“WormBase and WormBook provide information on Caenorhabditis elegans gene function, mutant strains, developmental biology, and experimental methodologies.”

WormBook also serves as the text companion to WormBase, the C.elegans model organism database. Objects such as genes, proteins and cells are linked to the relevant pages in WormBase, providing easily accessible background information. … The content of WormBook is divided into 10 sections: Genetics and Genomics, Molecular Biology, Cell Biology, Sex Determination, The Germ Line, Developmental Control, Signal Transduction, Neurobiology and Behavior, Evolution and Ecology, and WormMethods. Each section contains ∼10 chapters covering topics related to that subject area written by experts in the field. WormMethods includes a range of methods and protocols, accompanied by commentary, relevant to a range of studies including sections on Behavior, Genetic mapping, Cell Biology and Biochemistry.Abstract WormBook (www.wormbook.org) is an open-access, online collection of original, peer-reviewed chapters on the biology of Caenorhabditis elegans and related nematodes. Since WormBook was launched in June 2005 with 12 chapters, it has grown to over 100 chapters, covering nearly every aspect of C.elegans research, from Cell Biology and Neurobiology to Evolution and Ecology. WormBook also serves as the text companion to WormBase, the C.elegans model organism database. Objects such as genes, proteins and cells are linked to the relevant pages in WormBase, providing easily accessible background information. Additionally, WormBook chapters contain links to other relevant topics in WormBook, and the in-text citations are linked to their abstracts in PubMed and full-text references, if available. Since WormBook is online, its chapters are able to contain movies and complex images that would not be possible in a print version. WormBook is designed to keep up with the rapid pace of discovery in the field of C.elegans research and continues to grow. … ## CONTENT The content of WormBook is divided into 10 sections: Genetics and Genomics, Molecular Biology, Cell Biology, Sex Determination, The Germ Line, Developmental Control, Signal Transduction, Neurobiology and Behavior, Evolution and Ecology, and WormMethods. Each section contains ∼10 chapters covering topics related to that subject area written by experts in the field. WormMethods includes a range of methods and protocols, accompanied by commentary, relevant to a range of studies including sections on Behavior, Genetic mapping, Cell Biology and Biochemistry. The chapters are geared toward a wide audience ranging from high school students and interested laypeople to C.elegans researchers. FEATURES AND USER INTERFACE

The third incarnation was the creation of WormBook, a pioneering online compendium “created in response to the need to develop a publishing model that could keep pace with a rapidly growing knowledge base and provide a central repository for methods and protocols” (Girard et al. 2006). Chapters of WormBook were published beginning in 2005 in conjunction with WormBase, which began as a pioneering effort to expand the database of the genome-sequencing project database into a web-based one-stop shop for information about C. elegans, and is now thriving not only as the central repository for research data on all aspects of the biology, genetics, and genomics of C. elegans, but also for other nematode species (Howe et al. 2015).… elegans II,” published in 1996, grew to contain 30 chapters plus appendices. It also contains a preface in which Brenner remarked not only on the breadth of the biology encompassed in those pages but also on “the wonderful feature that I experienced first and which everyone has experienced since: that with a few toothpicks, some Petri dishes, and a microscope, you can open the door to all of biology.” How we worm people feel about our beast and our field cannot be said any better than that! The third incarnation was the creation of WormBook, a pioneering online compendium “created in response to the need to develop a publishing model that could keep pace with a rapidly growing knowledge base and provide a central repository for methods and protocols” (Girard et al. 2006). Chapters of WormBook were published beginning in 2005 in conjunction with WormBase, which began as a pioneering effort to expand the database of the genome-sequencing project database into a web-based one-stop shop for information about C. elegans, and is now thriving not only as the central repository for research data on all aspects of the biology, genetics, and genomics of C. elegans, but also for other nematode species (Howe et al. 2015). The publication of over 150 chapters in WormBook has furthered the WormBase mission to make information about the worm accessible and available to the community. This fourth incarnation, launched here as WormBook in GENETICS, is more than just “WormBook II.” It is an opportunity to respond to the ever-increasing pace and complexity of C. elegans research by treating information and discoveries in a more synthetic and interdisciplinary way. …

