Transcriptomics 1
RNA-seq: What is the transcriptome and why study it?
Molecular biologists study a broad spectrum of topics relating to the molecular regulation of cell biology, from DNA and RNA, to protein expression and protein-protein interactions. A dominant theme in molecular biology is how variation in nucleic acids (genotype) affects the biology of organisms (phenotype). A second major theme is the study of gene expression and the resulting change(s) in observed transcriptomics features of a studied sample.
Next Generation Sequencing (NGS) is a key technology enabling an unprecedented level of precision, and efficacy in understanding genomic and transcriptomic regulation. A Next Generation sequencer creates a digital file representing sequenced DNA or RNA. This file contains information where nucleotides are represented by letters corresponding to their “bases”.
Next Generation Sequencing data analysis is often referred to as “RNA-seq”. The purpose of this analysis is to map the short reads from raw sequence files to the reference genome, and then study the abundance of RNA mapped to a particular region. The abundance can represent levels of gene or isoform expression, and can be compared between samples or groups of samples.
Transcriptomics 1: Course objectives and methodology
The goal of this course is to prepare a student for real-world applications of RNA-seq. We will review methods of both quantitative and qualitative analysis of RNA in a sample, how data is generated using Next Generation Sequencing, and use a sample project “Patient Derived Xenograft: Transcriptomic Biomarkers of Breast Cancer” to practice generating a table of expression from raw FASTq files. We will also learn to preview and visualize the resulting data using Principal Component Analysis (PCA). To perform the example analysis detailed in the course, students will need access to the T-BioInfo platform. Account information can be requested by filling out the form on server.t-bio.info site. Microsoft Excel is also used for plotting results.
We would like to thank the following people who helped to prepare the projects, develop the tools, and compile the the learning resources for this course:
Dr. Leonid Brodsky and the Tauber Bioinformatics Research Center, Dr. Claudia Copeland, Dr. Ron Ferrucci, Julia Panov, Jaclyn Williams and Jo Calihan.
Course Features
- Lectures 9
- Quizzes 2
- Duration 6 hours
- Skill level All levels
- Language English
- Students 7654
- Certificate Yes
- Assessments Yes
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1. Biology of RNA and Next Generation Sequencing
Learn about the process of gene expression, alternative splicing and assays for mRNA detection and quantification
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2. Processing RNA-seq data and generating a table of expression
Learn about Next Generation Sequencing and the steps to analyze and interpret RNA-seq data
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3. Understanding The Table of Expression
Learn about working with the table of expression to get a high-level view of RNA-seq data
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4. Conclusion and Additional Resources
Additional resources for reading to review what we learned in Transcriptomics 1
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anthonyimolele
Godswill
Excellently crafted course,I have never developed such step-wise appreciation for a concept so complex. Its simply the best,without mincing my words.
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farhinsultana01066
Transcriptomics 1
This course is very much informative and very helpful to understand each step very easily. I have learned a lot of things from basic.
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sebrahim
Transcriptomics 1: Your First Step Towards RNA Sequencing
Transcriptomics 1 is surely the best way to start off when you are curious about RNA sequencing. It starts from the basic concept of transcription in the central dogma of life to the quantification of mRNA and analysis of RNA raw data. The course provides you with extensive content to brood over and then hands-on experience of the same which is extremely helpful to the point you understand the theoretical concept behind each topic. It is circumstantial but succinct and is a great continuation after Introduction to Bioinformatics course.
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dgowswami
transcriptomics 1
The first time learning this course was a bit difficult...but with thorough reading it was much clear.
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devalinahalder
A wonderful start to Transcriptomics
The course is well written and quite informative,it makes the concept easy to understand.
28 Comments
where are all the lessons?
How do I enroll?
There should be an enrollment button, but it appears to be missing for some users and certain courses. We are working on getting to the bottom of this issue..
issue fixed, you should be able to enroll now
This is simply awesome course. I loved this course. It made many of my concepts clear and the quiz was pretty exciting and challenging… looking forward to get enrolled in other courses too.
I recently took Transcriptomics 1 which helped me to clear my basics and gain an in-depth insight to what it is like to successfully handle data of any omics especially bioinformatics through excellent videos and quizzes. I look forward to utilizing the platform in research and gaining better knowledge of my core subjects.
This is really helpful data … I am very thankful for this
It’s very useful and help me to figure out my research project.
Thanks,
Glad to know that – hoping that your research project yields interesting results!
Transcriptomics 1 have helped me to get a clear knowledge about this topic and quiz is so interesting..
Interesting one.
I would suggest doing the (Principal Component Analysis) PCA course for the Interpretation of Output Data of Hands-on Project. and understand Transcriptomics 2.
Thank you!
I have started the assignment in transcriptomic 1 section 3.1 three days ago. My created pipeline (Test Run 1) has not yet finished and it is in its 50% processing step. Is there anything wrong?
There is nothing wrong, the pipeline run time is determined by data size, pipeline complexity and number of users simultaneously running analysis at the same time.
Extremely helpful course designed well to cover the basics on Transcriptomics which is a widely used technique that obtains information on the abundance of multiple mRNA transcripts within a biological sample simultaneously.There are various examples, pictorial representation to help us better comprehend the content. There are quizzes which are conceptual that will help you self access and get clarity over the subject. This course also allows you to work with hands on assignment where you can practically perform the analysis which helps in even better understanding of the subject on a whole. I would personally recommend it.
Is there a trouble-shooting page? I’ve been trying to run the RNA-seq pipeline, and it keeps getting hung up at 50% processing. I cannot get my results.
Each course has a forum for technical issues.
I was told that once we paid for a course that we would maintain access. Has this changed and we have to pay for a course a second time if we don’t complete it after a certain period of time?
We checked and your purchase was done via a subscription, which is a monthly fee. You can also purchase individual courses, those will not require to be purchased again until they are updated with new material (which happens, but rarely)
Hi can you please send me the certificate for this course as I can not access it?
you should be able to see your certificates under your profile: https://edu.t-bio.info/members/yana-gupta/courses/certificates/
Good day Sir, please why I grapple with the hands on assignment on transcriptomics 1, I started studying transcriptomics 2 contents,only to notice that my course progress didn’t increase at all,still o%, would that change to indicate all the progress I have made so far after in transcriptomics 2,after I get the correct answer? That was why I submitted earlier, to know if that will change, please how do I rectify this??
Dear Anthony, the course progress is only measured when you press “FINISH” (a button at the bottom of each lesson, or if you press “COMPLETE COURSE”
Good morning sir,
Please the section 4.1 on transcriptomics 1, keep logging me out automatically, I have not been able to assess its contents, or complete it, how can I correct this
Its “technical details on the method we used”
Sorry to hear that, please try again and let us know: support@pine.bio
This is simply amazing course!!! It provides a holistic approach to analyze RNA-seq raw data in the simplest manner. If someone is interested in learning the RNA-seq analysis in detail, one must take this course!!
I’m unable to upload the Breast_Cancer_Education1.svl file for transcriptomics 1 assignment. I keep getting server message: ”Please wait until the file is processed for use”.
Please refresh the server page and clear cache – I think everything is working, but if you are facing issues, you can email: support [at] pine.bio and post on the organization forum.
Hello Hyacinth, you have to wait until the file is uploaded and ready. For me, it takes a few seconds if I get that message after uploading the file.