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
Timeline
| Day 1 | Day 2 | Day 3 | |
|---|---|---|---|
| 9:00 AM-10:00 AM | Introduction to Omics (Lecture) | Introduction to Bioinformatics Pipelines – RNA-Seq (Lecture) | |
| 10:00 AM-11:00 AM | Introduction 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 PM | Sample 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 PM | Break | Break | Closing Group Lunch |
| 1:00 PM-2:00 PM | Sample and Library Preparation – Final (Hands-On) | Sample and Library Preparation – BioAnalyzer and qPCR (Hands-On) | |
| 2:00 PM-3:00 PM | Sample and Library Preparation – Final (Hands-On) | RNA-Seq Transcript Alignment and Assembly – Hands-On | |
| 3:00 PM-4:00 PM | Sample and Library Preparation – Final (Hands-On) | RNA-Seq Data Analysis – Hands-On |