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  1. Plasmids 101: Modular Cloning Applications and Kits

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    ...Moore, S. J., Lai, H. E., Kelwick, R. J., Chee, S. M., Bell, D. J., Polizzi, K. M., & Freemont, P. S. (2016...., Ehnert, T. M., Werner, S., Jones, J. D., Patron, N. J., & Marillonnet, S. (2014). A golden gate modular...C., Mortensen, S., Cram, E. J., Lee-Parsons, C. W. T., Stuttmann, J., & Marillonnet, S. (2020). High-efficiency..., E., Engler, C., Gruetzner, R., Werner, S., & Marillonnet, S. (2011). A modular cloning system for standardized... then the MoClo-YTK Kit specifically designed for S. cerevisiae is at your service (Lee et al., 2015)....al., 2017). In addition to additional elements for S. cerevisiae chromosomal integration and gene expression... D., Giménez-Oya, V., Bircheneder, M., Bachmaier, S., Studtrucker, T., Ryan, J., Sollweck, K., Leonhardt...
  2. Viral Vectors 101: AAV Variables That Matter

    Type
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    ...and happy optimizing!  Recommended Reading Issa, S. S., Shaimardanova, A. A., Solovyeva, V. V., & Rizvanov...Resources References Aschauer, D. F., Kreuz, S., & Rumpel, S. (2013). Analysis of Transduction Efficiency...10.1089/hum.2009.169 Dudek, A. M., Pillay, S., Puschnik, A. S., Nagamine, C. M., Cheng, F., Qiu, J., Carette... https://doi.org/10.1038/s41434-019-0075-6 Issa, S. S., Shaimardanova, A. A., Solovyeva, V. V., & Rizvanov...10.1371/journal.pone.0076310 Damdindorj, L., Karnan, S., Ota, A., Hossain, E., Konishi, Y., Hosokawa, Y.,...Fong, D. M., Mouravlev, A., Young, D., & O’Carroll, S. J. (2019). Astrocyte-selective AAV gene therapy through...cells12050785 Kanaan, N. M., Sellnow, R. C., Boye, S. L., Coberly, B., Bennett, A., Agbandje-McKenna, M...
  3. The Advances Behind The World's First Personalized CRISPR Treatment

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    ..., J. C., McCague, S., Burke, S. M., Wright, C. M., Bick, S., Indurthi, V., Sharma, S., … Ahrens-Nicklas...Edwards, A., Gehrke, J. M., Lee, S.-J., Liquori, A. J., Murray, R., Packer, M. S., Rinaldi, C., Slaymaker, I...Benjamin Kleinstiver’s lab engineered new variants of S. pyogenes Cas9. While the wild-type enzyme requires...Resources References Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang...Gaudelli, N. M., Komor, A. C., Rees, H. A., Packer, M. S., Badran, A. H., Bryson, D. I., & Liu, D. R. (2017...-020-0491-6  Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A., & Liu, D. R. (2016). Programmable .... https://doi.org/10.1038/nature17946  Lander, E. S. (2016). The Heroes of CRISPR. Cell, 164(1), 18–28...
  4. Cpf1: A New Tool for CRISPR Genome Editing

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    ...depletion assay to discover FnCpf1’s PAM sequence requirements. Cpf1’s preferred PAM is 5’-TTN, differing...RuvC-like endonuclease domain, but they lack Cas9’s second HNH endonuclease domain. Cpf1 cleaves DNA in... RuvC-like endonuclease domain, but it lacks Cas9’s other HNH endonuclease domain, indicating that Cpf1... nuclease could potentially overcome some of Cas9’s shortcomings - namely its blunt double stranded cleavage...nucleotides in length, about the same size as Cas9’s, but with the direct repeat preceding the spacer rather...crRNA is also much simpler in structure than Cas9’s; only a short stem-loop structure in the direct repeat... added another option to the CRISPR toolbox. Cpf1’s staggered cleavage pattern opens up the possibility...
  5. Microbiology Resources

