Applied-Genomic-Technologies

Compiled by Xingzhao Wen.

Acknowledgments

We thank BENG183 alumni: John David Lin, Samuel Beppler, Paige Dubelko, Pericles Corkos, Elisha Beebe, Mengyi Liu, Kelsey Dang, Katy Zou, Diego Quintero, Derek Jow, Victoria Tom, Joey Sun.

Chapter1 Molecular Biology

• Review of Molecular Biology from 3D Genome ebook.

Chapter2 DNA sequencing

• Sequencing technolegies from 3D Genome ebook.

Chapter3 RNA sequencing and data analysis

• 3.1 Overview of RNA sequencing.
• 3.2 Quantification of gene expression from 3D Genome ebook
• 3.3 Detection of differentially expressed genes from 3D Genome ebook
• 3.4 Single-cell transcriptomic analysis

Chapter4 ChIP-seq and data analysis

• 4.1 ChIP-seq

Chapter5 Introduction to precision medicine

• 5.1 An overview of precision medicine
• 5.2 Precision medicine in breast cancer
• 5.3 Precision medicine in diabetes
• 5.4 An overview of bioinformatic methods for precision medicine

Chapter6 Introduction to hypothesis testing

• 6.1 The instructor’s cheat sheet to hypothesis testing

Chapter7 Machine Learning

• 7.1 Intro to Machine Learning

Appendix: hands-on tutorials

• 1. Data files
• 2. Getting started with the Linux environment
• 3. Working with raw RNA sequencing data
• 4. Mapping RNA-seq reads and quantifying gene expression
• 5. Identifying differentially expressed genes
• 6. A tutorial for writing markdown (.md) files