Daul, Aric et al. (2017) International Worm Meeting "Caenorhabditis Genetics Center."

Knott, Julie, Daul, Aric, Stiernagle, Theresa, Rougvie, A.E.

[International Worm Meeting, 2017]

The goal of the Caenorhabditis Genetics Center (CGC) is to promote research on the small metazoan Caenorhabditis elegans by curating important, genetically characterized nematode stocks and distributing them upon request to researchers and science educators throughout the world. The CGC is housed at the University of Minnesota and is supported by the National Institutes of Health - Office of Research Infrastructure Programs (NIH-ORIP) and nominal user fees. There are now nearly 20,000 different strains in the collection. We strive to have at least one allele of every published gene and all useful chromosome rearrangements, duplications and deficiencies. Selected multiple-mutant stocks and transgenic strains are also available, such as strains that express various fluorescent protein reporter fusions. A small research component has enhanced the genetic tool-kit available to C. elegans researchers, in part by labeling existing balancer chromosomes with fluorescent markers. A searchable list of strains, including information about CGC stocks, is accessible through the CGC website (www.cbs.umn.edu/CGC/) and WormBase. Requests for strains should be made on-line through our website, using credit cards for payments whenever possible. We provide yearly reports to the NIH with statistics that reflect our services to the worm community. A key tracked parameter is the number of published papers that acknowledge the CGC for providing strains. Please help us retain our funding by remembering to acknowledge the CGC in your publications!

Daul, Aric L. et al. (2011) International Worm Meeting "Caenorhabditis Genetics Center."

Daul, Aric L., Knott, Julie, Rougvie, Ann E., Stiernagle, Theresa

[International Worm Meeting, 2011]

The Caenorhabditis Genetics Center (CGC), supported by the National Institutes of Health - National Center for Research Resources (NIH-NCRR), supplies Caenorhabditis strains and information to researchers throughout the world. The CGC continues to be housed at the University of Minnesota and will continue its duties of acquiring, maintaining and distributing worm stocks. The CGC now has over 13,000 different strains. We strive to have at least one allele of every published gene and all chromosome rearrangements, duplications and deficiencies. Selected multiple-mutant stocks and transgenic strains are also available, including some strains from the modENCODE project and strains that express various fluorescent protein reporter fusions. The CGC also has stocks of nematode species closely related to C. elegans and bacterial strains necessary for nematode growth. A searchable strains list, including information about CGC stocks, is accessible either through the CGC website (www.cbs.umn.edu/CGC/) or through WormBase. Requests for strains should be made via the on-line ordering system available through our website; the CGC no longer accepts orders submitted by fax. As mandated by NIH-NCRR, a small yearly user fee and charge per strain is assessed with each order. The CGC strongly encourages use of credit cards for these charges, and now accepts credit payments for invoices directly through the CGC website. Payments must be made by check or credit card; electronic bank transfer may not be used for making payment. We provide quarterly reports to the NIH with statistics that reflect our services to the worm community. We like to be acknowledged in papers for providing strains. We also like to receive pdf files of such papers, copies of which we provide to NIH.

Daul, Aric et al. (2015) International Worm Meeting "CGC ver 2.0: What you need to know."

Rougvie, Ann E, Awoyinka, Kemi, Knott, Julie, Daul, Aric, Stiernagle, Theresa

[International Worm Meeting, 2015]

The Caenorhabditis Genetics Center (CGC), supported by the National Institutes of Health - Office of Research Infrastructure Programs (NIH-ORIP) and housed at the University of Minnesota, supplies Caenorhabditis strains and information to researchers throughout the world. The CGC will be releasing a new website and on-line ordering system later this year. Our new system will include innovations such as enabling users and PIs to view their order history with ship dates, submit strain information when donating strains, and request lab codes directly through our site. There will be two types of accounts for each lab: A PI level account that will allow the PI or lab manager to edit lab information (billing and preferred shipping addresses, manage lab member accounts, view the order history for the entire lab, etc.) and a lab member level account that will allow each user to place orders, select or edit their preferred shipping address, view their personal order history, etc. The head of the lab must activate their PI account before lab members may set up their individual accounts. All users will be required to register and are encouraged to set up their lab's PI and personal accounts prior to our transition to the new site to avoid delays in placing or receiving their orders. We will provide an overview of our new website, outline key changes to the ordering system, and explain how to prepare your lab for the move to CGC 2.0!

