Project description:This submission contains datasets from several species used to demonstrate new features in compareMS2 2.0. Tandem mass spectrometry data from California sea lion, chimpanzee, dog, human, rock hyrax, and white-tailed deer sera were graciously provided with permission from an ongoing collaboration with Dr. Michael G. Janech (College of Charleston) as part of the CoMPARe Program (Comparative Mammalian Proteome Aggregator Resource). Specifically, the California sea lion sera were provided by The Marine Mammal Center (Sausalito, CA), the chimpanzee, rock hyrax, and white-tailed deer sera were provided by The Chattanooga Zoo, and the dog serum from Gus (Ohlandt Veterinary Clinic, Charleston, SC). In addition to institutional and NMFS permits and approval, data collection was performed under NIST ACUC MML-AR20-0001. The identification of certain commercial equipment, instruments, software, or materials does not imply recommendation or endorsement by the National Institute of Standards and Technology, nor does it imply that the products identified are necessarily the best available for the purpose.
Project description:The ongoing SARS-CoV-2 pandemic and subsequent demand for viral testing worldwide has led to major issues in scaling the efforts of diagnostic labs and even in securing basic supplies for collection and processing of samples. This has in turn led to worldwide efforts by the scientific community to establish improved protocols that are cheaper, more scalable, and not as resource intensive. One such effort resulted in an assay called “Swab-Seq”, which was so named because it was originally developed to work with dry nasal swab samples, but is actually flexible in terms of the sample type it can accommodate for testing. The assay adapts the existing gold standard (RNA extracted from a nasopharyngeal (NP) swab that is subjected to quantitative reverse transcription polymerase chain reaction, “qRT-PCR”) to a next-generation sequencing readout. By pairing this modification with extraction-free sampling techniques it is possible to achieve high scalability at low cost per sample, and a reasonable turnaround time for reporting results. We evaluated the effectiveness of this assay both on samples collected from asymptomatic individuals using the traditional NP swab and using alternative extraction-free sampling techniques, including saliva and a saline mouth gargle protocol, and found the assay to be highly sensitive (comparable to the standard qRT-PCR assay), flexible (adaptable to saliva and gargle samples stored at room temperature up to a week), and scalable (easily accommodating hundreds of samples at a time). Continued development in the future will lead to more effective testing regimes that reduce the burden of transmissible respiratory infections on the global community.
2022-02-23 | GSE176224 | GEO
Project description:SNP discovery in White-tailed deer
| PRJNA870086 | ENA
Project description:TICK MICROBIOME FROM WHITE-TAILED DEER
| PRJNA881327 | ENA
Project description:white tailed deer Raw sequence reads