ST NetWatch: Technical Information

American Type Culture Collection (ATCC)
ATCC is a non-profit biological resource center that collects, maintains, and distributes cells, microorganisms, seeds, and molecular reagents. Its collections contain human, animal, and plant cell lines, including feeder and support cells, cancer cell lines, hybridomas, and primary cells. Human and mouse stem cells available for purchase are listed in the ATCC Stem Cell Center along with protocols, FAQs, and links to online stem cell resources. ATCC also distributes microbiological reagents such as animal and plant viruses, bacterial strains, algae, protozoa, and fungi, plus molecular reagents such as cloned genes, libraries, and cloning vectors. Special Collections include microorganisms isolated from U. S. National Parks, a collection of strains and molecular reagents for yeast genetics research, and the Mantle Cell Lymphoma Cell Bank. The site includes technical information about how to maintain, subculture, transfect, and cryopreserve the reagents they distribute. The ATCC Standards Resource contains information about standardized bioassay and quality control methods that use microorganisms and cell lines available from ATCC. They also offer biological material storage patent deposit, and mycoplasma testing services.
Cell Biology Laboratory Manual
The Cell Biology Laboratory Manual, authored by William Heidcamp at Gustavus Adolphus College, was designed for use in cell biology laboratory courses. It is valuable as both a practical reference and a teaching tool because it covers a wide range of techniques and model systems used in cell and molecular biology research. The manual includes chapters on cell culture, the cytoskeleton, histochemistry, spectrophotometry, and photosynthesis and respiration. Basic methods such as gel electrophoresis are included as well as more advanced techniques such as cell fractionation and electron microscopy. There is a large collection of recipes and preparation instructions for many solutions and reagents in the Appendix, and a basic statistical analysis primer.
The American Society for Cell Biology (ASCB) has collected and organized links to online resources for cell biologists at CellBASE. The resources include those for general cell biologists, as well as those for specific subdisciplines. The "Research Resources" section lists diverse online resources ranging from forums and blogs to reagent and equipment vendors to model organism and genome databases to resources for performing simulations or creating animations. Additional resources are collected into subtopics, such as Cell Regulation, Microscopy, and Systems Biology, where the links are organized by the type of resources. There is even a section for Cell Biology Labs and users can suggest their lab or other relevant site for inclusion in this catalog of online resources for cell biology research.
Developmental Studies Hybridoma Bank (DSHB)
The DSHB, originally established as a repository for hybridomas produced by researchers at the National Institutes of Health (NIH), stores, maintains, and distributes hybridomas and the monoclonal antibodies they produce. The goal of the DSHB is to relieve researchers of such distribution responsibilities while making monoclonal antibodies inexpensive and easy to obtain. Their collection includes hybridomas that make antibodies that recognize antigens from various species, including slime mold, fruit fly, human, mouse, rat, chicken, and zebrafish; in many cases they have multiple hybridomas that produce antibodies directed against the same antigen. You may view a list of antigens for which antibodies are available or use the search box on the homepage to find a hybridoma line by name or to identify lines that produce antibodies that recognize a protein of interest. The information page for each hybridoma includes information about the contributor, the antigen, any known species cross-reactivity, the type of antibody secreted (for example, IgG or IgM), and references about that antibody or examples of its use in published works. Not all of the antibodies in the collection recognize a known antigen; some recognize specific cell types or structures and are thus useful as morphological markers. Supernatant, concentrated supernatant, ascites fluid, or live cells can be purchased for nominal fees by customers at non-profit institutions; corporate customers pay higher prices.
Developmental Therapeutics Program
For signaling researchers who focus on cancer, the Developmental Therapeutics Program (DTP) from the National Cancer Institute (NCI) and the National Institutes of Health (NIH) is a source of reagents and services for identifying compounds with anti-tumor activity. Researchers may order cells from the tumor catalog, acquire microarrays of sections of formalin-fixed, paraffin-embedded clinical tumor samples, or obtain samples from various NIH-sponsored repositories of chemical and biological substances. "Discovery Services" offered by the DTP also include in vitro and in vivo screening of compounds for anti-tumor activity and toxicity. Researchers may submit their own compounds for screening or choose from those available from the NIH-sponsored repositories. Data from anti-tumor screens are publicly available, as are data from screens for compounds that inhibit yeast growth and for compounds that show anti-HIV activity. A database of structural information includes compounds tested by the DTP or deposited in NIH-sponsored repositories, and there is a database of quantitative and qualitative measurements of molecular targets, such as changes in gene expression or protein activity, collected in DTS screens. The DTP provides links to tools for mining DTP data, including the COMPARE tool, with which users can search the DTP databases for compounds that show an activity profile similar to a compound or molecular target of interest. "Development Services" include information on partner organizations for every step of getting test compounds to clinical trial: designing and testing synthesis strategies, formulating dosages, and evaluating the toxicity, metabolism, and pharmacokinetics of test compounds.
