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Researcher's guide to DNA sequencing data

Candace Savonen, MS

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:

Read more

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.

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What's inside

Syllabus

Introduction
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.
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WGS and WXS
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.
DNA Methylation
In this section we dive into DNA methylation sequencing methods, also known more specifically as bisulfite sequencing.
Overview of Chromatin
In this section we cover the basics of chromatin evaluation methods. We contrast and compare chromatin sequencing methods.
Chromatin Methods part 1
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.
Chromatin Methods part 2
In this section we cover the basics of ChIP-seq and CUT & Tag and CUT & RUN.
Microarrays and Wrapping Up
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.

Good to know

Know what's good
, what to watch for
, and possible dealbreakers
Develops foundational skills for novices who have taken the prerequesite course, "Researcher's Guide to Fundamentals of Omic Data"
Strenghtens existing knowledge for intermediate learners who have taken the prerequesite course, "Researcher's Guide to Fundamentals of Omic Data"
Provides a comprehensive study of DNA informatics methods, including WGS, WXS, DNA methylation, and chromatin evaluation
Taught by an expert with an MS in the field
Examines traditional and contempory methods for DNA informatics and assessment
Explicitly advises students to take other courses first as prerequisites

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Activities

Be better prepared before your course. Deepen your understanding during and after it. Supplement your coursework and achieve mastery of the topics covered in Researcher's guide to DNA sequencing data with these activities:
Review introductory materials on DNA informatics
Solidify your foundation and prepare for success by reviewing introductory materials on DNA informatics, ensuring a strong understanding of the fundamental concepts.
Browse courses on DNA Sequencing
Show steps
  • Revisit your notes or textbooks from previous courses related to DNA informatics.
  • Explore online resources and tutorials that provide overviews of the field.
Review WGS data analysis techniques
Refine your understanding of WGS data analysis techniques through practice, reinforcing your knowledge.
Browse courses on Whole Genome Sequencing
Show steps
  • Set up a practice dataset with publicly available WGS data.
  • Perform variant calling and analysis using tools like GATK.
  • Interpret and visualize the results of your analysis.
Collaborate with peers on chromatin analysis projects
Strengthen your understanding and gain diverse perspectives by collaborating with peers on chromatin analysis projects, fostering a collaborative learning environment.
Browse courses on Epigenetics
Show steps
  • Form study groups or online forums with other students.
  • Choose a specific chromatin analysis project to work on together.
  • Share ideas, data, and insights to enhance your collective understanding.
Four other activities
Expand to see all activities and additional details
Show all seven activities
Lead study groups or mentor other students in DNA omics
Enhance your understanding and communication skills by leading study groups or mentoring other students in DNA omics, reinforcing your knowledge through teaching.
Browse courses on Mentoring
Show steps
  • Offer to lead study groups or provide one-on-one mentoring to peers.
  • Prepare materials and structure sessions to effectively convey DNA omics concepts.
  • Encourage active participation and answer questions to support the learning of others.
Explore advanced topics in DNA methylation analysis
Deepen your understanding of DNA methylation analysis by following guided tutorials, expanding your expertise in this specialized area.
Show steps
  • Identify reputable resources and tutorials on advanced DNA methylation analysis techniques.
  • Follow the tutorials and apply the methods to your own research or case studies.
  • Seek guidance from experts in the field through online forums or discussion groups.
Contribute to open-source DNA omics projects
Enhance your practical skills and contribute to the DNA omics community by actively participating in open-source projects.
Browse courses on Open-Source Software
Show steps
  • Identify open-source DNA omics projects that align with your interests.
  • Review the project documentation and select an area to contribute to.
  • Reach out to the project maintainers to discuss your contributions.
Design and conduct a small-scale DNA omics research project
Gain hands-on experience and apply your knowledge by designing and conducting a small-scale DNA omics research project, solidifying your understanding through practical implementation.
Show steps
  • Identify a specific research question or hypothesis related to DNA omics.
  • Design an experimental approach and select appropriate DNA omics techniques.
  • Collect and analyze the data to draw conclusions and interpret the results.

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Course image
Level
Intermediate
Via
Coursera
Institution
Fred Hutchinson Cancer Center
Instructor
Candace Savonen, MS
Session
August 12, 2024 - October 7, 2024
Language
English
Good to know
Develops foundational skills for novices who have taken the prerequesite course, "Researcher's Guide to Fundamentals of Omic Data"
Strenghtens existing knowledge for intermediate learners who have taken the prerequesite course, "Researcher's Guide to Fundamentals of Omic Data"
Provides a comprehensive study of DNA informatics methods, including WGS, WXS, DNA methylation, and chromatin evaluation
Taught by an expert with an MS in the field
Examines traditional and contempory methods for DNA informatics and assessment
Explicitly advises students to take other courses first as prerequisites
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