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  1. CRISPR 101: Making a Knock-In Cell Line

    Type
    Blog Post
    Published
    Dec. 22, 2022, 2:15 p.m.
    ...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...
  2. Viral Vectors 101: Optogenetic Tools

    Type
    Blog Post
    Published
    June 27, 2023, 1:15 p.m.
    ...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...
  3. CRISPR 101: Cytosine and Adenine Base Editors

    Type
    Blog Post
    Published
    Feb. 13, 2025, 2:15 p.m.
    ...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 ...
  4. The AAVantages of AAV in CRISPR Screens

    Type
    Blog Post
    Published
    Feb. 4, 2025, 2:15 p.m.
    ... 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...
  5. "Hall of Fame" AAV Enhancers from the Allen Institute for Brain Science

    Type
    Blog Post
    Published
    Sept. 9, 2025, 1:15 p.m.
    ...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...
  6. X-CHIME: Context Dependent Germline Knockout in Immune Cells

    Type
    Blog Post
    Published
    Jan. 16, 2024, 6:13 p.m.
    ...-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...
  7. Purple Plants that Report Pollutants

    Type
    Blog Post
    Published
    March 3, 2026, 2:14 p.m.
    ...Pathak, S., Swyers, N., Morgan, A., Meerdink, S., Kuzio, C., Calderon, S., Sheng, H., Kenney, S., Zare,...
  8. An Introduction to Adenovirus

    Type
    Blog Post
    Published
    Oct. 3, 2023, 1:15 p.m.
    ...., Bull, R. L., Garcia, K. Y., Goodrich, J. S., Lovett, S. P., Parker, K., Radune, D., Hatada, A., Pan...Reyes-Sandoval, A., Harris-McCoy, K. C., Hensley, S. E., Zhou, D., Lin, S. W., Bian, A., Zhi, Q. X., Iparraguirre...Scaria, A., Hermiston, T. W., Ryerse, J. S., Wold, L. J., & Wold, W. S. (1996). The adenovirus death protein...Implications for gene therapy. Proc Natl Acad Sci U S A, 95(19), 11377. https://doi.org/10.1073/PNAS.95.19.11377.../JVI.70.4.2296-2306.1996. PMID: 8642656. Wold, W. S. M., & Toth, K. (2013). Adenovirus Vectors for Gene...
  9. A New Generation of Adenine Base Editors Improves Editing in Primary Human Cells

    Type
    Blog Post
    Published
    May 7, 2020, 1:15 p.m.
    ...team replaced S. pyogenes Cas9 in the ABE complex with PAM-variant Cas9 proteins: the S. pyogenes NG-Cas9... TadA and TadA7.10, they designed one set of ABE8’s similarly (ABE8.x-d). In order to assess the effect...created ABE8 constructs using a catalytically “dead” S. pyogenes Cas9 (dC9-ABE8.x-m/d). The dC9-ABE8.x-m/...scope of adenine base editors The most commonly used S. pyogenes Cas9 requires the target site in the genomic...-Cas9 (PAM: NG) to create NG-ABE8.xm/d and the S. aureus Cas9 (PAM: NNGRRT) to create Sa-ABE8.x-m/d. With...NM, Barrera LA, Born DA, Edwards A, Gehrke JM, Lee S-J, Liquori AJ, Murray R, Packer MS, Rinaldi C, Slaymaker...
  10. CRISPR 101: Non-Homologous End Joining

    Type
    Blog Post
    Published
    April 16, 2015, 3:45 p.m.
    ...C-Y, Gootenberg JS, Konermann S, Trevino AE, Scott DA, Inoue A, Matoba S, Zhang Y, Zhang F (2013) Double.... https://doi.org/10.1038/ncomms5286 Yan M-Y, Li S-S, Ding X-Y, Guo X-P, Jin Q, Sun Y-C (2020) A CRISPR-Assisted...Piganeau M, Renouf B, Renaud J-B, Sallmyr A, Ruis B, Oh S, Tomkinson AE, Hendrickson EA, Giovannangeli C, Jasin...Pryor JM, Strom CN, Mieczkowski P, Burkhalter MD, Oh S, Qaqish BF, Moore DT, Hendrickson EA, Ramsden DA (...
  11. Some Like it Hot: Thermostable GeoCas9

    Type
    Blog Post
    Published
    Sept. 14, 2017, 12:40 p.m.
    ... et al for more examples of GeoCas9’s editing activity in HEK293’s. GeoCas9 stability in human plasma ...SpCas9 can tolerate. Harrington et al tested GeoCas9’s love of heat in two ways. The first set of experiments... mammalian cells. Harrington et al tested GeoCas9’s editing skills by transfecting HEK293 cells with GeoCas9...organisms at lower than optimal temperatures. GeoCas9’s thermostability could also be used with in vitro molecular...
  12. Prime Editing: Adding Precision and Flexibility to CRISPR Editing

    Type
    Blog Post
    Published
    Jan. 13, 2025, 9:49 p.m.
    ...Levesque, S., Jing, Y., Simpson, D., Zhao, A., Li, H., Yan, W., Goudy, L., Schmidt, R., Solley, S. C., Gilbert...domains derived from the E. coli Ec48 retron RT and the S. pombe Tf1 retrotransposon RT, respectively. Their...Newby, G. A., Sahin, M., Osborn, M. J., Weissman, J. S., Adamson, B., & Liu, D. R. (2021). Enhanced prime.../10.1038/s41587-021-01025-z Doman, J. L., Pandey, S., Neugebauer, M. E., An, M., Davis, J. R., Randolph...Raguram, A., Richter, M. F., Everette, K. A., Banskota, S., Tian, K., Tao, Y. A., Tolar, J., Osborn, M. J., .../doi.org/10.1016/j.cell.2023.07.039 Lin, Q., Jin, S., Zong, Y., Yu, H., Zhu, Z., Liu, G., Kou, L., Wang...021-00868-w Nelson, J. W., Randolph, P. B., Shen, S. P., Everette, K. A., Chen, P. J., Anzalone, A. V....
  13. Viral Vectors 101: Producing Your rAAV

