Transcriptomics 1
What is the transcriptome and why study it?
Molecular biologists study a broad spectrum of topics relating to the molecular regulation of cell biology, from DNA and RNA, to protein expression and protein-protein interactions. A dominant theme in molecular biology is how variation in nucleic acids (genotype) affects the biology of organisms (phenotype). The second major theme is the study of gene expression and the resulting change in observed features of a studied sample.
Next Generation Sequencing (NGS) is a key technology enabling an unprecedented level of precision and efficacy in understanding genomic and transcriptomic regulation. A Next Generation sequencer creates a digital file representing sequenced DNA or RNA. This file contains information where nucleotides are represented by letters corresponding to their “bases”.
Next Generation Sequencing data analysis is often referred to as “RNA-seq”. The purpose of this analysis is to map the short reads from raw sequence files to the reference genome and then study the abundance of RNA mapped to a particular region. The abundance can represent levels of gene or isoform expression and can be compared between samples or groups of samples.
Course objectives and methodology
The goal of this course is to prepare a student for real-world applications of RNA-seq. We will review methods of quantitative and qualitative analysis of RNA in a sample, how data is generated using Next Generation Sequencing and use a sample project “Patient Derived Xenograft: Transcriptomic Biomarkers of Breast Cancer” to practice generating a table of expression from raw FASTq files. We will also learn to preview and visualize the resulting data using Principal Component Analysis (PCA). To perform the example analysis detailed in the course, students will need access to the T-BioInfo platform. Account information can be requested in an email to info@pine-biotech.com. Microsoft Excel is also used for plotting results.
We would like to thank the following people who helped to prepare the projects, develop the tools, and compile the the learning resources for this course:
Dr. Leonid Brodsky and the Tauber Bioinformatics Research Center, Dr. Claudia Copeland, Dr. Ron Ferrucci, Julia Panov, Jaclyn Williams
Course Features
- Lectures 7
- Quizzes 2
- Duration 6 hours
- Skill level All levels
- Language English
- Students 1509
- Certificate Yes
- Assessments Yes
-
From biological samples to RNA reads
-
From raw RNA-seq reads to expression table
-
Glossary
-
khajapeer
shaik
its very good...i hope increase my knowledge
-
ahmadatallah
Ahmad
looks awesome and well organized materials
9 Comments
where are all the lessons?
How do I enroll?
There should be an enrollment button, but it appears to be missing for some users and certain courses. We are working on getting to the bottom of this issue..
issue fixed, you should be able to enroll now
This is simply awesome course. I loved this course. It made many of my concepts clear and the quiz was pretty exciting and challenging… looking forward to get enrolled in other courses too.
I recently took Transcriptomics 1 which helped me to clear my basics and gain an in-depth insight to what it is like to successfully handle data of any omics especially bioinformatics through excellent videos and quizzes. I look forward to utilizing the platform in research and gaining better knowledge of my core subjects.
This is really helpful data … I am very thankful for this
It’s very useful and help me to figure out my research project.
Thanks,
Basic stuff is very well covered. And the discussion on common algorithms was pretty good. One go and analyse data and also identify the problem statement to empower oneself in NGS RNA-seq analysis.