Daul, Aric et al. (2013) International Worm Meeting "Caenorhabditis Genetics Center."

Werre, Brittany, Rougvie, Ann E., Daul, Aric, Knott, Julie, Stiernagle, Theresa

[International Worm Meeting, 2013]

The Caenorhabditis Genetics Center (CGC), supported by the National Institutes of Health - Office of Research Infrastructure Programs (NIH-ORIP) and housed at the University of Minnesota, supplies Caenorhabditis strains and information to researchers throughout the world. The CGC has also initiated a small research component aimed at enhancing the genetic tool-kit available to C. elegans researchers. The CGC continues its duties of acquiring, maintaining and distributing worm stocks. There are now over 17,512 different strains in the collection. We strive to have at least one allele of every published gene and all chromosome rearrangements, duplications and deficiencies. Selected multiple-mutant stocks and transgenic strains are also available including strains that express various fluorescent protein reporter fusions. Greater than two thousand whole-genome sequenced strains, obtained from the Million Mutation Project and other sources, are available and have proved popular. The CGC also has stocks of nematode species closely related to C. elegans and bacterial strains necessary for nematode growth. A searchable strains list, including information about CGC stocks, is accessible either through the CGC website (www.cbs.umn.edu/CGC/) or through WormBase. Requests for strains should be made via the on-line ordering system available through our website. As mandated by NIH-ORIP, a small yearly user fee and charge per strain is assessed with each order. The CGC strongly encourages use of credit cards for payments. We provide yearly reports to the NIH with statistics that reflect our services to the worm community. A key tracked parameter is the number of published papers that acknowledge the CGC for providing strains. Please remember to acknowledge the CGC in your publications!.

Vargas, Marcus L. et al. (2019) International Worm Meeting "Generating microRNA deletions and transcriptional reporters using CRISPR-CAS9 technology."

Ambros, Victor, Vargas, Marcus L., Rougvie, Ann E., Knott, Julie

[International Worm Meeting, 2019]

MicroRNAs (miRNAs) are small, non-coding RNAs that regulate gene expression by targeting 3' UTRs of mRNAs, which leads to either mRNA degradation and/or inhibition of mRNA translation. Programs that predict miRNA-3' UTR interactions are readily available, and it is estimated that ~27% of C. elegans 3' UTRs are under selective pressure to maintain miRNA binding sites. However, there are many miRNA genes for which null mutations do not exist, providing an impediment to validation miRNA-mRNA interactions or to studies miRNA function. We have identified 244 bona fide miRNA loci by cross-referencing miRBase data, miRNA prediction algorithms, and published and unpublished expression data. Of those 244 loci, 131 do not have null mutations and a further 44 have mutations which are suboptimal (i.e. the mutation affects an additional gene). We are using two Crispr-Cas9 strategies to generate mutations in the 175 miRNAs identified above. The first strategy involves using Crispr-Cas9 to replace the pre-miRNA with a fluorescent protein to simultaneously delete the miRNA and generate a transcriptional reporter for expression read-out. We are using the heterochronic gene lin-4as a test-bed for assaying different fluorescent protein fusions designed to maximize protein expression while reporting the expected expression patterns. The other approach is to use Crispr-Cas9 to delete a single miRNA or clusters of miRNAs while inserting a visible marker to track the mutation. We have prioritized for deletion the 131 miRNA genes which do not have null alleles, starting with those loci that produce a single miRNA and have an optimal PAM site for Cas9 recognition that resides within the precursor (pre-miRNA). miRNA deletions that are requested by members of the worm community will be moved up in the queue, and once validated, all deletion strains will be deposited in the CGC.

Daul, Aric et al. (2015) International Worm Meeting "Caenorhabditis Genetics Center."

