Fall 2019 Epigenetics Workshops

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Next Generation Sequencing – Overview, Considerations and Best Practices

Instructor: Parisha Shah

Date / Time: Monday, December 9, 2019 from 9am-11am

Description: Are you planning NGS experiments? What constitutes a “good” sequencing library? How much coverage is needed? What practices yield quality sequencing data?  All this and more in a class that covers the basics of running your own NGS experiments.

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Bioinformatic Analysis Introduction

Instructors: Yemin Lan & Margaret Shaw

Date / Time: Tuesday, December 10, 2019 from 9am-11am

Description: The workshop will discuss how we make decisions on sequencing options such as sequencing depth, read length and strand choices. Additionally, we will briefly explain the characteristic analysis pipeline for RNA-seq and ChIP-seq data step by step, while we also explain how typical concerns.

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Bioinformatic Analysis Hands-On

Instructors: Yemin Lan & Margaret Shaw

Date / Time: Wednesday, December 11, 2019 from 9am-11am

Description: The workshop will use a test dataset to guide through a simple RNA-seq analysis pipeline from raw sequencing data to read count table. You are encouraged to bring your own laptop to follow the steps, including basic command lines, aligning reads, building genome browser tracks and counting reads.

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Basics of Proteomics

Instructor: Josue Baeza

Date / Time: Tuesday, December 17, 2019 from 9am-11am

Description: How do you identify and quantify thousands of proteins from a µg of sample? In this workshop, we will discuss how mass spectrometry (MS) has revolutionized protein analysis and made proteomics a central scientific discipline. The lecture will illustrate the principles of MS and how we identify/quantify proteins in a high throughput manner. Moreover, we will give an overview of all potential applications of MS for protein characterization, e.g. folding, interactions, turnover, cross-talk of post-translational modifications, tissue localization.

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Applied Proteomics

Instructor: Josue Baeza

Date / Time: Wednesday, December 18, 2019 from 9am-11am

Description: What should I consider when I plan a proteomics experiment? In this workshop, we will discuss pros and cons of all strategies in proteomics. This will include (i) What is the best preparation and quantification method depending on your sample and question; (ii) What experiments are possible with a given amount/type of starting material; (iii) How you can mine a proteomics dataset to extract information not obtainable with genomics data. Finally, we will briefly introduce metabolomics, an emerging field of applied MS to identify and quantify the cell metabolome.

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Workshop Selection



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