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    ...constructs for S. cerevisiae - Dueber Lab Yeast Prototrophy : Restoration of prototrophy in common S. cerevisiae...
  6. Tag Your Favorite Yeast Genes with Ease

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    ...integrate protein tags into the genomes of S. cerevisiae and S. pombe. The protocol is surprisingly simple...Yeast-optimized fluorophores for imaging Lee S, et al. (2013) PLoS ONE 8(7): e67902. Many imaging...al.(1) assessed many of these fluorescent tags in S. cerevisiae, looking at their performance in categories...plasmids for a wide variety of genome modifications in S. Pombe, including full and partial gene deletion, ...describe a complimentary set of plasmids for use in S. cerevisiae, with the additional benefit of multiple...system that isn't mentioned here? References: Lee S, Lim WA, Thorn KS. PLoS One. 2013 Jul 2;8(7):e67902...
  7. Advanced Uses of Cre-lox and Flp-FRT - A Neuroscientist’s View

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    ...to invert or ‘flip DNA’, is derived from the yeast S. cerevisiae (Gronostajski and Sadowski 1985). The ...References 1. Atasoy, D., Y. Aponte, H. H. Su, and S. M. Sternson. 2008. “A FLEX Switch Targets Channelrhodopsin...Ligand-Dependent Chimeric Cre Recombinase.” Proc Natl Acad Sci U S A 92(15): 6991–95. PubMed PMID: 7624356. PubMed Central...
  8. Live and Let Dye: Self-Labeling Protein Tags

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    ...Erdmann, R. S., Baguley, S. W., Richens, J. H., Wissner, R. F., Xi, Z., Allgeyer, E. S., Zhong, S., Thompson...F., Kromann, E. B., Allgeyer, E. S., Erdmann, R. S., Wood Baguley, S., Sirinakis, G., Schepartz, A., Baddeley...doi.org/10.1016/j.chembiol.2019.01.003  Gallagher, S. S., Sable, J. E., Sheetz, M. P., & Cornish, V. W. ... R., Bewersdorf, J., Rothman, J. E., Johnston, D. S., Schepartz, A., & Toomre, D. (2019). Labeling Strategies...10.1016/j.chembiol.2008.01.007  Griffin, B. A., Adams, S. R., & Tsien, R. Y. (1998). Specific Covalent Labeling...doi.org/10.1021/ar200099f  Keppler, A., Gendreizig, S., Gronemeyer, T., Pick, H., Vogel, H., & Johnsson,...s41467-023-40788-8  Ulrichs, H., Gaska, I., & Shekhar, S. (2023). Multicomponent regulation of actin barbed...
  9. Of Myc and Men

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    ...Schüchner, et al.’s results mean the end of 9E10’s time in the saga of the Myc tag? Hardly! 9E10’s accessibility...generated in an attempt to overcome some of Myc1-9E10’s shortcomings. Wait, 9E10 isn’t the Mary Poppins of... acids neighboring the Myc epitope influence 9E10’s affinity for the epitope, a phenomenon known as sequence...https://doi.org/10.1128/mcb.5.12.3610-3616.1985 Munro S, Pelham HR (1984) Use of peptide tagging to detect...doi.org/10.1002/j.1460-2075.1984.tb02263.x  Munro S, Pelham HRB (1986) An hsp70-like protein in the ER...https://doi.org/10.1016/0092-8674(86)90746-4 Munro S, Pelham HRB (1987) A C-terminal signal prevents secretion...//doi.org/10.1016/0092-8674(87)90086-9  Schüchner S, Behm C, Mudrak I, Ogris E (2020) The Myc tag monoclonal...
  10. Viral Vectors 101: Systemic Capsids