Daul, Aric, Stiernagle, Theresa, Awoyinka, Kemi, Knott, Julie, Rougvie, Ann E

[International Worm Meeting, 2015]

The Caenorhabditis Genetics Center (CGC) is supported by the National Institutes of Health - Office of Research Infrastructure Programs (NIH-ORIP) and housed at the University of Minnesota. Our primary aim is to acquire, curate, and maintain Caenorhabditis strains and distribute them upon request to researchers throughout the world. There are now nearly 19,000 different strains in the collection, including more than two thousand whole-genome sequenced strains obtained from the Million Mutation Project and other sources. We strive to have at least one allele of every published gene and all chromosome rearrangements, duplications and deficiencies. Selected multiple-mutant stocks and transgenic strains are also available, such as strains that express various fluorescent protein reporter fusions. The CGC has initiated a small research component aimed at enhancing the genetic tool-kit available to C. elegans researchers, including labeling balancer chromosomes with fluorescent markers (some of which are now available). The CGC also distributes stocks of nematode species closely related to C. elegans and bacterial strains necessary for nematode growth. A searchable list of strains, including information about CGC stocks, is accessible through the CGC website (www.cbs.umn.edu/CGC/) and WormBase. Requests for strains should be made on-line through our website. The CGC will be releasing a new on-line ordering system with enhanced user features later this summer. We will be offering a preview of our new website and inform users how to set up their required lab and individual accounts in preparation for the transition to our new ordering system.As mandated by NIH-ORIP, a small yearly user fee and charge per strain is assessed with each order. The CGC strongly encourages use of credit cards for payments. We provide yearly reports to the NIH with statistics that reflect our services to the worm community. A key tracked parameter is the number of published papers that acknowledge the CGC for providing strains. Please remember to acknowledge the CGC in your publications!.

Rougvie, Ann et al. (2021) International Worm Meeting "Caenorhabditis Genetics Center (CGC)"

Daul, Aric, Rougvie, Ann, Stiernagle, Theresa, Fox, Liz, Knott, Julie, Vargas, Marcus

[International Worm Meeting, 2021]

The Caenorhabditis Genetics Center (CGC) promotes C. elegans research by curating important, genetically characterized nematode stocks and distributing them upon request to researchers and science educators throughout the world. The CGC is housed at the University of Minnesota and is supported by the National Institutes of Health - Office of Research Infrastructure Programs (NIH-ORIP) and nominal user fees. We strive to have at least one allele of every published gene and all useful chromosome rearrangements, duplications and deficiencies. Our catalog of more than 23,000 different strains also includes selected multiple-mutant stocks, tagged endogenous loci, and genetic tool strains for various applications such as inducible gene expression. Despite a university-mandated 7-week closure due to the Covid-19 pandemic, we shipped over 21,500 strains in 2020. A small research component has enhanced the genetic tool-kit available to C. elegans researchers, in part by labeling existing balancer chromosomes with fluorescent markers and deleting or tagging miRNA loci. Requests for generation of specific miRNA deletions or balancer modifications are considered. A searchable list of strains, including information about each stock, is accessible through the CGC website (cgc.umn.edu) and WormBase. Orders should be placed on-line through our website, using credit cards for payments whenever possible. We provide yearly reports to the NIH with statistics that reflect our services to the worm community. A key tracked parameter is the number of published papers that acknowledge the CGC for providing strains. Please help us retain our funding by remembering to acknowledge the CGC in your publications!

Aurlie Blanc et al. (2005) International Worm Meeting "A French functional genomics platform."

Daniel Wong, Jerome Reboul, Jonathan Ewbank, Aurlie Blanc, Yohann Duverger

[International Worm Meeting, 2005]

For the last two years, we have offered a service of worm sorting based around the Union Biometrica COPAS platform. The COPAS machine is fully equipped with Zymark twister robot, allowing automated analysis of multiple 96 well plates, and the Profiler that generates 500 individual fluorescence measurements per worm. This equipment has been applied to a wide range of biological questions. They include quantifying the level of fluorescent reporter gene expression, large-scale RNAi and genetic screens and combinatorial library drug screening. Examples of each will be presented.This platform is now part of a fully integrated functional genomics facility open to the academic community (see http://www.ciml.univ-mrs.fr/EWBANK_jonathan/RIO.html). Other resources include the ORFeome (developed in Marc Vidals laboratory), and Julie Ahringers RNAi library, together with whole-genome microarrays. For the latter, through a collaboration with the Genome Sequencing Center at Washington, and the transcriptome platform at Nice, we have spotted the Illumina long oligo set onto glass slides and provide microarrays to the French C. elegans community.This French functional genomics platform has been made possible through funding from the National Genopole<sym02> network, Marseille-Nice genopole<sym02>, the CNRS and collaboration with Union Biometrica.