Another portal to WormBase is through WormBook (http://www.wormbook.org/). WormBook content is extensively linked to WormBase with Genes, Proteins and Cells linked to the relevant pages in WormBase. Links from WormBase back to WormBook have recently been implemented to provide users easy access to background and in-depth information. … Searching for strains at the Caenorhabditis Genetic Center (CGC) has been improved and is now hosted at WormBase. In addition to searching by strain name, users may now search for strains carrying a specific gene or allele, or other information found in the strain class (i.e. species, mutagen, data received and remarks). … The WormBase Wiki site (http://www.wormbase.org/wiki) provides a mechanism for users to easily add content to WormBase. Individuals can post experimental protocols, make posting about meetings and job openings, or add useful information about their favorite gene(s).… There are links to all the mirror sites and the main and development site on the WormBase homepage (Supplementary Figure 8). Another portal to WormBase is through WormBook (http://www.wormbook.org/). WormBook content is extensively linked to WormBase with Genes, Proteins and Cells linked to the relevant pages in WormBase. Links from WormBase back to WormBook have recently been implemented to provide users easy access to background and in-depth information. Improved searching … Google searches can be limited to WormBase results by using the format ‘site: www.wormbase.org [search terms]’. Google's page caching also provides an additional layer of redundancy during unexpected server interruptions at the WormBase site. Searching for strains at the Caenorhabditis Genetic Center (CGC) has been improved and is now hosted at WormBase. In addition to searching by strain name, users may now search for strains carrying a specific gene or allele, or other information found in the strain class (i.e. species, mutagen, data received and remarks). Improved data presentation … Some requests are for information for which WormBase simply does not have access, such as large-scale studies before publication. WormBase strives to have data available at the time of publication and encourages authors to contact WormBase about upcoming publications. The WormBase Wiki site (http://www.wormbase.org/wiki) provides a mechanism for users to easily add content to WormBase. Individuals can post experimental protocols, make posting about meetings and job openings, or add useful information about their favorite gene(s). A long-term goal is for the Wiki site to assume the role of the print version of the Worm Breeder's Gazette. SUPPLEMENTARY DATA

Much of this information, including gene expression, gene function, and references, is curated on WormBase (www.wormbase.org). Reviews on many topics of C. elegans biology are provided by WormBook (www.wormbook.org), which includes a collection of C. elegans methods (WormMethods) and current and past issues of the C. elegans Newsletter (The Worm Breeder's Gazette).… Right image shows an npr-1 mutant strain foraging in grouped masses (sometimes called a “social” feeding phenotype). Image from M. de Bono, taken from Schafer (2005). Sharing large amounts of genetic and cellular information has been central to the success of C. elegans research. The wealth of knowledge generated by past research is readily available to anyone via on-line resources (see Table 1). Much of this information, including gene expression, gene function, and references, is curated on WormBase (www.wormbase.org). Reviews on many topics of C. elegans biology are provided by WormBook (www.wormbook.org), which includes a collection of C. elegans methods (WormMethods) and current and past issues of the C. elegans Newsletter (The Worm Breeder's Gazette). No model organism can be used to answer every research question, and working with C. elegans has some limitations. Not all metazoan genes are found in the C. elegans genome (Ruvkun and Hobert 1998). For example, Hedgehog (Hh) signaling is important in vertebrates for the patterning of various organs during development, but C. elegans lacks many of the genes in the regulatory cascade (Bürglin and Kuwabara 2006). Although some C. …

Since its inception in March 2000, WormBase has provided the nematode research community with an online resource for gene, genome, and other biological information about Caenorhabditis elegans and related nematodes [1,2]. … The WormBase website provides quick and convenient access to the most important information for conducting research using C. elegans as a model system. The site presents a wide array of data both curated from the scientific literature and submitted to the consortium directly by users. These data range from whole genome sequences of C. elegans and a number of related nematodes and genomic-scale datasets down to the sequence of individual variations. Gene function and perturbation, expression, anatomy, phenotypes, literature, and researcher history and more are all directly accessible from a single search of the site.1. Introduction Since its inception in March 2000, WormBase has provided the nematode research community with an online resource for gene, genome, and other biological information about Caenorhabditis elegans and related nematodes [1,2]. WormBase offers abundant gene-centric information including gene structure models, gene homology data, gene expression data, gene-affiliated phenotypes, gene ontology annotations, and gene interactions (physical, regulatory, and genetic) as well as an anatomy ontology, a life stage ontology, human disease relevance, publication information, and C. elegans researcher information. … ## 2. The WormBase Website The WormBase website provides quick and convenient access to the most important information for conducting research using C. elegans as a model system. The site presents a wide array of data both curated from the scientific literature and submitted to the consortium directly by users. These data range from whole genome sequences of C. elegans and a number of related nematodes and genomic-scale datasets down to the sequence of individual variations. Gene function and perturbation, expression, anatomy, phenotypes, literature, and researcher history and more are all directly accessible from a single search of the site. 2.1. The Home Page

