GEP Tools | Using the RNA-Seq Tracks
Channel: Genomics Education Partnership
Date: 16/09/2021

A video describing RNA-Seq by Virtual GEP TA Christina Ray Santos. We start off with a guided navigation to the GEP UCSC Genome Browser, where GEP student annotators can view their gene models, and then take a step back to talk about how it’s obtained, how scientists can use it to analyze transcriptomes and how they vary between species, organisms, or even cells. This leads into the topic of alternative splicing, which results in unique isoforms that can be used for particular biological tasks. Next, a guide to using your RNA-Seq tracks to their full potential in the GEP UCSC Genome Browser, and finally, a brief summary of what we’ve found out about our example gene to show what we can ultimately take away from all this.

2:57 ~ RNA-Seq (for the TAs) - https://docs.google.com/presentation/d/1b5R85HQBfDvZRga9oUG796lxqwMM5r-KcNCzON_MuOQ/edit#slide=id.ge50c349ca7_0_0
2:57 ~ Encode - https://www.kurzweilai.net/images/EncodeNatureGraphic.png
2:42 ~ RNA-Seq Read Mapping - https://www.youtube.com/watch?v=4U6cNSuuBHE
3:30 ~ Sanger Sequencing - https://youtu.be/6ldtdWjDwes
3:31~ Next Generation Sequencing - https://youtu.be/-7GK1HXwCtEAnimation
3:32 ~ PacBio vs Nanopore - https://en.wikipedia.org/wiki/Third-generation_sequencing
3:34 ~ PacBio Sequencing – How it Works - https://youtu.be/_lD8JyAbwEo
3:34 ~ How nanopore sequencing works - https://youtu.be/RcP85JHLmnI
3:40 ~ Single-Cell RNA Seq Workflow - https://commons.wikimedia.org/wiki/File:Single-cell_RNA-Seq_workflow.pdf
4:11 ~ Life Stages - https://onlinelibrary.wiley.com/cms/asset/259dd4bb-506c-4713-94c0-72f7233b88db/wdev396-toc-0001-m.jpg
4:50 ~ Reverse Transcription - cDNA - https://www.mun.ca/biology/desmid/brian/BIOL4900/CB18_31.html
5:19 ~ PCR Cycle Count - https://theminione.com/wp-content/uploads/2019/02/M6005-PCR-Cycle-Count-main-800x800.jpg
5:36 ~ Alternative Splicing - https://www.ddw-online.com/full-length-isoform-sequencing-iso-seq-yields-a-more-comprehensive-view-of-gene-activity-1586-201608/
12:57 ~ Canonical Splice Site Donors and Acceptors - https://www.researchgate.net/figure/Non-canonical-splice-sites-identified-in-F-graminearum-A-Genes-with-non-canonical_fig7_234157021

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Spanish subtitles provided by REV.com and reviewed Mateo Antonio Lopez, GEP Virtual TA and biology student at Mount Saint Mary College, NY. 

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