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Researcher's guide to RNA sequencing data
Candace Savonen, MS
Candace Savonen, MS
This course is a follow up course to "Choosing genomics tools" which dives into further detail about RNA informatics methods!
This course is for individuals who:
- Have taken Researcher's Guide to Fundamentals of Omic Data
Read more
This course is a follow up course to "Choosing genomics tools" which dives into further detail about RNA informatics methods!
This course is for individuals who:
- Have taken Researcher's Guide to Fundamentals of Omic Data
Read more
This course is a follow up course to "Choosing genomics tools" which dives into further detail about RNA informatics methods!
This course is for individuals who:
- Have taken Researcher's Guide to Fundamentals of Omic Data
- Have RNA data and don’t know what to do with it.
- Want a basic overview of their RNA focused data type.
- Want to find resources for processing and interpreting RNA data
What this course will cover:
- Fundamentals of RNA 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.
Register for this course and see more details by visiting:
OpenCourser.com/course/py5qi9/researcher
What's inside
Syllabus
Introduction
In this first module we introduce the goals of this course an do an overview of the available methods for RNA methods, otherwise known as gene expression.
Read more
Syllabus
Introduction
In this first module we introduce the goals of this course an do an overview of the available methods for RNA methods, otherwise known as gene expression.
Read more
Bulk RNA-seq
In this module we dive into Bulk RNA-seq methods for evaluating gene expression of tissue.
Single Cell RNA-seq
In this module we dive into single cell RNA-seq methods for evaluating gene expression of single cells.
Spatial Transcriptomics
In this module we dive into gene expression of tissue but with spatial information.
Wrapping Up
To wrap up this course, we have a quick section about gene expression microarrays before we wrap up the course with a final course knowledge check.
Good to know
Good to know
Know what's good ,
what to watch for , and
possible dealbreakers
Provides foundational understanding of RNA methods for gene expression analysis
Suitable for learners with prior experience in genomics tools and RNA data
Emphasizes resources, tools, and considerations for RNA data analysis
Covers various RNA sequencing methods, including bulk, single cell, and spatial transcriptomics
Does not delve into technical details, such as coding or specific experimental designs
Taught by an experienced instructor specializing in omics data informatics
Save this course
Save Researcher's guide to RNA sequencing data to your list so you can find it easily later:
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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 RNA sequencing data with these
activities:
Review the structure and function of RNA
Show steps
Refresh your knowledge of the structure and function of RNA, including the different types of RNA molecules and their roles in gene expression.
Show steps
-
Read a textbook chapter or online article on RNA structure and function.
-
Watch a video tutorial on RNA structure.
Review Bulk RNA-seq
Show steps
Refresh your knowledge of Bulk RNA-seq methods to solidify your understanding of gene expression of tissue.
Show steps
-
Go over foundational principles of Bulk RNA-seq.
-
Review protocols and pipelines for Bulk RNA-seq.
Review RNA sequencing (RNA-seq)
Show steps
Refreshing your knowledge of the RNA-Seq technique is essential for getting the most out of this course.
Browse courses on
RNA-seq
Show steps
-
Re-read the basic principles of RNA-Seq.
-
Go over the different types of RNA-Seq experiments.
-
Review the data analysis workflow for RNA-Seq.
22 other activities
Expand to see all activities and additional details
Show all 25 activities
Review basic methods of gene expression
Show steps
Refresh your knowledge of the basic methods used to measure gene expression, such as RNA sequencing and microarrays.
Browse courses on
Gene Expression
Show steps
-
Read a textbook chapter or online article on RNA sequencing.
-
Watch a video tutorial on how to perform RNA sequencing.
-
Complete a practice exercise on RNA sequencing data analysis.
Discuss RNA-seq Analysis Techniques
Show steps
Gain diverse perspectives and insights into RNA-seq analysis techniques through discussions with peers.
Browse courses on
RNA-Seq Analysis
Show steps
-
Connect with classmates or peers in the field.
-
Host or join study groups to discuss specific RNA-seq analysis methods.
