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Abstract Detail


Baker, Stokes S [1].

Using RNA-seq data in an Ecology Laboratory Inquiry Investigation.

In recent years, organizations have been established to integrate next generation sequencing technology into the undergraduate curriculum (see URL links). In an upper level Ecology Laboratory (Bio4490) course taught at the University of Detroit Mercy undergraduates used next generation sequencing data to investigate the response of giant duckweed (Spirodela polyrhiza (L.) Schleiden) to the essential nutrient, phosphorous. Students used a database containing RNA-seq expression values from plants growing in sterile cultures containing modified 1/2X Schenk and Hildebrandt median with no-phosphorus, 50 μg/L phosphorus (as orthophosphate, corresponding to a eutrophic concentration), and 40,385 μg/L phosphorous (standard 1/2X Schenk and Hildebrandt media). Students were asked to develop criterions to identify ecologically significant genes and to use the RNA-seq expression profiles and the US Department of Energy Phytozome database (link below) to identify candidate genes. The students were asked to design and conduct an experiment to test a hypothesis derived from their data analysis. The students used reverse transcriptase quantitative polymerase chain reaction (rt-qPCR) to test one of their hypotheses. Qualitative assessment, in the form of open ended questions, was used as the main evaluation method because of a small class size. In response to the question, “What did you learn from the RNA-seq experiment?”, 8 of 11 students noted that aquatic plants change their gene expression in response to their environments and 6 of 11 students described technical aspects of the investigation (some students discussed both). To the question, “Why did we use RNA-seq in our investigation of greater duckweed”, 9 of 11 students replied that specific genes are part of an aquatic plant’s response to phosphorus water pollution.

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Related Links:
The Genome Consortium for Active Teaching
RNA-seq for the Next Generation
iPlant Collaborative DNA Subway
Genome Education Partnership
DOE Phytozome Spirodela Database

1 - University of Detroit Mercy, Biology Department, 4001 W. McNichols Rd., Detroit, MI, 48221, 313-993-1142

laboratory exercise

Presentation Type: Oral Paper
Session: 18, Teaching Section Papers Session I
Location: 101/Savannah International Trade and Convention Center
Date: Tuesday, August 2nd, 2016
Time: 8:30 AM
Number: 18003
Abstract ID:751
Candidate for Awards:None

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