WormBase (www.wormbase.org) is the central repository for the genetics and genomics of the nematode Caenorhabditis elegans. We provide the research community with data and tools to facilitate the use of C. elegans and related nematodes as model organisms for studying human health, development, and many aspects of fundamental biology. … Collecting variants and strains, and associating them with phenotypes, genomic location, papers, strains, laboratories, allows us to create variants which can be understood in the context of gene function, protein consequences, strain availability, publication, and phenotype, so that researchers can search for and obtain reagents suitable for their own research.Abstract WormBase (www.wormbase.org) is the central repository for the genetics and genomics of the nematode Caenorhabditis elegans. We provide the research community with data and tools to facilitate the use of C. elegans and related nematodes as model organisms for studying human health, development, and many aspects of fundamental biology. Throughout our 22-year history, we have continued to evolve to reflect progress and innovation in the science and technologies involved in the study of C. elegans. We strive to incorporate new data types and richer data sets, and to provide integrated displays and services that avail the knowledge generated by the published nematode genetics literature. … Our new Variants First Pass pipeline uses a neural network to identify potential new variant names in all new papers published each month. We regularly synchronize data with the CGC and National BioResource Project strain stock centers (https://cgc.umn.edu and https://shigen.nig.ac.jp/c.elegans), to be completely up-to-date with their strain, genotype, and variant contents. Finally, we curate variant and strain data directly from the literature. Collecting variants and strains, and associating them with phenotypes, genomic location, papers, strains, laboratories, allows us to create variants which can be understood in the context of gene function, protein consequences, strain availability, publication, and phenotype, so that researchers can search for and obtain reagents suitable for their own research. We have recently made significant improvements to the access and interpretation of variants at WormBase. Our new variant annotation pipeline, utilizing the Ensembl Variant Effect Predictor (McLaren et al. 2016), predicts the putative molecular consequences of variants (e.g. stop gained, missense, splice site loss, frameshift) in comparison to the latest reference annotation. …

WormBase (https://wormbase.org/) provides researchers using Caenorhabditis elegans as a model system a carefully curated and highly integrated view of decades of experimental data (1,2). … In addition, WormBase has incorporated many datasets unique to the system, such as the C. elegans developmental lineage and neuronal connectivity.INTRODUCTION WormBase (https://wormbase.org/) provides researchers using Caenorhabditis elegans as a model system a carefully curated and highly integrated view of decades of experimental data (1,2). With deep roots as an electronic resource pre-dating the rise of the web and driven by a scientific community well known for open sharing, WormBase has grown from supporting ∼300 active labs to over 1400 today. WormBase now spans multiple nematode species and annotations across the range of modern biology and a wealth of tools to assist in experimental design. In addition, WormBase has incorporated many datasets unique to the system, such as the C. elegans developmental lineage and neuronal connectivity. WormBase serves a global community of researchers and is an essential part of daily ‘worm work’. Backed by a team of biological curators, WormBase extracts experimental observations from the literature placing them in a searchable, highly cross-referenced and computable environment. To accelerate the rate and coverage of curation, WormBase solicits direct contributions from domain experts via community curation interfaces and relies on automated methods when feasible. …

The page can describe any or all of the following information, when available: identity of the gene's product; normal function of the gene's product; orthologs of the gene (if any); the gene's meiotic and physical location within the genome; its phenotype in classical mutations or RNAi screens; its spatial and temporal expression pattern, with microarray data; domains of its encoded protein; Gene Ontology (UNIT 7.2) terms describing its function; mutant alleles and strains carrying them … Finally, WormBook (http://www.wormbook.org) provides an on-line compendium of over 70 articles about C. elegans biology, covering genetics, genomics, molecular biology, cell biology, sex determination, developmental biology, neurobiology, and evolution. … WormBook's WormMethod chapter by Raymond Lee containing core web resources for C. elegans researchA Gene page is intended summarize everything of biological importance known about a given gene; it can thus be quite complex, although it is also meant to be concise ((http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_03.png) and The page can describe any or all of the following information, when available: identity of the gene's product; normal function of the gene's product; orthologs of the gene (if any); the gene's meiotic and physical location within the genome; its phenotype in classical mutations or RNAi screens; its spatial and temporal expression pattern, with microarray data; domains of its encoded protein; Gene Ontology (UNIT 7.2) terms describing its function; mutant alleles and strains carrying them; homologs identified by best BLASTP (UNIT 3.4) scores versus other proteomes; cDNA, STS, and antibody reagents; microarray probes; SAGE oligonucleotides; and references from the primary C. elegans research literature. … The WormAtlas database is intended to provide a comprehensive atlas of C. elegans anatomy, like the atlases that have long been available for human anatomy in medicine. It includes a collection of serial electron microscope sections, and several guides to cellular anatomy, including beautiful schematics of neuronal morphology. Finally, WormBook (http://www.wormbook.org) provides an on-line compendium of over 70 articles about C. elegans biology, covering genetics, genomics, molecular biology, cell biology, sex determination, developmental biology, neurobiology, and evolution. Other model organism databases … Web Resources for C. elegans- this link is not part of the original Wiley chapter WormBook's WormMethod chapter by Raymond Lee containing core web resources for C. elegans research ftp://ftp.wormbase.org/pub/wormbase

