# in vivo CRISPR (TRiP) ## expand\_more **[Quick link to Find CRISPR sgRNA search](http://www.flyrnai.org/crispr2/) [Quick link to TRiP-CRISPR sgRNA stock database](http://www.flyrnai.org/tools/grna_tracker/web/)** Using the TRiP pipeline, we are actively developing CRISPR fly stocks and resources for gene editing and other applications. These resources facilitate knockout, up-regulation (CRIPSRa), and other *Drosophila in vivo* CRISPR applications. Sort TRiP-CRISPR fly stock collections **Function** **sgRNA Vectors** **Cross to** **Notes** [TRiP-OE](/trip-overexpression-stocks) [VPR](/trip-overexpression-stocks) Gene Activation [pCFD4](/sgrna-vectors) Gal4+dCas9-VPR See [TRiP-CRISPR Toolbox](/trip-crispr-toolbox-fly-stocks) [flySAM1.0](/trip-overexpression-stocks) Gene Activation [U6B-sgRNA2.0](/sgrna-vectors) Gal4+flySAM See [TRiP-CRISPR Toolbox](/trip-crispr-toolbox-fly-stocks) [flySAM2.0](/trip-overexpression-stocks) Gene Activation [flySAM2.0](/sgrna-vectors) Gal4 flySAM2.0 lines contain both sgRNA and dCas9 (flySAM) [TRiP-KO](/trip-knockout) Gene Cutting [pCFD3](/sgrna-vectors), [pCFD4](/sgrna-vectors) Gal4+Cas9 See [TRiP-CRISPR Toolbox](/trip-crispr-toolbox-fly-stocks) **[Search](http://www.flyrnai.org/tools/grna_tracker/web/)** the DRSC/TRiP sgRNA Stock Database for TRiP-OE and TRiP-KO stocks [**Nominate genes for production** ](http://www.flyrnai.org/tools/grna_tracker/web/nominate)for TRiP-OE and TRiP-KO stocks **[Download](http://www.flyrnai.org/tools/grna_tracker/web/grna_tracker_finished_stocks.csv)** a .XLS file of currently available TRiP-OE and TRiP-KO stocks **[Protocols](/vivo-crispr-0)** for cloning, sequencing, and using TRiP-CRISPR lines Online tools for **[gRNA design](/find-crisprs)** and **[efficiency prediction](/crispr-efficiency)** See links below to relevant online tools, reagents, protocols, publications, and more. ![in vivo CRISPR](/sites/g/files/omnuum5366/files/fly/files/vpr-adult-wings_640_200.jpg) ## Online tools [### Find CRISPRs ](/find-crisprs) This tool provides access to a pre-computed database of short guide RNAs (gRNAs) for CRISPR approaches in Drosophila. The gRNAs are appropriate for CRISPR applications using S. pyogenes Cas9 (PAM sequence of NGG or NAG). You can view and filter gRNAs in... description [### CRISPR Efficiency Prediction ](/crispr-efficiency) Part of our "Find CRISPRs" design suite, our Efficiency Predictor evaluation tool compares the nucleotide sequence of short guide RNA (gRNA) designs against our algorithms for optimal efficiency. Note that this tool does not evaluate potential off targets... description ## Reagents [### in vivo CRISPR fly stocks ](/crispr-fly-stocks-and-vectors) The TRiP-CRISPR project aims to build genome scale collections of transgenic sgRNA fly lines, providing powerful, versatile and transformative tools for the fly community. For a detailed description of the the TRiP in vivo CRISPR approach click here. TRiP... description ## Protocols [### in vivo CRISPR ](/vivo-crispr-0) Here we describe the TRiP platform for the generation of genome scale collections of Drosophila sgRNA stocks. To search and obtain specific stocks, please visit the reagents page. Overview of TRiP-CRISPR collections (below) sgRNA vectors for in vivo sgRNA... description ## News [### Important new considerations for TRiP stock users ](/news/important-new-considerations-trip-stock-users) August 29, 2022 A handful of recent papers and preprints have highlighted some important considerations for using TRiP shRNA and sgRNA stocks. First, the Weake lab at Purdue University discovered that TRiP stocks contain a previously uncharacterized loss-of-function... ![in