...for attendees and helping societies help their members get the most out of their meetings. Amanda Gunn...Gunn ran randomized coffee trials for us at ASCB|EMBO 2019, matching Mentors with Singletons for short coffee... a culture that brings more value to ALL their members.  Shoutout to our mentors and supporters Thanks...
  11. Hot Plasmids: Summer 2024

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    Blog Post
    ... streptavidin-coated magnetic beads through an assembly of biotinylated SpyTag-SpyCatcher linkers and ...and target capture module (SpyTag-GFP nanobody) assembled on beads. C) Micrograph of H1.8-GFP nucleosomes...loss. Ci Ji Lim’s lab found that adding Late Embryogenesis Abundant (LEA) proteins, small proteins that...
  12. Hot Biosensors 2022: Year-End Roundup

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    Blog Post
    ...devised a “Modular fluorescence unit fused with TRansmembrane region-to-IntrAcellular loop linkers” (MTRIA...they observe fluorescence localizes to the plasma membrane only when the RTK is activated and the ITAM phosphorylated...relies on a change in localization to the cell membrane and not a direct change in the fluorescent properties...
  13. An Integrin Antibody Toolkit from IPI

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    Blog Post
    ...heads and long legs that protrude from the cell membrane, physically connecting the extracellular environment...the integrin, where it is resisted by the ligand embedded in the extracellular environment. This further...the extended open integrin conformation. During embryonic development, extended-open integrins enable tissue...
  14. Cutting Once Is Harder Than It Sounds: Your Guide to Minimizing Off-Target Effects

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    Blog Post
    ...make mistakes and cleave DNA sequences that only resemble the intended target. These unintended cuts cause...~5–10%, consider selecting a different target. Remember, if WT SpCas9 does not cleave the target efficiently...note When expressing gRNAs from a U6 promoter, remember that transcription typically requires a purine...
  15. The Fluorescent Vegetables in Aptamer Soup

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    Blog Post
    ...hydroxybenzylidene imidazolinone (DFHBI). DFHBI is membrane permeable and non toxic to cells. Because it rapidly...split aptamer that can be used to investigate RNA assembly. The split aptamer is composed of a “Top” and ...fluorescent split aptamer for visualizing RNA–RNA assembly in vivo." ACS synthetic biology 6.9 (2017): 1710...
  16. Neurodegeneration Research Collection

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    Collection
    ...Neurodegeneration Research Collection Addgene has assembled the following to help you find information and...cases having at least one other affected family member. These familial cases, usually inherited in an ...ER contact with other organelles. (Mattia et al. EMBO Rep. 2018) Study intrinsically disordered protein...
  17. CRISPR References and Information

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    Collection
    ...collection of protocols, materials, and publications by members of the Division of Signaling and Functional Genomics...cells pCas9_GFP ; gRNA empty vector Protocol at StemBook O'Connor-Giles Fly: gRNA and ssODNs design and...pSpCas9(BB) (pX330) PDF, 330 KB Parrott NEBuilder Assembly of CRISPR vectors using ssDNA oligos p201G Cas9...
  18. Hot Plasmids: Spring 2025

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    Blog Post
    ...deposited versions with both PDGFR and NGR fusions for membrane display, they recommend the NGR vectors for most... modulators of cell signaling pathways during embryonic development and cancer. But there is still much...intestinal peptide (VIP), or lysosomal-associated membrane protein 5 (LAMP5) — as well as cholinergic (choline...
Showing: 241 - 260 of 648 results