Note that some of the following sections contain material discussed in greater detail in other sections of WormBook such as Maintenance of C. elegans. … Wormbase provides information about specific mutations and alleles. A scale of one to three (ES1, ES2, ES3) is commonly used to designate the ease of scoring of the plate phenotype. … Consult WormBase or other sources for specifics concerning the defects associated with particular mutants.… In short, the answer is not entirely. Standard genetic procedures will continue to play an important role in the identification of mutants and for generating useful reagents for biological analysis. The principle difference will be one of degree, and this is good news for everyone. Note that some of the following sections contain material discussed in greater detail in other sections of WormBook such as Maintenance of C. elegans. Also, for these sections to be nominally useful, readers will need to possess a basic working knowledge of Mendelian genetics. Finally, for a concise review of some of the topics discussed, see Hodgkin (1999). 1.2. Fundamentals … One issue to always consider is the penetrance of the allele. If the penetrance is significantly below 100%, the marker may be difficult or even impossible to use for mapping. Another issue is the ease with which the mutation can be scored by its plate phenotype. Wormbase provides information about specific mutations and alleles. A scale of one to three (ES1, ES2, ES3) is commonly used to designate the ease of scoring of the plate phenotype. ES3 mutations are generally very easy to score, whereas most ES1 mutations require some level of clairvoyance and a pair of dowsing rods (Sigma catalog #DR502). ES2-rated mutations range from the reasonable to the ridiculous. For a more complete listing of mutants and phenotypes, see Wormbase. … Adult animals have a variably blistered cuticle, which can resemble a large bubble on the surface of the worm. The Bli phenotype can be suppressed by a number of dpy and rol mutations. lin Lineage defective (Lin). These can display any number of distinct defects in the pattern of cell divisions that occur during development. Consult WormBase or other sources for specifics concerning the defects associated with particular mutants. 1.5. Genetic shorthand

WormBook is a comprehensive online review of C. elegans biology, containing over 100 original, peer-reviewed chapters on a wide range of topics related to the biology of C. elegans and related nematodes; as well as WormMethods, a collection of laboratory methods and protocols useful for nematode researchers.Pasadena (CA): WormBook; 2005- 2018. WormBook is a comprehensive online review of C. elegans biology, containing over 100 original, peer-reviewed chapters on a wide range of topics related to the biology of C. elegans and related nematodes; as well as WormMethods, a collection of laboratory methods and protocols useful for nematode researchers. WormBook can be found on the web at http://www.wormbook.org Contents

WormBase (http://www.wormbase.org), the model organism database for information about Caenorhabditis elegans and related nematodes, continues to expand in breadth and depth. … WormBase is the model organism database for the biology and genomics of Caenorhabditis elegans and Caenorhabditis briggsae. It is a rapidly evolving resource, which is driven by the fact that C.elegans is widely used as a model organism for a variety of biomedical research topics, including development, neuroscience, apoptosis and aging (1–4), and an increasingly wide range of high-throughput data is available for it. … The Batch Genes page allows users to retrieve all biologically interesting gene data fields, ranging from external database IDs, to protein motifs, GO terms, genomic positions, phenotypes and underlying DNA and protein sequences.Abstract WormBase (http://www.wormbase.org), the model organism database for information about Caenorhabditis elegans and related nematodes, continues to expand in breadth and depth. Over the past year, WormBase has added multiple large-scale datasets including SAGE, interactome, 3D protein structure datasets and NCBI KOGs. … ## DESCRIPTION WormBase is the model organism database for the biology and genomics of Caenorhabditis elegans and Caenorhabditis briggsae. It is a rapidly evolving resource, which is driven by the fact that C.elegans is widely used as a model organism for a variety of biomedical research topics, including development, neuroscience, apoptosis and aging (1–4), and an increasingly wide range of high-throughput data is available for it. The genome sequence of C.elegans (5) has boosted genome-wide research projects including ORFeome (6), RNA interference (RNAi) (7), microarray (8), interactome (genome-wide protein–protein interactions) (9), serial analysis of gene expression (SAGE) (10,11) and other gene expression profiling techniques (11). … The advantage of working with WormBase this way is that the users can get detailed views and information about the items of interest. Batch retrieval. WormBase users increasingly need to obtain customized batch reports. To address this need, WormBase provides two web search pages: ‘Batch Genes’ and ‘Batch Sequences’ (2). The Batch Genes page allows users to retrieve all biologically interesting gene data fields, ranging from external database IDs, to protein motifs, GO terms, genomic positions, phenotypes and underlying DNA and protein sequences. This page gives users the option to download the results in plain text or the HTML format, and provides a variety of ways to select the set of genes of interest. The Batch Sequences page is ideal for retrieving sequence-based data such as UTRs, introns, putative promoter elements and so on. …