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    ... Kumar, S., Chen, X., Goertsen, D., Coughlin, G. M., Hori, A. M., Chuapoco, M. R., Otis, T. S., Miles,...Ichiki, T., Mazmanian, S. K., Osborne, P. B., Keast, J. R., Miller, C. T., Fox, A. S., Chiu, I. M., & Gradinaru... Bindu, D. S., Zhang, M., Taskin, N., Goertsen, D., Shay, T. F., Sullivan, E. E., Huang, S.-F., Ravindra...B. P., Kumar, S. R., Chan, K. Y., Banerjee, A., Wu, W.-L., Yang, B., Huber, N., Pasca, S. P., & Gradinaru...., Ng, C., Nammour, J., Maiz, D., Dujardin, S., Ramirez, S. H., Hudry, E., & Maguire, C. A. (2019). Selection...Liguore, W. A., Domire, J. S., Button, D., Wang, Y., Dufour, B. D., Srinivasan, S., & McBride, J. L. (2019...Stanton, A., King, E. M., Ye, S., Tellez, L., Krunnfusz, A., Tavakoli, S., Widrick, J. J., Messemer, K...
  11. CRISPR 101: Making a Knock-In Cell Line

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    ...viability of your cells. Enrich S-phase cells HR operates predominantly in S and G2 phase of the cell cycle....1016/j.jbiotec.2019.11.010 Wright, D. W., Shah, S. S., Heyer, W. D. Homologous recombination and the ...2018). 1 10.1074/jbc.TM118.000372 Yang, H., Ren, S., Yu, S., Pan, H., et al. Methods favoring homology-directed...regulatory proteins responsible for the transition out of S phase, so cells stay in an HDR-promoted cycle longer...., 21(18): 6461 (2020). 10.3390/ijms21186461 Lin, S., Staahl, B. T., Alla, R. K., Doudna, J. A. Enhanced...01836-2 Charpentier, M., Khedher, A. H. Y., Menerot, S., Brion, A., et al. CtIP fusion to Cas9 enhances transgene...
  12. Viral Vectors 101: Optogenetic Tools

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    ...10.1038/nn.2495 Marshel, J. H., Kim, Y. S., Machado, T. A., Quirin, S., Benson, B., Kadmon, J., Raja, C., ..., J. C., McKnight, D. J., Yoshizawa, S., Kato, H. E., Ganguli, S., & Deisseroth, K. (2019). Cortical layer-specific...following factors will help you determine which one(s) are candidates for your experiments.  Wavelengths....1007/978-1-0716-0755-8_2 Lehtinen, K., Nokia, M. S., & Takala, H. (2022). Red Light Optogenetics in Neuroscience...://doi.org/10.1007/978-1-0716-0755-8_2 Boyden, E. S., Zhang, F., Bamberg, E., Nagel, G., & Deisseroth,...Gunaydin, L. A., Yizhar, O., Berndt, A., Sohal, V. S., Deisseroth, K., & Hegemann, P. (2010). Ultrafast....1808 Nagel, G., Szellas, T., Huhn, W., Kateriya, S., Adeishvili, N., Berthold, P., Ollig, D., Hegemann...
  13. CRISPR 101: Cytosine and Adenine Base Editors

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    ...Zhang, S., Wu, H., Gao, H., Bai, S., Li, C., Ding, R., Xue, N., Lei, Z., Chen, Y., Guan, Y., Siwko, S., …...Edwards, A., Gehrke, J. M., Lee, S.-J., Liquori, A. J., Murray, R., Packer, M. S., Rinaldi, C., Slaymaker, I...Grünewald, J., Zhou, R., Lareau, C. A., Garcia, S. P., Iyer, S., Miller, B. R., Langner, L. M., Hsu, J. Y....McElroy, A. N., Pandey, S., Doman, J. L., Huang, T. P., Raguram, A., Banskota, S., Newby, G. A., Tolar,...Gaudelli, N. M., Komor, A. C., Rees, H. A., Packer, M. S., Badran, A. H., Bryson, D. I., & Liu, D. R. (2017...Kim, Y. B., Komor, A. C., Levy, J. M., Packer, M. S., Zhao, K. T., & Liu, D. R. (2017). Increasing the...10.1038/nbt.4172 Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A., & Liu, D. R. (2016). Programmable ...
  14. The AAVantages of AAV in CRISPR Screens