Review RNA extraction techniques
Show steps
Reviewing RNA extraction techniques will refresh your memory on the proper procedures and ensure that you have a solid foundation for the course.
Browse courses on
RNA Sequencing
Show steps
-
Read articles or watch videos on RNA extraction techniques.
-
Practice RNA extraction on a sample.
Identify a Mentor in the Field of RNA Bioinformatics
Show steps
Gain access to expert guidance and support by identifying a mentor in the field of RNA Bioinformatics.
Browse courses on
RNA Sequencing
Show steps
-
Research potential mentors at universities or research institutions.
-
Reach out to potential mentors via email or LinkedIn.
Follow tutorials on RNA analysis software
Show steps
Following tutorials on RNA analysis software will introduce you to the tools and techniques used in the course, giving you a head start.
Show steps
-
Identify a tutorial on an RNA analysis software tool.
-
Follow the tutorial step-by-step, practicing the commands and techniques.
Learn about gene expression microarrays
Show steps
This activity will help you understand the basics of gene expression microarrays, which is a closely related technique to RNA-Seq.
Browse courses on
Microarrays
Show steps
-
Find an online tutorial about gene expression microarrays.
-
Follow the tutorial to learn about the principles of microarrays.
-
Watch a video demonstration of a microarray experiment.
Follow a tutorial on spatial transcriptomics
Show steps
Spatial transcriptomics is a newer method for evaluating gene expression that provides spatial information. This tutorial will help you learn the basics of spatial transcriptomics.
Show steps
-
Find a tutorial on spatial transcriptomics
-
Follow the tutorial step-by-step
-
Complete the exercises or assignments included in the tutorial
Interpret Spatial Transcriptomics Data
Show steps
Develop your ability to analyze gene expression of tissue with spatial information by interpreting Spatial Transcriptomics data.
Show steps
-
Gather various sample Spatial Transcriptomics datasets.
-
Practice interpreting the data to identify patterns and insights.
Participate in a study group
Show steps
Participating in a study group will provide you with opportunities to discuss course concepts, ask questions, and learn from others.
Show steps
-
Find a study group or start your own with classmates.
-
Meet regularly to discuss course material, work on assignments, and prepare for exams.
Practice analyzing RNA sequencing data
Show steps
Practice your skills in analyzing RNA sequencing data to identify differentially expressed genes and other patterns of gene expression.
Browse courses on
Gene Expression Analysis
Show steps
-
Download an RNA sequencing dataset from a public repository.
-
Use a software package to analyze the dataset and identify differentially expressed genes.
-
Interpret the results of your analysis and write a brief report.
Practice Bulk RNA-seq techniques
Show steps
Bulk RNA-seq is a common method for evaluating gene expression. This practice will help reinforce learning from the Bulk RNA-seq module.
Browse courses on
RNA-seq
Show steps
-
Review the Bulk RNA-seq module materials
-
Use an online tool or software to practice analyzing Bulk RNA-seq data
-
Join a discussion forum or online community to discuss Bulk RNA-seq techniques with other learners
Enroll in a Single Cell RNA-seq Tutorial
Show steps
Supplement your understanding of gene expression of single cells by exploring Single Cell RNA-seq methods.
Show steps
-
Find reputable Single Cell RNA-seq tutorials online.
-
Follow the tutorial, making notes and asking questions as needed.
Create a visualization of Single Cell RNA-seq data
Show steps
Creating a visualization of Single Cell RNA-seq data will help you understand the relationships between different cell types and their gene expression profiles.
Browse courses on
RNA-seq
Show steps
-
Review the Single Cell RNA-seq module materials
-
Use a visualization tool or software to create a visualization of Single Cell RNA-seq data
-
Share your visualization with others and get feedback
Summarize course lectures
Show steps
Creating summaries of course lectures will help you retain information and identify key concepts.
Show steps
-
After each lecture, take notes on the main points.
-
Within 24 hours, expand your notes into a concise summary.
-
Review your summaries regularly to reinforce your understanding.
