Genomics and Bioinformatics

As a long-time leader in the growing field of bioinformatics, ATCC recognizes the importance of this discipline in solving critical problems in biology. In order for ATCC to maintain its critical role in providing reference reagents and associated databases for the scientific enterprise it must pursue processes that integrate computational technologies with genomic and clinical databases; molecular, cellular, and metabolic processes; protein structure analysis; and other systems biology and biological pathway analyses methods.
 
Recognizing this essential capability, ATCC has invested in the development of a Genomics and Bioinformatics resource built on a foundation of experienced scientists and staff who are committed to serving the disciplines that depend on this important resource.

Databases

Molecular Genomics

STR

Ribosomal DNA Database

Viral Database

Functional and Computational Genomics
 
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Databases
    Molecular Genomics*
    1. ATCC hosts the Mammalian Gene Collection (MGC), a trans-NIH initiative, to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes. We also have many specific collections of isolated gene DNA libraries, vectors, and patented constructs.
    2. Our Genomics and Bioinformatics team uses a systems biology approach for the systematic mining of information. This approach allows us to provide the current state of knowledge relevant to the queried gene as well as the pertinent multidimensional network with biological molecules and pathways. In addition, FL-ORF clones of the genes involved in several of the well-known pathways are available as part of our collection.
    *Please contact us for more information and an ATCC expert will respond with a price quote and the expected lead time.

    STR
    1. To initiate and facilitate the long overdue effort to authenticate commonly used cell lines, ATCC has developed a comprehensive database of DNA fingerprints of Short Tandem Repeat (STR) loci for all of the human cell lines in our collection. STR loci are among the most informative polymorphic markers in the genome. The fingerprinting process used at ATCC involves simultaneously amplifying nine STR loci in a multiplex PCR reaction. This process allows for discrimination of less than 1 in 108 individuals (Lins, A.M., et al. J. Forensic Sci. 43: 1168-1180, 1998).

      The amplicons are separated by electrophoresis and analyzed using Genotyper® 2.0 software from Applied Biosystems. Each peak in the resulting gel represents an allele that is alphanumerically scored and entered into our database. We vigilantly monitor our collection of cell lines by STR authentication. When inconsistencies in the fingerprint profiling of a cell line are uncovered (i.e., the fingerprint is similar or identical to that of an unrelated cell line), we promptly post our findings in Misidentified Cell Lines. These data are available to the scientific community as part of our service to help ensure the quality and integrity of their research.

      We hope that the availability of this database will make cell line authentication a routine process in cell biology research. Scientists and researchers can submit their cells for fingerprint analyses and compare the results to our database. If you have any questions about STR loci or this database, please contact us.

    Ribosomal DNA Database*
    1. The Ribosomal DNA Database of ATCC encompasses DNA sequences of the small subunit (SSU) and large subunit (LSU) ribosomal RNA subunits of bacteria and other microorganisms that are available in our collection. This database facilitates confirmation and identification of specific strains and /or specific mutations within a given organism.
    2. The bacteriology collection comprises more than 18,000 distinct organisms. Sequencing of the small (SSU) ribosomal RNA subunit is part of our quality control process and is performed regularly upon stock replenishment. Our database currently consists of SSU rRNA sequencing records from Escherichia coli and. Access to our database will be available as part of our authentication services to enable our customers to compare their strains with those available in our catalog. We welcome suggestions and information relevant to newly characterized SSU or LSU rRNA sequences. This information will be incorporated into the database for the benefit of the scientific community.
    3. Restriction digestion patterns from riboprinter analyses are stored and available in a searchable mode in our database. The DNA patterns generated for riboprinter analyses are another tool for further genotypic characterization and confirmation of species. Our database includes patterns comprising more than 550 genera and 1230 species.

    *Please contact us for more information and an ATCC expert will respond with a price quote and the expected lead time.

    Viral Database*
    1. ATCC is defining genetic identification methods for all viruses within its Animal Virology Collection, using published sequence and molecular epidemiology data. Sets of primers identified from the literature or designed de novo are used to amplify a 500-1000 bp amplicon by PCR/RT-PCR, sequenced at high definition to provide a product-specific signature sequence. This signature sequence is employed to confirm the identity of each new product lot as it is manufactured. Sequence data are collected from a diverse series of viruses, including adenoviruses from a variety of animal species, murine cytomegalovirus, human respiratory syncitial virus, and recombinant amphotropic murine leukemia virus.

    *Please contact us for more information and an ATCC expert will respond with a price quote and the expected lead time.
Functional and Computational Genomics
  • Our Genomics and Bioinformatics team is comprised of experts in systems biology and biological pathway analysis. The team specializes in extraction and evaluation of meaningful patterns from high-throughput data sets, including mRNA, miRNA, protein and small analyte profiling. We have successfully completed a number of projects involving analysis of genetic and physical gene maps, comparative genomics, pedigree analysis, protein-protein interactions and ligand-receptor interactions, interpretation of the mass spectrometry data, high throughput profiling of gene expression, and an analysis of the protein binding to DNA and RNA. Please contact us for more information or potential collaboration opportunities.


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