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    ... Hanlon, K. S., Kleinstiver, B. P., Garcia, S. P., Zaborowski, M. P., Volak, A., Spirig, S. E., Muller...Sousa, A. A., Tsai, S. Q., Bengtsson, N. E., Lööv, C., Ingelsson, M., Chamberlain, J. S., Corey, D. P., Aryee.../s41467-019-12449-2 Pupo, A., Fernández, A., Low, S. H., François, A., Suárez-Amarán, L., & Samulski, ...Rose, I. V., Teyssier, N., Pan, A., Danner-Bocks, S., Sanghal, T., Yadanar, L., Tian, R., Ma, K., Palop... J., Klingler, E., Kuhn, M., Farouni, R., Lagler, S., Kalamakis, G., Lischetti, U., Jabaudon, D., & Platt...
  15. Fluorescent Protein Guide: Biosensors

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    ...657. Douglas Kim , GENIE Project Calcium GCaMP6f/m/s calcium sensors for imaging neural activity (Constitutive...Calcium Intersectional viral expression of GCaMP6m/s in cells depdent on Cre, Flp, or Vcre Comprehensive... encoded fluorescent sensor. Proc Natl Acad Sci U S A. 2004 Dec 14;101(50):17404-9. Ca 2+ indicators based...genetically encoded sensors. Proc Natl Acad Sci U S A. 2011 May 3;108(18):7351-6. Amy Palmer Zinc Cytosolic...single GFP-linked biosensors. Proc Natl Acad Sci U S A. 2008 Jan 8. Wolfgang Dostmann cGMP (cyclic GMP)...neurons of Caenorhabditis elegans. Proc Natl Acad Sci U S A. 2019 Aug 1. Alexander Gottschalk Return to top ...constructing highly-tunable GPCR-based biosensors in S. cerevisiae cpFRET Kit includes plasmids to construct...
  16. "Hall of Fame" AAV Enhancers from the Allen Institute for Brain Science

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    ...Ben-Simon, Y., Hooper, M., Narayan, S., Daigle, T. L., Dwivedi, D., Way, S. W., Oster, A., Stafford, D. A....Opitz-Araya, X., Martinez, R. A., Way, S. W., Thyagarajan, B., Otto, S., … Ting, J. T. (2025). Enhancer AAV...-Araya, X., Roth, J. R., Alexander, J. R., Allen, S., Amster, A., Arbuckle, J., Ayala, A., Baker, P. M...Johansen, N. J., Hooper, M., Omstead, V., Vargas, S., Lerma, M. N., Taskin, N., Weed, N., Laird, W. D....Bendrick, J. L., Kim, T. K., Zhou, T., Mortrud, M., Yao, S., Siverts, L. A., Larsen, R., Gore, B. B., Szelenyi...Mahoney, J. T., Kojima, Y., Ding, Y., Somasundaram, S., Miller, J. A., Kalmbach, B. E., Radaelli, C., Gore...Shapovalova, N. V., Martinez, R. A., Fong, O., Yao, S., Mortrud, M., . . . Levi, B. P. (2021). Functional...
  17. X-CHIME: Context Dependent Germline Knockout in Immune Cells

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    ...-excited GFP (vex) Lineage-Cre; Rosa26-Cas9 S-CHIME Knocks out pairs of genes sequentially pXPR...hindering studies post embryogenesis. Using C-CHIME and S-CHIME, we discovered that double knockout of PTPN1...References LaFleur, M. W., Lemmen, A. M., Streeter, I. S. L., Nguyen, T. H., Milling, L. E., Derosia, N. M...., Z. M., Gillis, J. E., Tjokrosurjo, Q., Markson, S. C., Huang, A. Y., Anekal, P. V., Montero Llopis, ...Coxe, M. A., Yates, K. B., Trombley, J. D., Weiss, S. A., Brown, F. D., Gillis, J. E., Coxe, D. J., Doench...
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