WormBook: The Online Review of C. elegans Biology [Internet]. Pasadena (CA): WormBook; 2005-2018. … Here we have compiled a set of protocols that broadly fit under the category of Cell Biology. We begin with a brief discussion of various microscopical techniques employed by C. elegans researchers to study aspects of the cell. We then describe methods for studying protein-protein and protein-DNA interactions in C. elegans.NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health. WormBook: The Online Review of C. elegans Biology [Internet]. Pasadena (CA): WormBook; 2005-2018. WormBook: The Online Review of C. elegans Biology [Internet]. … A serious obstacle to studying cell biological phenomena in C. elegans is the small size of its cells. However, advances in imaging techniques have allowed faint signals to be significantly amplified, and small structures to be visualized, allowing examination of transport, export, and import processes, as well as examination of cytoskeletal and chromatin structure. Here we have compiled a set of protocols that broadly fit under the category of Cell Biology. We begin with a brief discussion of various microscopical techniques employed by C. elegans researchers to study aspects of the cell. We then describe methods for studying protein-protein and protein-DNA interactions in C. elegans. We also describe methods used to study specific cell biological problems (e.g. endocytosis, chromatin, programmed cell death). Finally, we conclude this chapter with a discussion of primary embryonic cell culture and its uses. Contributors of sections or protocols are acknowledged in parentheses following the section or protocol titles. In some cases, protocols are based on previously published work, which is then cited after the protocol title. …

WormBase is the major public online database resource for the Caenorhabditis research community. The database was developed primarily for the nematode C. elegans but expanded to host genomes and biological data from other closely related nematode species including C. briggsae, C. remanei, C. brenneri , C. japonica and Pristionchus pacificus . … The aim of this is to produce a abstract like summary of the gene and it' s function so that WormBase users get a good understanding of the gene, with a minimum amount of effort. WormBook is the online text companion to WormBase, the C. elegans model organism database. WormBook contains original reviews on all aspects of C. elegans biology and up-to-date descriptions of technical procedures used to study this animal.Abstract Curation Anomaly display (see sequence curation poster for more details) Phenotype ontology WormBook WormBase is the major public online database resource for the Caenorhabditis research community. The database was developed primarily for the nematode C. elegans but expanded to host genomes and biological data from other closely related nematode species including C. briggsae, C. remanei, C. brenneri , C. japonica and Pristionchus pacificus . WormBase has developed tools to mine the data held within the database and compare the hosted species. Over the years we have developed a variety of curation pipelines which often begin in a "first-pass" literature curation step. This involves a brief overview of the literature before directing it to specialised data curators who extract all relevant information. … Phenot ypes are l i nked t o genes t hrough al l el e or R N Ai curat i on Curators are working to produce a manually generated concise description for all C. elegans genes (extending to include tier II nematodes). The aim of this is to produce a abstract like summary of the gene and it' s function so that WormBase users get a good understanding of the gene, with a minimum amount of effort. WormBook is the online text companion to WormBase, the C. elegans model organism database. WormBook contains original reviews on all aspects of C. elegans biology and up-to-date descriptions of technical procedures used to study this animal. No coding gene at this loci

Dauer diapause is a stress-resistant, developmentally quiescent, and long-lived larval stage adopted by Caenorhabditis elegans when conditions are unfavorable for growth and reproduction. This chapter contains methods to induce dauer larva formation, to isolate dauer larvae, and to study pre- and post-dauer stages. … The convergence of these pathways to regulate the dauer formation is reviewed in Dauer; and Fielenbach and Antebi (2008), whereas specific pathways are reviewed in the following WormBook chapters: TGF-β signaling in C. elegans, Insulin/insulin-like growth factor signaling in C. elegans, and Nuclear receptor signal transduction in C. elegans.§ To whom correspondence should be addressed. Email: ude.hcimc@x1prak (dev@null) Dauer diapause is a stress-resistant, developmentally quiescent, and long-lived larval stage adopted by Caenorhabditis elegans when conditions are unfavorable for growth and reproduction. This chapter contains methods to induce dauer larva formation, to isolate dauer larvae, and to study pre- and post-dauer stages. 1. Introduction … #### 2.1.2. Signaling pathways Dauer-promoting environmental cues impact several signal transduction pathways that regulate dauer formation including cGMP, TGFβ, insulin-like, and nuclear hormone receptor pathways. The convergence of these pathways to regulate the dauer formation is reviewed in Dauer; and Fielenbach and Antebi (2008), whereas specific pathways are reviewed in the following WormBook chapters: TGF-β signaling in C. elegans, Insulin/insulin-like growth factor signaling in C. elegans, and Nuclear receptor signal transduction in C. elegans. 2.2. Timing of the dauer formation decision