vivo](/sites/g/files/omnuum5366/files/styles/hwp_16_9__480x270/public/fly/files/invivo-tile.jpg?itok=ZEK1O34D) [### Read the DRSC/TRiP Report to the Fly Board 2022 ](/news/read-drsctrip-report-fly-board-2022) March 31, 2022 Below we share with the community at large the report we provided to the Fly Board in advance of the 2022 Fly Meeting. As always, your feedback on our technologies and services is welcome. We are here to help. DRSC/TRiP Functional Genomics Resources at... ![Decorative cartoon drawn with BioRender depicting DRSC-BTRR technology concepts](/sites/g/files/omnuum5366/files/styles/hwp_16_9__480x270/public/fly/files/drsc-btrr_499-350.jpeg?itok=kyu_pmTs) [### DRSC/TRiP and DRSC-BTRR Office Hours ](/OfficeHours2021) September 13, 2021 New this fall: Online office hours! Do you have questions about modifying Drosophila cell lines with CRISPR or performing large-scale cell screens? Questions about in vivo RNAi with TRiP fly stocks or CRISPR knockout or activation with our sgRNA fly... ![Graphical image of tissue culture, fly pushing, and computer, and the team of people who work with them](/sites/g/files/omnuum5366/files/styles/hwp_16_9__480x270/public/fly/files/team.jpeg?itok=NLIA2Ora) [### DRSC/TRiP presentations from June 2020 Boston Area Drosophila Meeting ](/news/drsctrip-presentations-june-2020-boston-area-drosophila-meeting) June 12, 2020 Did you miss the presentations from Claire Hu and Jonathan Zirin at the June 2020 Boston Area Drosophila Meeting? No problem! The slides can be accessed from this post. Click the title above to view the whole post, then scroll down to access the PDFs... ![Image of an anesthetized male Drosophila fruit fly](/sites/g/files/omnuum5366/files/styles/hwp_16_9__480x270/public/fly/files/semohr-website-images_semohr-website-image009_raw_ch00_male-square-1_0.jpg?itok=W-Mmt7xK) [### Transgenic Fly Stocks for Double Knockout of Paralog Pairs ](/news/call-gene-nominations%E2%80%94transgenic-fly-stocks-double-knockout-paralog-pairs) May 18, 2020 Paralogs can be defined as related genes within a genome that are thought to arise from gene duplication events. Because paralogous proteins share amino acid identity, they can have redundant functions. But the picture is not necessarily so... ![from Figure 1 in Ewen-Campen et al. in Dev Cell](/sites/g/files/omnuum5366/files/styles/hwp_16_9__480x270/public/fly/files/gr1_lrg-smaller.jpg?itok=GzlguEJ6) [### DRSC-Biomedical Technology Research Resource ](/news/drsc-biomedical-technology-research-resource) October 21, 2019 We are pleased to announce that we have been funded by NIH NIGMS to form the Drosophila Research & Screening Center-Biomedical Technology Research Resource (DRSC-BTRR). The P41-funded DRSC-BTRR (N. Perrimon, PI; S. Mohr, Co-I) builds upon and extends past... ![Graphical image of tissue culture, fly pushing, and computer, and the team of people who work with them](/sites/g/files/omnuum5366/files/styles/hwp_16_9__480x270/public/fly/files/team.jpeg?itok=NLIA2Ora) ## Contact Us Please [contact us](/contact) for any questions. ## Publications Download 6 citations download- [BibTeX](/bibcite/export?pager_style=no_pager&number_of_items=6&sort_field=bibcite_year--desc&taxonomy_filters%5Bfield_hwp_c_technology%5D%5B0%5D%5Btarget_id%5D=114116&&&format=bibtex) - [EndNote X3 XML](/bibcite/export?pager_style=no_pager&number_of_items=6&sort_field=bibcite_year--desc&taxonomy_filters%5Bfield_hwp_c_technology%5D%5B0%5D%5Btarget_id%5D=114116&&&format=endnote8) - [EndNote 7 XML](/bibcite/export?pager_style=no_pager&number_of_items=6&sort_field=bibcite_year--desc&taxonomy_filters%5Bfield_hwp_c_technology%5D%5B0%5D%5Btarget_id%5D=114116&&&format=endnote7) - [Endnote