|
| Status |
Public on Oct 15, 2010 |
| Title |
Validation data for Lawrence Livermore Microbial Detection Array version 2 |
| Platform organism |
synthetic construct |
| Sample organisms |
Chlorocebus aethiops; Homo sapiens; Vaccinia virus Lister; Bovine viral diarrhea virus 1; Human betaherpesvirus 6B |
| Experiment type |
Other
|
| Summary |
We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phage), bacteria, and plasmids. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms. The array has wider coverage of bacterial and viral targets based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. In blinded lab testing on spiked samples with single or multiple viruses, the MDA was able to correctly identify species or strains. In clinical fecal, serum, and respiratory samples, the MDA was able to detect and characterize multiple viruses, phage, and bacteria in a sample to the family and species level, as confirmed by PCR.
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| |
|
| Overall design |
Testing of microbial detection array with mixtures of known viruses, blinded clinical samples and viral cell culture samples.
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| |
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| Contributor(s) |
Gardner SN, Jaing CJ, McLoughlin KS, Slezak TR |
| Citation(s) |
21108826 |
| |
| Submission date |
Oct 12, 2010 |
| Last update date |
Mar 22, 2012 |
| Contact name |
Kevin McLoughlin |
| E-mail(s) |
mcloughlin2@llnl.gov
|
| Phone |
(925)423-5486
|
| Organization name |
Lawrence Livermore National Laboratory
|
| Department |
Global Security
|
| Lab |
Pathogen Bioinformatics
|
| Street address |
PO Box 808
|
| City |
Livermore |
| State/province |
CA |
| ZIP/Postal code |
94551 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL11040 |
Lawrence Livermore Microbial Detection Array version 2 |
|
| Samples (19)
|
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| This SubSeries is part of SuperSeries: |
| GSE24700 |
Validation data for Lawrence Livermore Microbial Detection Arrays |
|
| Relations |
| BioProject |
PRJNA133581 |
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