Yohann Duverger et al. (2007) International Worm Meeting "A French functional genomics platform."

Yohann Duverger, Jonathan Ewbank, Jerome Reboul, Sarah Scaglione, Daniel Wong

[International Worm Meeting, 2007]

For the last four years, we have offered a service of worm sorting based around the Union Biometrica COPAS platform. The COPAS machine is fully equipped with Zymark twister robot, allowing automated analysis of multiple 96 well plates, and the Profiler that generates up to 1000 individual fluorescence measurements per worm. This equipment has been applied to a wide range of biological questions. They include quantifying the level of fluorescent reporter gene expression, large-scale RNAi and genetic screens and combinatorial library drug screening. Examples of each will be presented. This platform is now part of a fully integrated functional genomics facility open to the academic community (see http://www.ciml.univ-mrs.fr/EWBANK_jonathan/RIO.html). Other resources include the ORFeome (developed in Marc Vidals laboratory), and Julie Ahringers RNAi library, together with whole-genome microarrays. For the latter, through a collaboration with the Genome Sequencing Center at Washington, and the transcriptome platform at Nice, we have spotted the Illumina long oligo set onto glass slides and provide microarrays to the French C. elegans community. This French functional genomics platform has been made possible through funding from the National Genopole&#174; network, Marseille-Nice genopole&#174;, INSERM, the CNRS and support from Union Biometrica.

Au, Vinci et al. (2021) International Worm Meeting "Crispr-ing C. elegans genes conserved to humans"

Au, Vinci, Moerman, Donald, Rougvie, Ann, Edgley, Mark, Doell, Claudia, Vargas, Marcus, Palma, Wilber, Hutter, Harald, Park, Heenam, Knott, Julie, Sternberg, Paul, Fernando, Lisa, Juciute, Viktorija, Li-Leger, Erica, Flibotte, Stephane, Martin, Kiana

[International Worm Meeting, 2021]

We are continuing our community resource project to generate gene deletions of high value to those interested in human biology and disease. Our highly coordinated three-site knockout (KO) production strategy has branches in California, Minnesota, and British Columbia, with the Canadian branch transitioning from the University of British Columbia to Simon Fraser University upon the retirement of KO legend Don Moerman. We employ a dual-pipeline strategy to generate KOs, with the Minnesota and Canadian sites using a scheme based on the Calarco Lab's dual selection cassette method. It deletes all or most of the target gene, effectively eliminating function. In addition, it replaces the gene with a fluorescent reporter, allowing simple tracking of the allele in cases where the mutation results in homozygous lethality or sterility, or fails to cause a discernible phenotype, facilitating genetic manipulation of the alleles. Alternatively, the California site developed and uses a "STOP-IN" cassette that places stop codons in all three reading frames near the beginning of the coding region, eliminating activity. This method does not allow visual tracking of alleles but has the advantage in that it inserts a unique guide RNA recognition site, enabling reversion of the locus to wild-type allowing the phenotype to be reassessed. This feature is desired by some users, for example those performing metabolomics experiments requiring quantitation of phenotypes that are sensitive to strain background effects. Each gene edit is carefully confirmed, and validated strains are grossly phenotyped and promptly deposited into the Caenorhabditis Genetics Center (CGC) strain collection along with detailed strain information. To date, 1,040 of our KOs are available through the CGC. Going forward, we plan to target an additional 2500 C. elegans orthologs of human genes, prioritizing known or suspected human disease genes, druggable gene classes, as well as understudied genes that are conserved to humans but that have no actionable information. Finally, we will consider community requests to prioritize specific genes.