Deletion strains are listed on Wormbase, which should be consulted first to determine if an allele is already available for a gene of interest. … The Mos1-insertion strains are annotated on MosLocator (http://www.ciml.univ-mrs.fr/applications/MosLocator/) and Wormbase, and they are available to researchers through the Consortium (http://ums3421.univ-lyon1.fr/). … This chapter should be cited as: Kutscher L. M., Shaham S. Forward and reverse mutagenesis in C. elegans (January 17, 2014), WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.167.1, http://www.wormbook.org.… elegans Knockout Consortium are available from the Caenorhabditis Genetics Center (CGC, http://www.cbs.umn.edu/research/resources/cgc) under the allele designation ok or gk. Strains generated by the NBRP, with allele designation tm, are available after submission of a Materials Transfer Agreement (Mitani, 2009). Deletion strains are listed on Wormbase, which should be consulted first to determine if an allele is already available for a gene of interest. If not, one may request a deletion strain from the Consortium. Upon receiving a strain, it should be outcrossed to remove irrelevant mutations. It is always important to verify the presence of the mutation in a strain. … elegans gene of interest (Robert and Bessereau, 2007). A strain containing a genomic Mos1-insertion near or in a target gene is identified. The NemaGENETAG Consortium created a collection of over 13,000 Mos1-tagged alleles (Bazopoulou and Tavernarakis, 2009; Vallin et al., 2012). The Mos1-insertion strains are annotated on MosLocator (http://www.ciml.univ-mrs.fr/applications/MosLocator/) and Wormbase, and they are available to researchers through the Consortium (http://ums3421.univ-lyon1.fr/). Once the strain of interest is received, it is transformed with a transposase used to remobilize the transposon and with a transgene containing a repair template with a specific mutation in the region of the Mos1 insertion. … --- *Edited by Oliver Hobert Last revised January 16, 2014, Published January 17, 2014. This chapter should be cited as: Kutscher L. M., Shaham S. Forward and reverse mutagenesis in C. elegans (January 17, 2014), WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.167.1, http://www.wormbook.org. Copyright: © 2014 Lena M. Kutscher and Shai Shaham. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

WormBook: The Online Review of C. elegans Biology [Internet]. Pasadena (CA): WormBook; 2005-2018. … This chapter describes protocols for the isolation and culture of C. elegans embryonic and larval stage cells. … Isolated cells are easy to access with patch pipettes for single channel to whole cell recording (see WormMethods chapter, Culture of embryonic C. elegans cells for electrophysiological and pharmacological analyses: doi/10.1895/wormbook.1.122.1, http://www.wormbook.org).NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health. WormBook: The Online Review of C. elegans Biology [Internet]. Pasadena (CA): WormBook; 2005-2018. WormBook: The Online Review of C. elegans Biology [Internet]. … Recent advances have allowed for large-scale isolation and culture of primary C. elegans cells from both embryos and all four larval stages. Isolated cells can be used for single-cell profiling, electrophysiology, and high-resolution microscopy to assay cell autonomous development and behavior. This chapter describes protocols for the isolation and culture of C. elegans embryonic and larval stage cells. Our protocols describe isolation of embryonic and L1 stage cells from nematodes grown on high-density NA22 bacterial plates and isolation of L2 through L4 stage cells from nematodes grown in axenic liquid culture. … Although recording of voltages and ion currents through thin glass pipettes can be done in individual filleted animals (Goodman et al., 1998; Richmond and Jorgensen, 1999), the filleting technique is extremely demanding. In contrast, isolated neurons can be produced in abundance and followed for two weeks in culture. Isolated cells are easy to access with patch pipettes for single channel to whole cell recording (see WormMethods chapter, Culture of embryonic C. elegans cells for electrophysiological and pharmacological analyses: doi/10.1895/wormbook.1.122.1, http://www.wormbook.org). The protocols outlined here will extend isolated-cell electrophysiology to postembryonic lineages. Neuronal genesis in vivo is complete by stage L2 (Sulston and Horvitz, 1977), but neurons undergo dramatic post-mitotic changes over the course of development (White et al., 1986; Varshney et al., 2011). …

WormBook: The Online Review of C. elegans Biology [Internet]. Pasadena (CA): WormBook; 2005-2018. … This chapter should be cited as: Huang, L. S. and Sternberg, P. W. Genetic dissection of developmental pathways (June 14, 2006), WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.88.2, http://www​.wormbook.orgNCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health. WormBook: The Online Review of C. elegans Biology [Internet]. Pasadena (CA): WormBook; 2005-2018. WormBook: The Online Review of C. elegans Biology [Internet]. … * Edited by David Fay. WormMethods editor, Victor Ambros. Last revised April 22, 2005. Published June 14, 2006. This chapter should be cited as: Huang, L. S. and Sternberg, P. W. Genetic dissection of developmental pathways (June 14, 2006), WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.88.2, http://www​.wormbook.org [PMC free article: PMC4781082] [PubMed: 18050452]. §

