in vivo CRISPR (TRiP)

Quick link to Find CRISPR sgRNA search
Quick link to TRiP-CRISPR sgRNA stock database

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.

TRiP-CRISPR fly stock collections

Function

sgRNA Vectors

Cross to

Notes

TRiP-OE

VPR

Gene Activation

pCFD4

Gal4+dCas9-VPR

See TRiP-CRISPR Toolbox

flySAM1.0

Gene Activation

U6B-sgRNA2.0

Gal4+flySAM

See TRiP-CRISPR Toolbox

flySAM2.0

Gene Activation

flySAM2.0

Gal4

flySAM2.0 lines contain both sgRNA and dCas9 (flySAM)

TRiP-KO

Gene Cutting

pCFD3, pCFD4

Gal4+Cas9

See TRiP-CRISPR Toolbox

Search the DRSC/TRiP sgRNA Stock Database for TRiP-OE and TRiP-KO stocks
Nominate genes for production for TRiP-OE and TRiP-KO stocks
Download a .XLS file of currently available TRiP-OE and TRiP-KO stocks
Protocols for cloning, sequencing, and using TRiP-CRISPR lines
Online tools for gRNA design and efficiency prediction

See links below to relevant online tools, reagents, protocols, publications, and more.

in vivo CRISPR

Online tools

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...

CRISPR Efficiency Prediction
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...

Reagents

in vivo CRISPR fly stocks
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...

Protocols

in vivo CRISPR
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...

News

Important new considerations for TRiP stock users
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

Read the DRSC/TRiP Report to the Fly Board 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

DRSC/TRiP and DRSC-BTRR Office Hours
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

Transgenic Fly Stocks for Double Knockout of Paralog Pairs
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

DRSC-Biomedical Technology Research Resource
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

Contact Us

Please contact us for any questions.

Publications

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”. 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”. Trends Genet, 38, 5, Pp. 437-53. doi:10.1016/j.tig.2021.11.006
Justin A. Bosch, Norbert Perrimon, and Christian Dahmann. 2022. “Prime Editing for Precise Genome Engineering in 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”. In Drosophila: Methods and Protocols, Pp. 113-34. New York, NY: Springer US

2021

J. A. Bosch, G. Birchak, and N. Perrimon. 2021. “Precise Genome Engineering in 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”. Proc Natl Acad Sci U S A, 118
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”. 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”. BioRxiv

2020

R. Viswanatha, M. Zaffagni, J. Zirin, N. Perrimon, and S. Kadener. 2020. “CRISPR-Cas13 Mediated Knock Down in 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”. BioRxiv
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”. 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”. Genetics. doi:10.1534/genetics.119.302964
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