TY - JOUR
T1 - Microbes, metagenomes and marine mammals
T2 - Enabling the next generation of scientist to enter the genomic era
AU - Edwards, Robert Alan
AU - Haggerty, John Matthew
AU - Cassman, Noriko
AU - Busch, Julia Christine
AU - Aguinaldo, Kristen
AU - Chinta, Sowmya
AU - Vaughn, Meredith Houle
AU - Morey, Robert
AU - Harkins, Timothy T.
AU - Teiling, Clotilde
AU - Fredrikson, Karin
AU - Dinsdale, Elizabeth Ann
PY - 2013/9/4
Y1 - 2013/9/4
N2 - Background: The revolution in DNA sequencing technology continues unabated, and is affecting all aspects of the biological and medical sciences. The training and recruitment of the next generation of researchers who are able to use and exploit the new technology is severely lacking and potentially negatively influencing research and development efforts to advance genome biology. Here we present a cross-disciplinary course that provides undergraduate students with practical experience in running a next generation sequencing instrument through to the analysis and annotation of the generated DNA sequences.Results: Many labs across world are installing next generation sequencing technology and we show that the undergraduate students produce quality sequence data and were excited to participate in cutting edge research. The students conducted the work flow from DNA extraction, library preparation, running the sequencing instrument, to the extraction and analysis of the data. They sequenced microbes, metagenomes, and a marine mammal, the Californian sea lion, Zalophus californianus. The students met sequencing quality controls, had no detectable contamination in the targeted DNA sequences, provided publication quality data, and became part of an international collaboration to investigate carcinomas in carnivores.Conclusions: Students learned important skills for their future education and career opportunities, and a perceived increase in students' ability to conduct independent scientific research was measured. DNA sequencing is rapidly expanding in the life sciences. Teaching undergraduates to use the latest technology to sequence genomic DNA ensures they are ready to meet the challenges of the genomic era and allows them to participate in annotating the tree of life.
AB - Background: The revolution in DNA sequencing technology continues unabated, and is affecting all aspects of the biological and medical sciences. The training and recruitment of the next generation of researchers who are able to use and exploit the new technology is severely lacking and potentially negatively influencing research and development efforts to advance genome biology. Here we present a cross-disciplinary course that provides undergraduate students with practical experience in running a next generation sequencing instrument through to the analysis and annotation of the generated DNA sequences.Results: Many labs across world are installing next generation sequencing technology and we show that the undergraduate students produce quality sequence data and were excited to participate in cutting edge research. The students conducted the work flow from DNA extraction, library preparation, running the sequencing instrument, to the extraction and analysis of the data. They sequenced microbes, metagenomes, and a marine mammal, the Californian sea lion, Zalophus californianus. The students met sequencing quality controls, had no detectable contamination in the targeted DNA sequences, provided publication quality data, and became part of an international collaboration to investigate carcinomas in carnivores.Conclusions: Students learned important skills for their future education and career opportunities, and a perceived increase in students' ability to conduct independent scientific research was measured. DNA sequencing is rapidly expanding in the life sciences. Teaching undergraduates to use the latest technology to sequence genomic DNA ensures they are ready to meet the challenges of the genomic era and allows them to participate in annotating the tree of life.
KW - DNA sequencing
KW - Metagenome
KW - Sea lion
KW - Undergraduate education
UR - http://www.scopus.com/inward/record.url?scp=84883285468&partnerID=8YFLogxK
U2 - 10.1186/1471-2164-14-600
DO - 10.1186/1471-2164-14-600
M3 - Letter
C2 - 24007365
AN - SCOPUS:84883285468
SN - 1471-2164
VL - 14
JO - BMC Genomics
JF - BMC Genomics
M1 - 600
ER -