DNASU Plasmid Repository
The DNASU Plasmid Repository of the Biodesign Institute at Arizona State University stores and distributes plasmids from individual researchers and consortia. Researchers may deposit plasmids containing DNA from any species into the repository as a way of both archiving the plasmids and reducing the responsibility of distributing them from their own labs. The repository includes empty vectors, individual clones, and collections of plasmids, such as the cystic fibrosis transmembrane conductance regulator (CFTR) expression library, human kinase collections, and yeast ORF libraries. Browse the plasmid collections or search the entire repository by gene, sequence, vector properties, keyword, or species. Information for each plasmid includes details about the vector, appropriate applications, provenance, usage restrictions, and links to additional information in other databases such as PubMed or the Worldwide Protein Data Bank. Most plasmids are available to all researchers for a nominal fee, but some are restricted for use only by those at academic and non-profit institutions. Complete instructions for depositing constructs into the repository are available on the site.
Do you want to know if a drug you are using in experiments affects only one pathway, or several? Do you want to find drugs that act on your favorite pathway? DrugBank is a database of drug-target interactions that researchers using pharmacological agents may find useful. Search the site by gene name or sequence to find drugs that affect a particular protein target, or search by drug name or structure to determine what pathways are affected by a particular drug. The database includes information for many FDA-approved and experimental drugs, biotech drugs, illicit substances and small molecule drugs. DrugBank is supported by Genome Alberta and Genome Canada in cooperation with GenomeQuest, Inc.
E-RNAi is an online tool for designing and evaluating both dsRNAs and short siRNAs. Design RNAi reagents by entering the sequence of the target or its gene identifier, or choose a target sequence from a genome browser that includes organisms such as yeasts, fruit fly, nematode, planarian, mouse, and human. The tool returns suggested RNA sequences based on predicted specificity, efficiency, and map position. Users can adjust the settings to exclude repetitive sequences and regions of low sequence complexity, choose the length of the RNAs, and set predicted efficiency thresholds. The tool also includes an RNAi reagent evaluator that analyzes user-defined dsRNA or siRNA sequences, reports on their genome map position, and predicts specificity and efficiency. The "Help" pages include detailed information about using the tool and interpreting results. E-RNAi was developed by the laboratory of Michael Boutros and is hosted by the German Cancer Research Center.
To comply with funding regulations and publishing guidelines, researchers are usually required to deposit published nucleotide sequences into publicly accessible data banks. Nucleotide sequences, including genomic DNA, mRNA, and noncoding RNA sequences may be deposited into GenBank. Sequences in GenBank are shared with the European Molecular Biology Laboratory (EMBL) and the DNA Data Bank of Japan (DDBJ) as part of the International Nucleotide Sequence Database Collaboration, and data contained in each database are accessible through the partners' search and retrieval tools. Detailed instructions for submitting data and specifications about the file types accepted by GenBank can be found under the "Submit to GenBank" link on the main page.
Gene Expression Omnibus (GEO)
Many granting agencies and publishers require researchers to deposit data from high throughput sequencing analyses and microarray studies into public data banks. These types of data, including those from ChIP-Seq and expression profiling experiments, can be deposited into the Gene Expression Omnibus (GEO). Detailed instructions for submitting data are available in the "Submission Guide" section.
Ki Database
The Ki database is a searchable index of affinity information about drugs and the receptors, channels and enzymes they target. You can search the database by receptor, species, ligand, Ki, expressing tissue or any combination of these descriptors. References for the reported Kis are clearly indicated so that users can determine under what conditions they were obtained . The database was generated by Bryan Roth's lab at UNC and includes information from published research as well as data from the National Institute of Mental Health (NIMH) Psychoactive Drug Screening Program. A selection of cDNA clones of receptors and transporters identified by this large-scale NIMH screen are available for academic use.
