Researcher's guide to DNA sequencing data
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Researcher's guide to DNA sequencing data
This course is part of Researcher's Guide to Omic Data Specialization
Instructor: Candace Savonen, MS
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What you'll learn
You will be able to understand the goals and general workflows of DNA based methods and know tools and resources you should consider.
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There are 7 modules in this course
This course is a follow up course to "Researcher's Guide to Fundamentals of Omic Data" which dives into further detail about DNA informatics methods!
This course is for individuals who: - Have taken Researcher's Guide to Fundamentals of Omic Data - Have DNA data and don’t know what to do with it. - Want a basic overview of their DNA focused data type. - Want to find resources for processing and interpreting DNA data What this course will cover: - Fundamentals of DNA methods. - Resources you may consider looking into for your own purposes. - Questions you should ask yourself and your colleagues about your goals and experimental design. What this course will NOT cover: - Code needed to process your data. - Details about every type of experimental design. - Everything you’d need to know to make you a computational biologist. In other words we still highly encourage you to consult your informatics and computational colleagues, especially those who may have done any handling of data you are trying to learn about.
In this module we discuss what this course covers and encourage you to make your own goals for what you'd like to learn. Then we start with some generalities about DNA focused methods.
What's included
3 videos3 readings2 assignments1 discussion prompt
3 videos•Total 6 minutes
- Welcome!•1 minute
- Intro to this course•1 minute
- DNA Overview•4 minutes
3 readings•Total 19 minutes
- Considerations for your DNA goals•5 minutes
- Video covering types of mutations•2 minutes
- DNA Overview•12 minutes
2 assignments•Total 11 minutes
- DNA Overview•5 minutes
- DNA Overview•6 minutes
1 discussion prompt•Total 15 minutes
- Goals for this course•15 minutes
In this module we cover the details of whole genome sequencing and whole exome sequencing. We compare and contrast the methods and discuss what kinds of questions these data types might answer.
What's included
2 readings2 assignments1 discussion prompt
2 readings•Total 20 minutes
- DNA Sequencing Video•5 minutes
- WGS and WXS•15 minutes
2 assignments•Total 13 minutes
- WGS vs WXS•5 minutes
- WGS vs WXS Quiz•8 minutes
1 discussion prompt•Total 10 minutes
- Imagine a WXS/WGS study•10 minutes
In this section we dive into DNA methylation sequencing methods, also known more specifically as bisulfite sequencing.
What's included
2 readings2 assignments1 discussion prompt
2 readings•Total 23 minutes
- Video on basics of DNA Methylation•8 minutes
- DNA Methylation•15 minutes
2 assignments•Total 13 minutes
- DNA Methylation•5 minutes
- DNA methylation quiz•8 minutes
1 discussion prompt•Total 10 minutes
- Imagine a DNA methylation study•10 minutes
In this section we cover the basics of chromatin evaluation methods. We contrast and compare chromatin sequencing methods.
What's included
1 video2 readings2 assignments1 discussion prompt
1 video•Total 2 minutes
- Chromatin Overview•2 minutes
2 readings•Total 15 minutes
- Chromatin Methods Overview•10 minutes
- Video about the basics of chromatin•5 minutes
2 assignments•Total 13 minutes
- Chromatin Overview•5 minutes
- Chromatin Overview Quiz•8 minutes
1 discussion prompt•Total 10 minutes
- Imagine a chromatin study•10 minutes
In this module, we discuss details of the different ways chromatin can be assessed. We go through the basics of ATAC-seq, and scRNA-seq.
What's included
2 videos3 readings2 assignments
2 videos•Total 4 minutes
- ATAC-seq Overview•2 minutes
- Single cell ATAC-seq Overview•3 minutes
3 readings•Total 38 minutes
- Video about Basics of ATAC-seq •10 minutes
- ATAC-Seq•15 minutes
- scATAC-Seq•13 minutes
2 assignments•Total 13 minutes
- ATAC-seq and scATAC-seq•5 minutes
- ATAC-seq and scATAC-seq•8 minutes
In this section we cover the basics of ChIP-seq and CUT & Tag and CUT & RUN.
What's included
1 video4 readings2 assignments
1 video•Total 2 minutes
- ChIP-Seq Overview•2 minutes
4 readings•Total 31 minutes
- Video about the Basics of ChIP-seq •6 minutes
- ChIP-seq•10 minutes
- Video: CUT & RUN Basics•5 minutes
- CUT&RUN/Tag•10 minutes
2 assignments•Total 13 minutes
- ChIP-seq and CUT & RUN/Tag•5 minutes
- ChIP-seq and CUT & RUN/Tag Quiz•8 minutes
In this section, In this module we discuss when microarrays should be used for assaying DNA instead of sequencing methods. and then we will wrap up this course with a final quiz to assess your absorption of the material. We also point you to our Tool Glossary that has a list of tools you may want to consider for your next steps of your DNA omics study.
What's included
3 readings1 assignment2 discussion prompts
3 readings•Total 14 minutes
- Consider Microarrays•8 minutes
- About the authors•2 minutes
- Tool Glossary•4 minutes
1 assignment•Total 15 minutes
- Summary of DNA tools Quiz•15 minutes
2 discussion prompts•Total 20 minutes
- Are SNP arrays for you?•10 minutes
- Which DNA Tools?•10 minutes
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