Institute of Systems Biology

 Institute of Systems Biology

Workshop Outline

This workshop will focus on topics ranging from basic experimental design to advanced downstream analyses of RNA-seq data as well as tips to publish in high-impact journals.

Upon the completion of this 3-day online workshop, participants will be capable of the following:

  • Conceptualising a transcriptome experiment with different considerations
  • Understanding a complete workflow of RNA-seq data acquisition, processing, assembly, functional annotation, analysis, and interpretation
  • Aware of the different analysis workflows and software packages in RNA-seq analysis
  • Exposure to different approaches for integrating transcriptomics with other omics towards systems understanding 
  • Network opportunity with other researchers in the field & sharing of knowledge via voluntary flash talks
  • Hands-on in de novo transcriptomic analysis and mining data
  • Hands-on in downstream functional analyses: WEGO, KEGG pathway, clustering, functional enrichment

HIGHLIGHTS

  1. Principles of transcriptomics
  2. Experimental design & considerations
  3. Complete workflow of transcriptomic analysis
  4. Functional annotation & enrichment analysis
  5. Biologist-friendly approach to downstream analyses using MS Excel & Perseus

Why you should attend?

  • You're a researcher, academician, or student interested in transcriptomics and its applications.
  • You're interested in advanced skills in RNA-seq analysis.
  • You want user-friendly platforms for the interpretation of RNA-seq data.
  • You got the transcriptome results from the sequencing vendor but not sure how to interpret them.
  • You wish to analyse the transcriptome data hands-on, especially as a biologist instead of a data scientist.
  • You want to learn on how to mine for biological knowledge from transcriptome data without programming/coding.
  • You work on a transcriptomic project and want to learn on how to publish your results as a high-impact journal article.

This workshop is opened to local & international participants, from beginner to advanced researchers in molecular biology / omics. The content of this workshop is transferable to other omics studies such as proteomics.

Speaker Biography

  • Associate Professor Dr. Goh Hoe Han is a plant molecular biologist who obtained his PhD from the University of Sheffield, United Kingdom in 2011 before starting his first acedemic position at the Institute of Systems Biology, Universiti Kebangsaan Malaysia. Upon joining INBIOSIS, he pioneered the Plant Functional Genomics Research Group focusing on the molecular exploration of tropical plants and crop improvement using functional genomics approaches. Some of the tropical plant species include kesum, ketum, Rafflesia, and Nepenthes pitcher plants, as well as important crops, such as mangosteen, papaya, rice, tomato, and oil palm. Fundamental understandings on the molecular aspects of these plants are crucial for their bioprospecting, industrial application, and crop improvement.

  • Dr Goh is keen on industrial collaboration in precision biotechnology for tropical plant improvement and also the commercialisation of novel recombinant plant enzymes. If you are interested to collaborate or be part of the plant functional genomics group, please email to gohhh@ukm.edu.my.

Programme

5th July 2022 (Tuesday)

Time Activity
8.30 am Registration
9.00 am Introduction

Lecture 1: Principles of transcriptomics

10.30 am Morning break
10.45 am Lecture 2: A crash course on RNA-seq analysis
12.30 pm Technical Talk 1 : Current developments of NGS (Apical Scientific)
1.00 pm Lunch break
2.30 pm Practical 1 : Data pre-processing/exploration

Practical 2 : Transcriptome assembly

4.00 pm Afternoon break
4.15 pm Participant flash talks, summary, discussions, and wrap-up
5.00 pm END OF DAY 1

6th July 2022 (Wednesday)

Time Activity
9.00 am Introduction to Day 2 & Recap
9.10 am Lecture 3: Exploring RNA-seq analysis for biological discovery (Functional Annotation & Downstream Analyses)
10.30 am Morning break
10.45 am Practical 3 : Mining RNA-seq data with Excel
12.30 pm Technical Talk 2 : Single-cell RNA-seq (Bio3 Scientific Sdn Bhd)
1.00 pm Lunch break
2.30 pm Practical 4 : WEGO & KEGG pathway analysis
4.o0 pm Afternoon break
4.15 pm Participant flash talks, summary, discussions, and wrap-up
5.00 pm END OF DAY 2

7th July 2022 (Thursday)

Time Activity
9.00 am Introduction to Day 3 & Recap
9.10 am Lecture 4 : RNA-seq downstream analyses using Perseus
10.30 am Morning break
10.45 am Practical 5 : Cluster analysis
12.30 pm Technical talk 3 – Applications of RNA-seq (Neoscience Sdn Bhd)
1.00 pm Lunch break
2.30 pm Practical 6 : Functional enrichment analysis
4.00 pm Afternoon break
4.15 pm Summary, discussions, and conclusion
5.00 pm END OF WORKSHOP

 

Workshop Requirements

For this online workshop, please download and install Webex for the online sessions. You won't need a computer with very high specifications. Minimum requirements: Windows OS (ideally 64-bit Windows 10 and above) with minimum 2 GB RAM and 10 GB hard disk storage to run MS Excel (2016 and above) and Perseus software for day 2 and day 3 practicals, respectively. For Mac users, please run Windows via Parallels or Bootcamp etc.

We will be using Perseus v1.6.7. Installers can be downloaded here. You just need to unzip the Perseus folder.

It's recommended that you use two devices (e.g., desktop/smartphone + laptop) or dual monitor setup to allow easy following of online demos during practicals.

For hands-on practicals, make sure that all software (Excel & Perseus) can run on your laptop before the workshop. Due to time constraint we don't have the time to individually troubleshoot software installation. As a pre-workshop training, you can try out this tutorial with the demo dataset to get familiar with Perseus basic functions. You can refer to Perseus demo videos Part 1 & Part 2.

Don't worry if your laptop cannot run Perseus, you can still learn a lot from this workshop on transcriptomics, different technologies, analysis workflow, applications, data interpretation, and visualisation.

​You can email me if facing any difficulty, I will try my best to help.

Register now or contact us for more details