Practice interpreting RNA-Seq data
Show steps
This activity will give you hands-on experience with interpreting RNA-Seq data.
Browse courses on
RNA-seq
Show steps
-
Download a publicly available RNA-Seq dataset.
-
Use a software package to analyze the dataset.
-
Write a report summarizing your findings.
Develop a research proposal using RNA methods
Show steps
This will help you apply the concepts you have learned in the course to a real-world research question.
Show steps
-
Identify a research question that you are interested in
-
Develop a hypothesis and specific aims
-
Choose the appropriate RNA methods to use
-
Design your experiment
-
Write a research proposal
Explore Gene Expression Microarrays
Show steps
Expand your knowledge in gene expression analysis by familiarizing yourself with Gene Expression Microarrays.
Show steps
-
Find educational resources on Gene Expression Microarrays.
-
Review the principles, methods, and applications of microarrays.
Practice RNA analysis problems
Show steps
Solving RNA analysis problems will improve your understanding of the concepts and techniques covered in the course.
Browse courses on
Data Interpretation
Show steps
-
Find practice problems online or in textbooks.
-
Attempt to solve the problems on your own.
-
Check your solutions against the provided answer key.
Create a Visual Representation of RNA-seq Results
Show steps
Enhance your understanding of RNA-seq results by creating a visual representation of the data.
Browse courses on
RNA-seq
Show steps
-
Select appropriate data visualization tools for your chosen data.
-
Create visualizations that effectively communicate the key findings of your RNA-seq analysis.
Create a visualization for your RNA-Seq data
Show steps
This activity will help you to improve your data visualization skills and communicate your findings more effectively.
Browse courses on
RNA-seq
Show steps
-
Choose a type of visualization that is appropriate for your data.
-
Use a software package to create the visualization.
-
Present your visualization to your classmates or colleagues.
Design an Experiment Using RNA-seq Data
Show steps
Apply your understanding of RNA-seq data by designing an experiment that utilizes it.
Browse courses on
RNA-seq
Show steps
-
Identify a specific research question you want to address.
-
Determine the appropriate RNA-seq approach for your experiment.
-
Design the experiment, including sample preparation, sequencing parameters, and data analysis methods.
Create a research proposal on an RNA-related topic
Show steps
Creating a research proposal will allow you to apply the knowledge and skills learned in the course to a real-world problem.
Browse courses on
Research Proposal
Show steps
-
Identify a research question related to RNA.
-
Research the topic, including relevant literature and data.
-
Write a proposal outlining your research question, methods, and expected outcomes.
Review the structure and function of RNA
Show steps
Refresh your knowledge of the structure and function of RNA, including the different types of RNA molecules and their roles in gene expression.
Show steps
Show steps
Show steps
- Read a textbook chapter or online article on RNA structure and function.
- Watch a video tutorial on RNA structure.
Review Bulk RNA-seq
Show steps
Refresh your knowledge of Bulk RNA-seq methods to solidify your understanding of gene expression of tissue.
Show steps
Show steps
Show steps
- Go over foundational principles of Bulk RNA-seq.
- Review protocols and pipelines for Bulk RNA-seq.
Review RNA sequencing (RNA-seq)
Show steps
Refreshing your knowledge of the RNA-Seq technique is essential for getting the most out of this course.
Browse courses on
RNA-seq
Show steps
Show steps
Show steps
- Re-read the basic principles of RNA-Seq.
- Go over the different types of RNA-Seq experiments.
- Review the data analysis workflow for RNA-Seq.
22 other activities
Expand to see all activities and additional details
Show all 25 activities
Review basic methods of gene expression
Show steps
Refresh your knowledge of the basic methods used to measure gene expression, such as RNA sequencing and microarrays.
Browse courses on
Gene Expression
Show steps
Show steps
Show steps
- Read a textbook chapter or online article on RNA sequencing.
- Watch a video tutorial on how to perform RNA sequencing.
- Complete a practice exercise on RNA sequencing data analysis.
Discuss RNA-seq Analysis Techniques
Show steps
Gain diverse perspectives and insights into RNA-seq analysis techniques through discussions with peers.