tagged](/bibcite/export?pager_style=no_pager&number_of_items=6&sort_field=bibcite_year--desc&taxonomy_filters%5Bfield_hwp_c_technology%5D%5B0%5D%5Btarget_id%5D=114116&&&format=tagged) - [Marc](/bibcite/export?pager_style=no_pager&number_of_items=6&sort_field=bibcite_year--desc&taxonomy_filters%5Bfield_hwp_c_technology%5D%5B0%5D%5Btarget_id%5D=114116&&&format=marc) - [PubMedId](/bibcite/export?pager_style=no_pager&number_of_items=6&sort_field=bibcite_year--desc&taxonomy_filters%5Bfield_hwp_c_technology%5D%5B0%5D%5Btarget_id%5D=114116&&&format=pubmed_id) - [RIS](/bibcite/export?pager_style=no_pager&number_of_items=6&sort_field=bibcite_year--desc&taxonomy_filters%5Bfield_hwp_c_technology%5D%5B0%5D%5Btarget_id%5D=114116&&&format=ris) ### 2022 Jonathan Zirin, Justin Bosch, Raghuvir Viswanatha, Stephanie Mohr, and Norbert Perrimon. 2022. “[State-of-the-Art CRISPR for in Vivo and Cell-Based Studies in Drosophila](/publications/state-art-crispr-vivo-and-cell-based-studies-drosophila)”. Trends Genet, 38, 5, Pp. 437-53. doi:10.1016/j.tig.2021.11.006 Jonathan Zirin, Justin Bosch, Raghuvir Viswanatha, Stephanie Mohr, and Norbert Perrimon. 2022. “[State-of-the-Art CRISPR for in Vivo and Cell-Based Studies in Drosophila](/publications/state-art-crispr-vivo-and-cell-based-studies-drosophila)”. Trends Genet, 38, 5, Pp. 437-53. doi:10.1016/j.tig.2021.11.006 - add\_circle do\_not\_disturb\_on Abstract For more than 100 years, the fruit fly, Drosophila melanogaster, has served as a powerful model organism for biological and biomedical research due to its many genetic and physiological similarities to humans and the availability of sophisticated... Justin A. Bosch, Norbert Perrimon, and Christian Dahmann. 2022. “[Prime Editing for Precise Genome Engineering in Drosophila](/publications/prime-editing-precise-genome-engineering-drosophila)”. In Drosophila: Methods and Protocols, Pp. 113-34. New York, NY: Springer US Justin A. Bosch, Norbert Perrimon, and Christian Dahmann. 2022. “[Prime Editing for Precise Genome Engineering in Drosophila](/publications/prime-editing-precise-genome-engineering-drosophila)”. In Drosophila: Methods and Protocols, Pp. 113-34. New York, NY: Springer US - add\_circle do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://doi.org/10.1007/978-1-0716-2541-5_5) Editing the Drosophila genome is incredibly useful for gene functional analysis. However, compared to gene knockouts, precise gene editing is difficult to achieve. Prime editing, a recently described CRISPR/Cas9-based technique, has the potential to make... - [ descriptionPublisher's Version](https://doi.org/10.1007/978-1-0716-2541-5_5) ### 2021 J. A. Bosch, G. Birchak, and N. Perrimon. 2021. “[Precise Genome Engineering in Drosophila Using Prime Editing](/publications/precise-genome-engineering-drosophila-using-prime-editing)”. Proc Natl Acad Sci U S A, 118 J. A. Bosch, G. Birchak, and N. Perrimon. 2021. “[Precise Genome Engineering in Drosophila Using Prime Editing](/publications/precise-genome-engineering-drosophila-using-prime-editing)”. Proc Natl Acad Sci U S A, 118 - add\_circle do\_not\_disturb\_on Abstract Precise genome editing is a valuable tool to study gene function in model organisms. Prime editing, a precise editing system developed in mammalian cells, does not require double-strand breaks or donor DNA and has low off-target effects. Here, we applied... Jun Xu, Ah-Ram Kim, Ross W. Cheloha, Fabian A. Fischer, Joshua Shing Shun Li, Yuan Feng, Emily Stoneburner, Richard Binari, Stephanie E. Mohr, Jonathan Zirin, Hidde Ploegh, and Norbert Perrimon. 