Minimum Information for Biological and Biomedical Investigations (MIBBI)
Full understanding and interpretation of data sets requires basic information about the experimental methods, conclusions, and context in addition to the actual data. Minimum information (MI) checklists are gaining in popularity as a way to specify the metadata that must be included with data sets, and some funding agencies and journals even require researchers to use proscribed checklists. Many discipline- and technique-specific checklists have been developed and are still evolving, and they differ in the amount of detail they include. Many are partially overlapping, so it can be challenging to determine which checklist to use for a particular data set. The Minimum Information for Biological and Biomedical Investigations (MIBBI) project was established to centralize the discussion about development and implementation of MI checklists, to encourage collaborations between groups developing checklists, and to promote standardization of checklists. Information about various MI projects from across the bioscience community is compiled in the MIBBI Portal. In the MIBBI Foundry, members of a community can collectively develop standard checklist modules that are then made publicly available through the MICheckout page, through which researchers can identify the checklist modules appropriate to their research.
Missouri S&T cDNA Resource Center
The Missouri S&T cDNA Resource Center maintains and distributes cDNA clones encoding human signaling proteins. The center was established by the Department of Biological Sciences of the Missouri University of Science and Technology to save researchers the time spent generating, sequencing, and verifying expression of cDNAs for their experiments. The collection mainly comprises G protein–coupled receptors and their associated downstream components, such as heterotrimeric G proteins, G protein regulators, and small G proteins, but also includes nuclear receptors. All cDNAs are provided in a vector that supports both transient and stable expression in mammalian cells. Most of the untranslated regions have been removed from the cDNAs to improve reliability and uniformity of expression, and mutant and epitope-tagged versions of most of the proteins are available in addition to the wild-type sequences. Clones are available for academic use at low cost.
Molecular Libraries Program (MLP)
The Molecular Libraries Program (MLP), part of the NIH Roadmap for Medical Research, helps researchers identify small molecules that modulate gene expression or signaling pathways. The goal of the MLP is to bring the large-scale screening resources once available only to researchers at private institutions into the public research realm. The MLP builds and maintains the Molecular Libraries Small Molecule Repository (MLSMR), a library that currently contains over 300,000 compounds. The contents of the MLSMR are not directly available to researchers, but investigators may work with the MLP to screen this library for compounds that show activity in their biological assay of interest. Screens are performed through the Molecular Libraries Probe Production Center Network (MLPCN), a group of research centers located throughout the U.S. that have a wide range of technical capabilities and support various assay formats. Scientists at these centers work with researchers to develop the assays and specialized instrumentation used for the high-throughput assays, perform the screen, analyze the data, and release the data to the public through PubChem. Information about how the MLSMR compounds were selected for inclusion in the library is available, as are probe reports for compounds that have been identified as having biological activity, some of which are commercially available. The "MLP Overview" page includes a glossary of terms used to describe the screening processes, and the "Access MLPCN Resources" page provides information about how researchers can apply for the opportunity to develop assays or submit their high-throughput-ready assay for consideration. provides links to animations that illustrate molecular and cellular events as well as a series of tutorials for life scientists who would like to create their own 3D animations. The tutorials include instructions and tips for using various animation software, including Maya, After Effects, and Cinema 4D. The tutorials are in PDF or video format and are organized by topic, by animation software, and by animator skill level. The site also provides free tools for using the Autodesk Maya animation software for molecular animations. The animations featured in the "Showcase" section are useful as teaching or learning tools for high school through college levels, or for scientists who would like to brush up on topics outside their field of expertise. Topics include receptor tyrosine kinases, apoptosis, and cell adhesion.
NCBI Minicourses
NCBI offers several mini-courses that teach users how to get the most out of NCBI's bioinformatics tools such as BLAST, Greengene and Entrez Gene. Most of these courses are offered in the real world at various host institutions around the United States, but some have online components that could serve as stand-alone tutorials for novices or as a refresher for those who may not have used all of NCBI's bioinformatics tools recently. There are BLAST, Entrez Gene and structural analysis QuickStart guides available. For casual users of bioinformatics tools, these mini-courses reveal the deeper capabilities of the applications and highlight just how much information a well-informed user can glean from bioinformatics. If you cannot attend a mini-course, check out the online components that are available. Make sure you are getting the most out of your sequence data by learning more about the software you use for analysis.