Browse courses on
RNA-Seq Analysis
Show steps
Show steps
Show steps
- Connect with classmates or peers in the field.
- Host or join study groups to discuss specific RNA-seq analysis methods.
Review RNA extraction techniques
Show steps
Reviewing RNA extraction techniques will refresh your memory on the proper procedures and ensure that you have a solid foundation for the course.
Browse courses on
RNA Sequencing
Show steps
Show steps
Show steps
- Read articles or watch videos on RNA extraction techniques.
- Practice RNA extraction on a sample.
Identify a Mentor in the Field of RNA Bioinformatics
Show steps
Gain access to expert guidance and support by identifying a mentor in the field of RNA Bioinformatics.
Browse courses on
RNA Sequencing
Show steps
Show steps
Show steps
- Research potential mentors at universities or research institutions.
- Reach out to potential mentors via email or LinkedIn.
Follow tutorials on RNA analysis software
Show steps
Following tutorials on RNA analysis software will introduce you to the tools and techniques used in the course, giving you a head start.
Show steps
Show steps
Show steps
- Identify a tutorial on an RNA analysis software tool.
- Follow the tutorial step-by-step, practicing the commands and techniques.
Learn about gene expression microarrays
Show steps
This activity will help you understand the basics of gene expression microarrays, which is a closely related technique to RNA-Seq.
Browse courses on
Microarrays
Show steps
Show steps
Show steps
- Find an online tutorial about gene expression microarrays.
- Follow the tutorial to learn about the principles of microarrays.
- Watch a video demonstration of a microarray experiment.
Follow a tutorial on spatial transcriptomics
Show steps
Spatial transcriptomics is a newer method for evaluating gene expression that provides spatial information. This tutorial will help you learn the basics of spatial transcriptomics.
Show steps
Show steps
Show steps
- Find a tutorial on spatial transcriptomics
- Follow the tutorial step-by-step
- Complete the exercises or assignments included in the tutorial
Interpret Spatial Transcriptomics Data
Show steps
Develop your ability to analyze gene expression of tissue with spatial information by interpreting Spatial Transcriptomics data.
Show steps
Show steps
Show steps
- Gather various sample Spatial Transcriptomics datasets.
- Practice interpreting the data to identify patterns and insights.
Participate in a study group
Show steps
Participating in a study group will provide you with opportunities to discuss course concepts, ask questions, and learn from others.
Show steps
Show steps
Show steps
- Find a study group or start your own with classmates.
- Meet regularly to discuss course material, work on assignments, and prepare for exams.
Practice analyzing RNA sequencing data
Show steps
Practice your skills in analyzing RNA sequencing data to identify differentially expressed genes and other patterns of gene expression.
Browse courses on
Gene Expression Analysis
Show steps
Show steps
Show steps
- Download an RNA sequencing dataset from a public repository.
- Use a software package to analyze the dataset and identify differentially expressed genes.
- Interpret the results of your analysis and write a brief report.
Practice Bulk RNA-seq techniques
Show steps
Bulk RNA-seq is a common method for evaluating gene expression. This practice will help reinforce learning from the Bulk RNA-seq module.
Browse courses on
RNA-seq
Show steps
Show steps
Show steps
- Review the Bulk RNA-seq module materials
- Use an online tool or software to practice analyzing Bulk RNA-seq data
- Join a discussion forum or online community to discuss Bulk RNA-seq techniques with other learners
Enroll in a Single Cell RNA-seq Tutorial
Show steps
Supplement your understanding of gene expression of single cells by exploring Single Cell RNA-seq methods.
Show steps
Show steps
Show steps
- Find reputable Single Cell RNA-seq tutorials online.
- Follow the tutorial, making notes and asking questions as needed.
Create a visualization of Single Cell RNA-seq data
Show steps
Creating a visualization of Single Cell RNA-seq data will help you understand the relationships between different cell types and their gene expression profiles.
