RI-INBRE Workforce Development Training (WDT) Summer 2023 Syllabus

Module Title: Next-Gen Sequencing and Omics Data Analysis

Instructor: Christopher Hemme, PhD, and Janet Atoyan, MS

Course Overview

This WDT Module aims to train students in next-generation sequencing (NGS) and omics data analysis methods. The module will include lectures on NGS methods, hands-on laboratory experience with library prep and sequencing (genome sequencing), and genome assembly and annotation (genomics), and RNA-seq (transcriptomics). The module is intended for students new to omics data generation and analysis and will provide sufficient background for students to pursue further training in these and related research areas. This module also complements the separate module on Proteomics. The module will be completed over 2.5 days and participants who complete the module will receive an RI-INBRE Certificate of completion.

Learning Outcomes

  • Learn background on NGS methods sufficient to understand basic sequencing techniques and terminology.
  • Prepare bacterial genomic sequencing sample libraries for sequencing on the Illumina MiSeq.
  • Process NGS data using hands-on learning modules (RNA-seq)
  • Analyze bioinformatics data using established methods such as differential expression analysis

Lab Report

Students will be expected to maintain detailed laboratory notes to include:

  • Library preparation protocols
  • Data analysis protocols (e.g., workflows, software used, etc.)
  • Quality control metrics for sequencing and data analysis
  • Results of bioinformatics analysis

Resources Used in this Module:

  • Standard Operating Procedure – NGS Sample and Library Prep
  • Jupyter Notebooks for Hands-On Bioinformatics Data Analysis
  • Slide Decks for Lectures


 Day 1Day 2Day 3
9:00 AM-10:00 AMIntroduction to Omics (Lecture)Introduction to Bioinformatics Pipelines – RNA-Seq (Lecture)
10:00 AM-11:00 AMIntroduction to Next-Gen Sequencing (Lecture)Intro to Unix Command Line (Hands-On)Sample and Library Preparation – Final QC Analysis (Hands-On)
11:00 AM-12:00 PMSample and Library Preparation – Initial Quality Control and Robot Setup (Hands-On)Pre-Processing and Quality Control of NGS Data (Lecture/Hands-On)Frontiers in Bioinformatics (Open Discussion)
12:00 - 1:00 PMBreakBreakClosing Group Lunch
1:00 PM-2:00 PMSample and Library Preparation – Final (Hands-On)Sample and Library Preparation – BioAnalyzer and qPCR (Hands-On)
2:00 PM-3:00 PMSample and Library Preparation – Final (Hands-On)RNA-Seq Transcript Alignment and Assembly – Hands-On
3:00 PM-4:00 PMSample and Library Preparation – Final (Hands-On)RNA-Seq Data Analysis – Hands-On