Peptidome was a public repository of tandem mass spectrometry (MS) data created by the National Center for Biotechnology Information (NCBI) for sharing MS data in a standardized format and ensuring long-term preservation of MS data. This repository is no longer accepting submissions, and the online browser, query, and display interfaces are not available. The existing contents of the database can be downloaded through an FTP server, where the files are named according to their Peptidome accession number. Data sets include a list of the proteins identified in each sample, the peptides used to identify the proteins, the original spectra, information about the biological sample, and details about the instrumentation and methods used to collect the data.
Proteome Commons Tranche Repository
As of the spring 2013, this site and Proteome Commons are no longer available.
Proteomics Identifications Database (PRIDE)
Many funding agencies require investigators to archive proteomics data sets and make them publicly available upon publication. Investigators may deposit their mass spectrometry (MS)–based proteomics data sets into the Proteomics Identifications Database (PRIDE). The site includes complete information on submitting peptide and protein identification information data. PRIDE offers access control, so that contributors can restrict data access to reviewers and collaborators until the data are made public upon publication. Users may search the database by keyword, sample type, species, GO term, disease, or UniProt, ENSEMBL, REFSEQ, or NCBI IDs or accession numbers. Each data set includes experimental details, MS spectra, and lists of identified peptides. Data sets may be viewed through a web browser or PRIDE Inspector, a free desktop application that allows users to visualize MS data prior to submission and to explore PRIDE's public data sets. PRIDE is part of the EMBL-EBI European Bioinformatics Institute collection of online databases and tools.
Protocol Online
These free protocols are contributed by academic research labs, biotechnology companies, and scientific community-based programs such as genome sequencing projects and model organism databases. Scroll past the advertisements that appear at the top of each page and you will find a variety of protocols relevant to many areas of cell biology, biochemistry, and molecular biology. The collection includes basic information, such as recipes for common molecular biology reagents, but also provides many protocols for advanced and specialized techniques. You can find protocols on topics that range from transforming lymphocytes, to culturing cerebellar neurons, to doing erythrophagocytosis assays, to performing surgical procedures such as xenografts. There are numerous yeast and C. elegans protocols listed under the "Model Organisms" category. Most protocols are provided in the usual style step-by-step written instructions, but several are provided as video tutorials, such as those describing laser-capture microdissection and hanging-drop culture of embryoid bodies. So if you would like to find out how to process histology samples in the microwave or isolate chloroplasts from spinach, take a look around this site.
ProtParam is a tool from the ExPASy Proteomics Server that determines various chemical and physical parameters for a protein of interest. Proteins can be defined by their Swiss-Prot accession number or sequence identifier, or by entering sequence. If the protein is specified by its Swiss-Prot identifier or accession number, then the calculations can be limited to specific domains or applied to the entire protein; for proteins specified by sequence, the tool returns calculations for the entire input sequence. The computed values include molecular weight, amino acid composition, isoelectric point (pI), charge distribution, extinction coefficients, estimated half-life, instability index, aliphatic index, and hydropathicity. This tool is a practical asset for researchers doing biochemistry with well-studied, previously uncharacterized, or synthetic proteins or peptides.
Worldwide Protein Data Bank (wwPDB)
Submission of certain types of experimental data into public data banks is often required by funding agencies as a condition for awarding grants and by publishers as a prerequisite for publishing research. The Worldwide Protein Data Bank (wwPDB) is a repository for protein structural information and is a collaborative effort of the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Protein Data Bank Europe (PDBe), Protein Data Bank Japan (PDBj), and BioMagResBank (BMRB). RCSB PDB, PDBe, and PDBj accept structural information from x-ray diffraction, nuclear magnetic resonance (NMR), and electron microscopy (EM) studies as well as data from less common techniques such as electron, neutron, or powder diffraction. The BMRB contains NMR spectroscopy data for proteins, peptides, and nucleic acids. Links to each of the four databases' submission sites, which include detailed submission instructions, are available from the wwPDB main page.
WormMethods is part of the WormBook web site, produced by and for the C. elegans research community. This page contains standard methods used for genetics, neurophysiology, and cell biology in the worm, as well as some molecular biology methods that can be used with any system. Worm-specific protocols include design of genetic screens, RNA in situ analysis, and husbandry. Protocols for procedures such as yeast two-hybrid and microarray screening are readily adaptable to other systems and thus would be useful to molecular and cell biologists outside the worm community.