Cell-based CRISPR

2018 Dec 08

DRSC&TRiP at ASCB|EMBO 2018

Sat Dec 8 (All day) to Wed Dec 12 (All day)

Location: 

San Diego, CA, USA
The DRSC & TRiP will be represented at the ASCB|EMBO 2018 conference in the form of a poster that includes information about our collaboration with O. Kanca in the H. Bellen lab at Baylor College of Medicine to tag Drosophila S2R+ cell lines with GFP using a CRISPR-based strategy. We have 'painted' a number of subcellular localizations green with this approach! If you're at the meeting, check out P1482 at Board Number B494, presented by Baolong Xia of the Perrimon lab.
flySAM

Missed us at ADRC 2018? View our workshop slides!

April 19, 2018
Thank you to all those who attended our workshop at last week's Annual Drosophila Research Conference in Philadelphia, PA, USA. It was great to talk fly stocks, cell screens, and bioinformatics with the community. We are here to help and look forward to continued feedback on the resources we are building to empower your research. PDFs of our workshop presentations are attached to this news item. The slides will help you learn more about our in vivo resources for CRISPR, new pooled cell-based CRISPR screen technology, and bioinformatics resources at our facility.  Feel free to contact... Read more about Missed us at ADRC 2018? View our workshop slides!
Cartoon of essential gene pooled screen (made using BioRender.io)

Pooled-format CRISPR screens in Drosophila cells

March 22, 2018

The DRSC/TRiP-FGR is pleased to support collaborations on pooled CRISPR screens using the method recently, reported in eLife by Viswanatha et al. (PDF download file below).

From the abstract: "... Here, we developed a site-specific integration strategy for library delivery and performed a genome-wide CRISPR knockout screen in Drosophila S2R+ cells. Under basal growth conditions, 1235 genes were essential for cell fitness...

Read more about Pooled-format CRISPR screens in Drosophila cells
2018 Apr 13

DRSC & TRiP Workshop at ADRC

1:45pm to 3:45pm

Location: 

Philadelphia, PA, USA
The DRSC & TRiP will be hosting a workshop at the Annual Drosophila Research Conference in Philadelphia, PA. The workshop is scheduled for Friday, April 13th from 1:45 to 3:45 PM. Come hear from DRSC & TRiP leaders Norbert Perrimon, Jonathan Zirin (organizer), Claire Yanhui Hu, and Stephanie Mohr. At the workshop, you will learn about new opportunities for community nomination and experiments using CRISPR knockout and activation, as well as learn what's new and popular among our online software and database tools. There will be something for everyone -- we will provide information... Read more about DRSC & TRiP Workshop at ADRC
Ben Ewen-Campen, Stephanie E Mohr, Yanhui Hu, and Norbert Perrimon. 10/9/2017. “Accessing the Phenotype Gap: Enabling Systematic Investigation of Paralog Functional Complexity with CRISPR.” Dev Cell, 43, 1, Pp. 6-9.Abstract
Single-gene knockout experiments can fail to reveal function in the context of redundancy, which is frequently observed among duplicated genes (paralogs) with overlapping functions. We discuss the complexity associated with studying paralogs and outline how recent advances in CRISPR will help address the "phenotype gap" and impact biomedical research.
Huajin Wang, Michel Becuwe, Benjamin E Housden, Chandramohan Chitraju, Ashley J Porras, Morven M Graham, Xinran N Liu, Abdou Rachid Thiam, David B Savage, Anil K Agarwal, Abhimanyu Garg, Maria-Jesus Olarte, Qingqing Lin, Florian Fröhlich, Hans Kristian Hannibal-Bach, Srigokul Upadhyayula, Norbert Perrimon, Tomas Kirchhausen, Christer S Ejsing, Tobias C Walther, and Robert V Farese. 2016. “Seipin is required for converting nascent to mature lipid droplets.” Elife, 5.Abstract

How proteins control the biogenesis of cellular lipid droplets (LDs) is poorly understood. Using Drosophila and human cells, we show here that seipin, an ER protein implicated in LD biology, mediates a discrete step in LD formation-the conversion of small, nascent LDs to larger, mature LDs. Seipin forms discrete and dynamic foci in the ER that interact with nascent LDs to enable their growth. In the absence of seipin, numerous small, nascent LDs accumulate near the ER and most often fail to grow. Those that do grow prematurely acquire lipid synthesis enzymes and undergo expansion, eventually leading to the giant LDs characteristic of seipin deficiency. Our studies identify a discrete step of LD formation, namely the conversion of nascent LDs to mature LDs, and define a molecular role for seipin in this process, most likely by acting at ER-LD contact sites to enable lipid transfer to nascent LDs.

CRISPR sgRNA design tool now based on Drosophila genome assembly 6

December 21, 2016

We have updated our CRISPR sgRNA design tool. The results and JBrowse display are now based on Drosophila melanogaster FlyBase genome assembly release 6. We have also added seed scores in addition to efficiency prediction scores and other values available on detailed views of sgRNA designs. Quick tips: start a search with a gene symbol or other identifier, use the...

Read more about CRISPR sgRNA design tool now based on Drosophila genome assembly 6
Benjamin E Housden, Matthias Muhar, Matthew Gemberling, Charles A Gersbach, Didier YR Stainier, Geraldine Seydoux, Stephanie E Mohr, Johannes Zuber, and Norbert Perrimon. 10/31/2016. “Loss-of-function genetic tools for animal models: cross-species and cross-platform differences.” Nat Rev Genet. Publisher's VersionAbstract

Our understanding of the genetic mechanisms that underlie biological processes has relied extensively on loss-of-function (LOF) analyses. LOF methods target DNA, RNA or protein to reduce or to ablate gene function. By analysing the phenotypes that are caused by these perturbations the wild-type function of genes can be elucidated. Although all LOF methods reduce gene activity, the choice of approach (for example, mutagenesis, CRISPR-based gene editing, RNA interference, morpholinos or pharmacological inhibition) can have a major effect on phenotypic outcomes. Interpretation of the LOF phenotype must take into account the biological process that is targeted by each method. The practicality and efficiency of LOF methods also vary considerably between model systems. We describe parameters for choosing the optimal combination of method and system, and for interpreting phenotypes within the constraints of each method.

2016 Sep 23

Boston Area Drosophila Meeting

1:00pm to 4:30pm

Location: 

University of Massachusetts Boston

The DRSC-Functional Genomics Resources (formerly DRSC & TRiP) will be participating in the Boston Area Drosophila Meeting, which was organized by Alexey Verakas of UMass Boston and Jim Walker of Harvard Medical School. Hear about what's new in technologies and online tools at this regional meeting of experts in Drosophila research.

Search results for the term oogenesis at the Drosophila protocols portal

Beta-testing a "Drosophila Protocols Portal"

June 16, 2016

The DRSC-FGR has developed a beta version of a database and online search for protocols, the Drosophila Protocols Portal, relevant to Drosophila research. The goal is to provide a central portal for protocols distributed across the web. We collected protocols from protocol databases, lab websites, YouTube, Drosophila Information Service (DIS), and relevant journals. You can view the results by topic or search for specific terms.

Longer-term goals...

Read more about Beta-testing a "Drosophila Protocols Portal"

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