WormBase has been the major repository and knowledgebase of information about the genome and genetics of Caenorhabditis elegans and other nematodes of experimental interest for over 2 decades. … These data include genes (including basic gene in formation like name, symbol, synonyms, and descriptions), alleles and variants (including transgenic alleles and their constructs), models (including strains and genotypes), gene expression anno tations (low- and high-throughput), disease model annotations, phenotype annotations, and interactions (molecular and genetic).†Surnames are in alphabetical order starting with Sternberg. WormBase has been the major repository and knowledgebase of information about the genome and genetics of Caenorhabditis elegans and other nematodes of experimental interest for over 2 decades. We have 3 goals: to keep current with the fast-paced C. elegans re search, to provide better integration with other resources, and to be sustainable. Here, we discuss the current state of WormBase as well as progress and plans for moving core WormBase infrastructure to the Alliance of Genome Resources (the Alliance). As an Alliance mem ber, WormBase will continue to interact with the C. elegans community, develop new features as needed, and curate key information … The data currently loaded into the Alliance Neo4J database re present the initially harmonized data types from WormBase: a subset of all data types and, within a data type, a subset of data type properties. These data include genes (including basic gene in formation like name, symbol, synonyms, and descriptions), alleles and variants (including transgenic alleles and their constructs), models (including strains and genotypes), gene expression anno tations (low- and high-throughput), disease model annotations, phenotype annotations, and interactions (molecular and genetic). Data type harmonization for the remaining data types and prop erties is ongoing among Alliance members, and the resulting har monized data are being deposited into the persistent PostgreSQL database to act as the primary curation database and eventual source of truth for Alliance-curated data. …

Single molecule fluorescent in situ hybridization (smFISH) of C. elegans worms and embryos WormBook. Published: 2012-12-13. 111 citations. … The following protocol covers the 5 major steps of smFISH: A. Probe design and synthesis, B. Fixation of C. elegans worms and embryos, C. Hybridization, D. Image acquisition, E. Data analysis.Single molecule fluorescent in situ hybridization (smFISH) of C. elegans worms and embryos WormBook. Published: 2012-12-13. 111 citations. Authors … ## Protocols The following protocol covers the 5 major steps of smFISH: A. Probe design and synthesis, B. Fixation of C. elegans worms and embryos, C. Hybridization, D. Image acquisition, E. Data analysis. This protocol is largely adapted from the general smFISH protocol detailed in Raj and Tyagi (2010) , with notes and modifications specific to C. elegans. Unless otherwise noted, all reagents listed can be made in bulk ahead of time and stored at room temperature (RT). Probe design and synthesis

Over 350,000 C. elegans gene-phenotype associations have been imported from our sister site, Wormbase. These gene-phenotype associations have also been propagated between orthologues for all Wormbase Parasite species.Phenotype data - Over 350,000 C. elegans gene-phenotype associations have been imported from our sister site, Wormbase. These gene-phenotype associations have also been propagated between orthologues for all Wormbase Parasite species. Gene Name Synonyms

A gene summary is a brief description of the key functional aspects of a gene and appears in the “Overview” widget of every gene page in WormBase. … Please see the microPublication that describes these updates to the gene summaries for C. elegans and other nematodes in the WS294 release of WormBase.November 21, 2024 by Ranjana Kishore Leave a Comment A gene summary is a brief description of the key functional aspects of a gene and appears in the “Overview” widget of every gene page in WormBase. Recently we changed the rules for inclusion of data such as large scale expression cluster data and protein domain data in gene summaries. When functional data as represented by Gene Ontology (GO) process, function or cellular component annotations are available for a gene, these are used to generate a gene summary. When no GO annotations are available for a gene, then functional data from the orthologous human gene is included in the gene summary. Further, if no tissue or cellular expression is available for the gene, expression cluster and protein domain data are included in the gene summary. Please see the microPublication that describes these updates to the gene summaries for C. elegans and other nematodes in the WS294 release of WormBase.