Browse courses on
RNA-seq
Show steps
Show steps
Show steps
- Review the Single Cell RNA-seq module materials
- Use a visualization tool or software to create a visualization of Single Cell RNA-seq data
- Share your visualization with others and get feedback
Summarize course lectures
Show steps
Creating summaries of course lectures will help you retain information and identify key concepts.
Show steps
Show steps
Show steps
- After each lecture, take notes on the main points.
- Within 24 hours, expand your notes into a concise summary.
- Review your summaries regularly to reinforce your understanding.
Practice interpreting RNA-Seq data
Show steps
This activity will give you hands-on experience with interpreting RNA-Seq data.
Browse courses on
RNA-seq
Show steps
Show steps
Show steps
- Download a publicly available RNA-Seq dataset.
- Use a software package to analyze the dataset.
- Write a report summarizing your findings.
Develop a research proposal using RNA methods
Show steps
This will help you apply the concepts you have learned in the course to a real-world research question.
Show steps
Show steps
Show steps
- Identify a research question that you are interested in
- Develop a hypothesis and specific aims
- Choose the appropriate RNA methods to use
- Design your experiment
- Write a research proposal
Explore Gene Expression Microarrays
Show steps
Expand your knowledge in gene expression analysis by familiarizing yourself with Gene Expression Microarrays.
Show steps
Show steps
Show steps
- Find educational resources on Gene Expression Microarrays.
- Review the principles, methods, and applications of microarrays.
Practice RNA analysis problems
Show steps
Solving RNA analysis problems will improve your understanding of the concepts and techniques covered in the course.
Browse courses on
Data Interpretation
Show steps
Show steps
Show steps
- Find practice problems online or in textbooks.
- Attempt to solve the problems on your own.
- Check your solutions against the provided answer key.
Create a Visual Representation of RNA-seq Results
Show steps
Enhance your understanding of RNA-seq results by creating a visual representation of the data.
Browse courses on
RNA-seq
Show steps
Show steps
Show steps
- Select appropriate data visualization tools for your chosen data.
- Create visualizations that effectively communicate the key findings of your RNA-seq analysis.
Create a visualization for your RNA-Seq data
Show steps
This activity will help you to improve your data visualization skills and communicate your findings more effectively.
Browse courses on
RNA-seq
Show steps
Show steps
Show steps
- Choose a type of visualization that is appropriate for your data.
- Use a software package to create the visualization.
- Present your visualization to your classmates or colleagues.
Design an Experiment Using RNA-seq Data
Show steps
Apply your understanding of RNA-seq data by designing an experiment that utilizes it.
Browse courses on
RNA-seq
Show steps
Show steps
Show steps
- Identify a specific research question you want to address.
- Determine the appropriate RNA-seq approach for your experiment.
- Design the experiment, including sample preparation, sequencing parameters, and data analysis methods.
Create a research proposal on an RNA-related topic
Show steps
Creating a research proposal will allow you to apply the knowledge and skills learned in the course to a real-world problem.
Browse courses on
Research Proposal
Show steps
Show steps
Show steps
- Identify a research question related to RNA.
- Research the topic, including relevant literature and data.
- Write a proposal outlining your research question, methods, and expected outcomes.
Career center
Learners who complete Researcher's guide to RNA sequencing data will develop knowledge and skills
that may be useful to these careers:
For more career information including salaries, visit:
OpenCourser.com/course/py5qi9/researcher
Reading list
We haven't picked any books for this reading list yet.
For more information about how these books relate to this course, visit:
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Introduction to Genomic Technologies
Level
Intermediate
Via
Coursera
Institution
Fred Hutchinson Cancer Center
Instructor
Candace Savonen, MS
Session
August 12, 2024
- September 23, 2024
Language
English
Good to know
Provides foundational understanding of RNA methods for gene expression analysis
Suitable for learners with prior experience in genomics tools and RNA data
Emphasizes resources, tools, and considerations for RNA data analysis
Covers various RNA sequencing methods, including bulk, single cell, and spatial transcriptomics
Does not delve into technical details, such as coding or specific experimental designs
Taught by an experienced instructor specializing in omics data informatics
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