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Peregrine: A rapid and unbiased method to produce strand-specific RNA-Seq libraries from small quantities of starting material

RNA Biology

Langevin, Stanley A.; Bent, Zachary; Solberg, Owen D.; Curtis, Deanna J.; Lane, Pamela; Williams, Kelly P.; Schoeniger, Joseph S.; Lane, Todd; Sinha, Anupama

Use of second generation sequencing (SGS) technologies for transcriptional profiling (RNA-Seq) has revolutionized transcriptomics, enabling measurement of RNA abundances with unprecedented specificity and sensitivity and the discovery of novel RNA species. Preparation of RNA-Seq libraries requires conversion of the RNA starting material into cDNA flanked by platform-specific adaptor sequences. Each of the published methods and commercial kits currently available for RNA-Seq library preparation suffers from at least one major drawback, including long processing times, large starting material requirements, uneven coverage, loss of strand information and high cost. We report the development of a new RNA-Seq library preparation technique that produces representative, strand-specific RNA-Seq libraries from small amounts of starting material in a fast, simple and cost-effective manner. Additionally, we have developed a new quantitative PCR-based assay for precisely determining the number of PCR cycles to perform for optimal enrichment of the final library, a key step in all SGS library preparation workflows. © 2013 Landes Bioscience.

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TYPE Journal Article YEAR 2013
OSTIScopus

Characterization of Pathogens in Clinical Specimens via Suppression of Host Background for Efficient Second Generation Sequencing Analyses

Branda, Steven S.; Jebrail, Mais J.; Van De Vreugde, James L.; Langevin, Stanley A.; Bent, Zachary; Curtis, Deanna J.; Lane, Pamela; Carson, Bryan; La Bauve, Elisa; Patel, Kamlesh; Ricken, Bryce; Schoeniger, Joseph S.; Solberg, Owen D.; Williams, Kelly P.; Misra, Milind; Powell, Amy J.; Pattengale, Nicholas D.; May, Elebeoba; Lane, Todd; Lindner, Duane L.; Young, Malin M.; Vandernoot, Victoria A.; Thaitrong, Numrin; Bartsch, Michael S.; Renzi, Ronald F.; Tran-Gyamfi, Mary; Meagher, Robert M.

Abstract not provided.

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TYPE Conference YEAR 2012
OSTI

Automated Molecular Biology Platform Enabling Rapid & Efficient SGS Analysis of Pathogens in Clinical Samples

Branda, Steven S.; Jebrail, Mais J.; Van De Vreugde, James L.; Langevin, Stanley A.; Bent, Zachary; Curtis, Deanna J.; Lane, Pamela; Carson, Bryan; La Bauve, Elisa; Patel, Kamlesh; Ricken, Bryce; Schoeniger, Joseph S.; Solberg, Owen D.; Williams, Kelly P.; Misra, Milind; Powell, Amy J.; Pattengale, Nicholas D.; May, Elebeoba; Lane, Todd; Lindner, Duane L.; Young, Malin M.; Vandernoot, Victoria A.; Thaitrong, Numrin; Bartsch, Michael S.; Renzi, Ronald F.; Tran-Gyamfi, Mary; Meagher, Robert M.

Abstract not provided.

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TYPE Conference YEAR 2012
OSTI

Copy of Automated Molecular Biology Platform Enabling Rapid & Efficient SGS Analysis of Pathogens in Clinical Samples

Branda, Steven S.; Jebrail, Mais J.; Van De Vreugde, James L.; Langevin, Stanley A.; Bent, Zachary; Curtis, Deanna J.; Lane, Pamela; Carson, Bryan; La Bauve, Elisa; Patel, Kamlesh; Ricken, Bryce; Schoeniger, Joseph S.; Solberg, Owen D.; Williams, Kelly P.; Misra, Milind; Powell, Amy J.; Pattengale, Nicholas D.; May, Elebeoba; Lane, Todd; Lindner, Duane L.; Young, Malin M.; Vandernoot, Victoria A.; Thaitrong, Numrin; Bartsch, Michael S.; Renzi, Ronald F.; Tran-Gyamfi, Mary; Meagher, Robert M.

Abstract not provided.

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TYPE Presentation YEAR 2012
OSTI

Quantitative laboratory measurements of biogeochemical processes controlling biogenic calcite carbon sequestration

Lane, Pamela; Lane, Todd; Zendejas, Frank Z.

The purpose of this LDRD was to generate data that could be used to populate and thereby reduce the uncertainty in global carbon cycle models. These efforts were focused on developing a system for determining the dissolution rate of biogenic calcite under oceanic pressure and temperature conditions and on carrying out a digital transcriptomic analysis of gene expression in response to changes in pCO2, and the consequent acidification of the growth medium.

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TYPE SAND Report YEAR 2010
DOIOSTI

Hyperspectral imaging of oil producing microalgae under thermal and nutritional stress

Powell, Amy J.; Davis, Ryan W.; Lane, Todd; Lane, Pamela; Keenan, Michael R.; Van Benthem, Mark H.

This short-term, late-start LDRD examined the effects of nutritional deprivation on the energy harvesting complex in microalgae. While the original experimental plan involved a much more detailed study of temperature and nutrition on the antenna system of a variety of TAG producing algae and their concomitant effects on oil production, time and fiscal constraints limited the scope of the study. This work was a joint effort between research teams at Sandia National Laboratories, New Mexico and California. Preliminary results indicate there is a photosystem response to silica starvation in diatoms that could impact the mechanisms for lipid accumulation.

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TYPE SAND Report YEAR 2008
DOIOSTIDOIOSTI
Results 51–75 of 76
Results 51–75 of 76
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