WormBook: The Online Review of C. elegans Biology [Internet]. Pasadena (CA): WormBook; 2005-2018. … - Making compound mutants - Mapping with deficiencies and duplications - SNPs: Introduction and two-point mapping - SNPs: Three-point mapping - Suppressor mutations - Synthetic and enhancer mutations - Classical genetic methods - Genetic balancers - Genetic dissection of developmental pathways - Maintenance of C. elegansWormBook: The Online Review of C. elegans Biology [Internet]. Pasadena (CA): WormBook; 2005-2018. - Contents WormMethods - Behavior - Assaying mechanosensation - Keeping track of worm trackers - Microfluidics as a tool for C. elegans research - Methods for measuring pharyngeal behaviors - Biochemistry and molecular biology - Introduction and basics - Two-point mapping with genetic markers - Three-point mapping with genetic markers - Dominant mutations - Making compound mutants - Mapping with deficiencies and duplications - SNPs: Introduction and two-point mapping - SNPs: Three-point mapping - Suppressor mutations - Synthetic and enhancer mutations - Classical genetic methods - Genetic balancers - Genetic dissection of developmental pathways - Maintenance of C. elegans - Nomarski images for learning the anatomy, with tips for mosaic analysis - Profiling C. elegans gene expression with DNA microarrays - Immunohistochemistry - Protocols for large scale in situ hybridization on C. elegans larvae - Reporter gene fusions - RNA in situ hybridization of dissected gonads - Single molecule fluorescent in situ hybridization (smFISH) of C. elegans worms and embryos - Methods in cell biology - Cell isolation and culture …

Want to know more about worm research? - WormWiring - WormBook - WormAtlas - Nematodes.org - Nematode.net - NEMABASE - Caenorhabditis Genetics Center (CGC) … Explore online resources supporting the C. elegans research community [Read more] … ## Species » C. elegans(Genome assembly: WBcel235)- Gene Name Changes - Release Schedule - Release notes - News (Blog) Want to know more about worm research? - WormWiring - WormBook - WormAtlas - Nematodes.org - Nematode.net - NEMABASE - Caenorhabditis Genetics Center (CGC) Directory … Community Explore online resources supporting the C. elegans research community [Read more] Directories … - open all - layout - show empty fields - hide sidebar - page settings Species » C. elegans(Genome assembly: WBcel235) --

Want to know more about worm research? - WormWiring - WormBook - WormAtlas - Nematodes.org - Nematode.net - NEMABASE - Caenorhabditis Genetics Center (CGC) … Explore online resources supporting the C. elegans research community [Read more]- Gene Name Changes - Release Schedule - Release notes - News (Blog) Want to know more about worm research? - WormWiring - WormBook - WormAtlas - Nematodes.org - Nematode.net - NEMABASE - Caenorhabditis Genetics Center (CGC) Directory … Community Explore online resources supporting the C. elegans research community [Read more] Directories

As of WS236, published and unpublished allele phenotypes from the books, C. elegans I and II, will be available through gene and allele pages displayed in the phenotype widget. … As these descriptions constitute valuable gene function information, we are pleased to have these data available for query and computational analysis.February 5, 2013 by Ranjana Kishore Leave a Comment As of WS236, published and unpublished allele phenotypes from the books, C. elegans I and II, will be available through gene and allele pages displayed in the phenotype widget. This focused effort added 4,819 phenotype annotations to 1,431 genes. Until now, these data had been hidden in legacy information from C. elegans I and II, and were available in WormBase as a block of text under the concise description in the overview widget of the gene page. As these descriptions constitute valuable gene function information, we are pleased to have these data available for query and computational analysis.

The data we currently include in a gene description are – orthology to human for C. elegans genes and orthology to C. elegans for non-elegans species genes (such as C. briggsae), biological process, molecular function and cellular localization (based on Gene Ontology (GO) annotations), and tissue expression data.… When we realized we couldn’t keep up with both updating and writing new gene descriptions, we developed an automated gene descriptions data pipeline that looks at primary data from the most recent WormBase release, in order to write gene descriptions for the next WormBase release (eg., the gene descriptions for the WS262 release of WormBase are based on the WS261 WormBase data release). The data we currently include in a gene description are – orthology to human for C. elegans genes and orthology to C. elegans for non-elegans species genes (such as C. briggsae), biological process, molecular function and cellular localization (based on Gene Ontology (GO) annotations), and tissue expression data. For poorly studied genes with no functional data, we include expression and regulation data summaries from large scale experiments such as microarray, tiling array and RNA sequencing. For every new release, scripts add new data that has been curated between the releases, in the above categories, to the gene descriptions. We currently have over 140,000 gene descriptions for nine species. The descriptions for the non-elegans genes such as C. briggsae, C. japonica, etc. …

Genetics, Strains, and Phenotypes - RNAi - Phenotypes - Strain Report - SNPs, Markers, and Strains - Variation Report - Clone Report - Rearrangements - Genetic interval Some Basic Numbers For C. elegans- Expression profile - Expression Pattern - Neurons - Cell and Pedigree Genetics, Strains, and Phenotypes - RNAi - Phenotypes - Strain Report - SNPs, Markers, and Strains - Variation Report - Clone Report - Rearrangements - Genetic interval Some Basic Numbers For C. elegans - Worm numbers