2021. “[Protein Visualization and Manipulation in Drosophila through the Use of Epitope Tags Recognized by Nanobodies](/publications/protein-visualization-and-manipulation-drosophila-through-use-epitope-tags)”. BioRxiv Jun Xu, Ah-Ram Kim, Ross W. Cheloha, Fabian A. Fischer, Joshua Shing Shun Li, Yuan Feng, Emily Stoneburner, Richard Binari, Stephanie E. Mohr, Jonathan Zirin, Hidde Ploegh, and Norbert Perrimon. 2021. “[Protein Visualization and Manipulation in Drosophila through the Use of Epitope Tags Recognized by Nanobodies](/publications/protein-visualization-and-manipulation-drosophila-through-use-epitope-tags)”. BioRxiv - add\_circle do\_not\_disturb\_on Abstract - [ picture\_as\_pdf2021.04.16.440240v1.full\_...](/sites/g/files/omnuum5366/files/fly/files/2021.04.16.440240v1.full_.pdf) Expansion of the available repertoire of reagents for visualization and manipulation of proteins will help understand their function. Short epitope tags installed on proteins of interest and recognized by existing binders such as nanobodies facilitate... - [ picture\_as\_pdf2021.04.16.440240v1.full\_...](/sites/g/files/omnuum5366/files/fly/files/2021.04.16.440240v1.full_.pdf) ### 2020 R. Viswanatha, M. Zaffagni, J. Zirin, N. Perrimon, and S. Kadener. 2020. “[CRISPR-Cas13 Mediated Knock Down in Drosophila Cultured Cells](/publications/crispr-cas13-mediated-knock-down-drosophila-cultured-cells)”. BioRxiv R. Viswanatha, M. Zaffagni, J. Zirin, N. Perrimon, and S. Kadener. 2020. “[CRISPR-Cas13 Mediated Knock Down in Drosophila Cultured Cells](/publications/crispr-cas13-mediated-knock-down-drosophila-cultured-cells)”. BioRxiv - add\_circle do\_not\_disturb\_on Abstract - [ picture\_as\_pdf2020.11.01.364166v1.full\_...](/sites/g/files/omnuum5366/files/fly/files/2020.11.01.364166v1.full_.pdf) Manipulation of gene expression is one of the best approaches for studying gene function *in vivo*. CRISPR-Cas13 has the potential to be a powerful technique for manipulating RNA expression in diverse animal systems *in vivo*, including *Drosophila*... - [ picture\_as\_pdf2020.11.01.364166v1.full\_...](/sites/g/files/omnuum5366/files/fly/files/2020.11.01.364166v1.full_.pdf) Jonathan Zirin, Yanhui Hu, Luping Liu, Donghui Yang-Zhou, Ryan Colbeth, Dong Yan, Ben Ewen-Campen, Rong Tao, Eric Vogt, Sara VanNest, Cooper Cavers, Christians Villalta, Aram Comjean, Jin Sun, Xia Wang, Yu Jia, Ruibao Zhu, Ping Peng, Jinchao Yu, Da Shen, Yuhao Qiu, Limmond Ayisi, Henna Ragoowansi, Ethan Fenton, Senait Efrem, Annette Parks, Kuniaki Saito, Shu Kondo, Liz Perkins, Stephanie Mohr, Jianquan Ni, and Norbert Perrimon. 2020. “[Large-Scale Transgenic Resource Collections for Loss- and Gain-of-Function Studies](/publications/large-scale-transgenic-resource-collections-loss-and-gain-function-studies)”. Genetics. doi:10.1534/genetics.119.302964 Jonathan Zirin, Yanhui Hu, Luping Liu, Donghui Yang-Zhou, Ryan Colbeth, Dong Yan, Ben Ewen-Campen, Rong Tao, Eric Vogt, Sara VanNest, Cooper Cavers, Christians Villalta, Aram Comjean, Jin Sun, Xia Wang, Yu Jia, Ruibao Zhu, Ping Peng, Jinchao Yu, Da Shen, Yuhao Qiu, Limmond Ayisi, Henna Ragoowansi, Ethan Fenton, Senait Efrem, Annette Parks, Kuniaki Saito, Shu Kondo, Liz Perkins, Stephanie Mohr, Jianquan Ni, and Norbert Perrimon. 2020. “[Large-Scale Transgenic Resource Collections for Loss- and Gain-of-Function Studies](/publications/large-scale-transgenic-resource-collections-loss-and-gain-function-studies)”. Genetics. doi:10.1534/genetics.119.302964 - add\_circle do\_not\_disturb\_on Abstract The Transgenic RNAi Project (TRiP), a functional genomics platform at Harvard Medical School, was initiated in 2008 to generate and distribute a genome-scale collection of RNAi fly stocks. To date, the TRiP has generated >15,000 RNAi fly stocks. As this... [ More arrow\_circle\_right ](/publications/technology/fly-in-vivo-crispr)