This course has two primary goals:
1) Students will learn to understand the molecular biology methods that form the basis for biotechnology products used in the production of high-throughput sequencing data
2) Students will carry out the sample processing steps required to make a 'library' and sequencing it on and Ion Torrent Personal Genome Machine, including the quality control assays that guarantee a high-quality set of data.  

  By the end of the course the student should be able to: follow basic safety rules while working in the lab; prepare reagent solutions; extract and purify DNA and RNA; design genomic experiments that include adequate biological and technical replicates; explain the steps in a published protocol for making genomic or copy DNA; explain how to design PCR primers and microarray probes; describe how hybridization conditions affect microarray analysis; describe the steps for making a HTS library and how they shape the data interpretation steps; process an Ion Torrent library for basic quality control features; present research results in written and verbal form; explain where ELSI requirements limit experiments or demand specific protections that are specifically relevant to genomics.  

Motivation: Genomics usually implies the production of sequence data in a highly parallel fashion, to produce a simultaneous snapshot of a sample or set of samples. One advantage to handling the samples together is the elimination of technical variability in those steps. For historical reasons the sample applied to the sequencer is usually called a library, and the art of genomics lies in library construction: the way in which it is carried out will significantly affect the analyses that are appropriate and the conclusions that can be made. To have deep understanding of the process students need to understand and practice the individual steps, and carry out problem-solving methods when results fail to meet expectations.

Description: In this class you will learn to understand how to read and carry out a library preparation protocol and carry it through to the production of sequence. We will introduce molecular biotechnology methods used to prepare and process samples for high-throughput sequencing (‘genomics’) studies, and the bioinformatics tools used to design experiments, reagents, perform quality control on intermediate steps, and analyze the resulting data. We will focus on methods that characterize DNA and RNA. Protocols and application papers using the methods will be posted, describing the manipulation of the designated class of biomolecules, along with tutorials and Web sites describing the instrumentation. The goal is to learn to understand and perform methods used to manipulate/purify and characterize the given classes of biomolecules, specifically the laboratory methods used to produce the transformations, and bioinformatics tools used throughout in processing and analyzing data for quality assurance and validation.