    Type
    Blog Post
    Published
    July 16, 2024, 1:15 p.m.
    ....1101/2023.03.20.533580 Goodwin, M. S., Croft, C. L., Futch, H. S., Ryu, D., Ceballos-Diaz, C., Liu, X...Truong, V., Rostonics, E., Hernandez, A., Boye, S. L., Boye, S. E., Levites, Y., … Golde, T. E. (2020). Utilizing...producer cells for further processing. What component(s) you need to collect will depend on the serotype, ....1089/hum.2020.120 Lock, M., Alvira, M. R., Chen, S.-J., & Wilson, J. M. (2014). Absolute determination...doi.org/10.1089/hgtb.2013.131 Lock, M., McGorray, S., Auricchio, A., Ayuso, E., Beecham, E. J., Blouin-Tavel...
  14. Using AAV for Neuronal Tracing

    Type
    Blog Post
    Published
    Aug. 9, 2018, 1:04 p.m.
    ... B.-Y., Viswanathan, S., Gaj, T., Lavzin, M., Ritola, K.D., Lindo, S., Michael, S., Kuleshova, E., Ojala...complications. References Aschauer, D.F., Kreuz, S., and Rumpel, S. (2013). Analysis of transduction efficiency...Okada, T., Kawasaki, K., Ishibashi, H., Yuasa, S., Takeda, S., Hasegawa, I., and Nakahara, K. (2011). Local...PubMed Central PMCID: PMC2293646. Jin, J., and Maren, S. (2015). Prefrontal-Hippocampal Interactions in Memory...Mise, N., Obata, Y., Wickersham, I.R., and Tonegawa S. (2014). Cell type-specific genetic and optogenetic...22196330. PubMed Central PMCID: PMC3275419. Maday, S., Twelvetrees, A.E., Moughamian, A.J., and Holzbaur...Harris, J.A., Ng, L., Winslow, B., Cain, N., Mihalas, S., Wang, Q., Lau, C., Kuan, L., Henry, A.M., Mortrud...
  15. SARS-CoV-2/COVID-19 Detection Methods Based on CRISPR/Cas

    Type
    Blog Post
    Published
    May 5, 2020, 1:15 p.m.
    ..., Valois, E., Solley, S. C., Braig, F., Lach, R. S., Baxter, N. J., Kosik, K. S., Arias, C., Acosta-Alvear...coronavirus using CRISPR-based SHERLOCK (Specific ​H​igh ​s​ensitivity ​E​nzymatic ​R​eporter un​LOCK​ing) technique... amplification kit. In this case, regions of gene S and Orf1ab gene are amplified. RPA reactions also ...A. H., Sinha, D., Sharma, N., Kumar, M., … Maiti, S. (2020). Rapid, field-deployable nucleobase detection...-Gonzalez A, Zorn K, Gopez A, Hsu E, Gu W, Miller S, Pan C-Y, Guevara H, Wadford DA, Chen JS, Chiu CY ...2020.04.20.052159 Zhang, F., Abudayyeh, O. O. & Gootenberg, J. S. A protocol for detection of COVID-19 using CRISPR...
  16. Deaminet 2026: Breakthroughs in Base Editing, Deaminase Biology, and Therapeutic Translation

    Type
    Blog Post
    Published
    March 10, 2026, 1:14 p.m.
    .../doi.org/10.1101/2023.03.16.532918 Pierce, S. E., Erwood, S., Oye, K., An, M., Krasnow, N., Zhang, E.,....1101/gr.280164.124 Wang, T., Jessa, S., Marinov, G. K., Klemm, S., Kundaje, A., & Greenleaf, W. J. (2025...Resources References Arantes, P. R., Chen, X., Sinha, S., Saha A., Patel A.C., Sample M., Nierzwicki L., Lapinaite...McRae, F., Wang, J., Hirsch, T., Portell, A., Kumar, S., & Mali, P. (2025). Regulatable in vivo gene expression.../10.64898/2025.12.21.695777 Doman, J. L., Pandey, S., Neugebauer, M. E., An, M., Davis, J. R., Randolph...Raguram, A., Richter, M. F., Everette, K. A., Banskota, S., Tian, K., Tao, Y. A., Tolar, J., Osborn, M. J., ..., da Silva, E. M., Selenica, P., & Chandarlapaty, S. (2025). APOBEC3 mutagenesis drives therapy resistance...
  17. Overcoming the AAV Size Limitation for CRISPR Delivery

    Type
    Blog Post
    Published
    Sept. 16, 2020, 1 p.m.
    ...Cho H-Y, Song DW, Lee KJ, Jung MH, Kim S, Kim JH, Kim JH, Kim J-S (2017) In vivo genome editing with a ...doi.org/10.1038/nmeth.3993  Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini...Boyaval P, Fremaux C, Horvath P, Magadán AH, Moineau S (2010) The CRISPR/Cas bacterial immune system cleaves...019-0908-x  Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, Nureki...doi.org/10.1038/nature14299  Senís E, Fatouros C, Große S, Wiedtke E, Niopek D, Mueller A-K, Börner K, Grimm...doi.org/10.1002/biot.201400046  Strecker J, Jones S, Koopal B, Schmid-Burgk J, Zetsche B, Gao L, Makarova...
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