USF Genomics

USF Genomics Program Training

The USF Genomics Program offers three of training workshops, the RNA-seq Illumina Sequencing Laboratory Workshop, the RNA-seq Data Analysis Computational Workshop, and the Microbiome Analysis Training. The RNA-seq workshops are offered three times a year in February, May, and September. The first Microbiome Analysis Training will be offered in November 2019. These workshops are open to all in the USF community. The RNA-seq Illumnia Sequencing Laboratory Workshop is required for access to use the USF Genomics Equipment Core (more information here).


  • RNA-seq Illumina Sequencing Laboratory Workshop

    Goal

    This 5-day intensive hands-on training to enables participants to confidently prepare high-quality sample libraries for sequencing.

    Description

    This training course includes presentations on technology theory and practical experience with entire laboratory sample prep workflow. Experienced trainers will lead you through using TapeStation and Miseq equipment. By the end of this training, you will be able to: complete Illumina library preparation process and  set up a sequencing run using Illumina Miseq Control Software.


    Participant Requirements

    • To maximize effectiveness, this training is limited to 6 participants at a time.  
    • A basic knowledge of biochemistry and molecular biology and familiarity with laboratory equipment usage are pre-requisites.  
    • Participants will need to bring your own micropipettes (10µl, 200µl and 1000µl) 
    • Participants may use this to test their own experimental samples, each      participant can prep two samples.sequence analysis or command line experience are not required. 


    Workshop Structure:

    Day 1 Morning (Monday): Illumina sequencing technology introduction (open to non-registered participants)
    Day 1 Afternoon (Monday): Illumina sequencing technology overview and RNA sample prep
    Day 3 (Tuesday): Library Prep (1) - mRNA purification, 1st, 2nd strand cDNA synthesis
    Day 4 (Wednesday): Libarary Prep (2) - A-Tailing, ligation, PCR amplification, Beads purification
    Day 5 (Thursday): qPCR quantification, Normalize & pool, Set up Miseq run, Base-Space
  • RNA-seq Data Analysis Computational Workshop

    Goal

    This 5-day in-depth course will instruct participants on the theoretical and practical concepts related to RNA sequencing analysis, enabling them to perform these analyses independently.


    Description

    The first workshop module is an introduction to data analysis using Linux, assuring that all participants are able to follow the practical parts. The second module discusses advantages and disadvantages of current sequencing technologies and their implications on data analysis. The third module introduces preprocessing raw reads, read mapping, visualization of mapped reads and one proceeds with first hands-on analyses (QC, mapping, visualization). The fourth module introduces ‘R’ a programming language to perform statistical computing  and visualization, and ‘Bioconductor’ an R based toolshed for analyzing genomic data. The last module addresses quantification of gene expression and predict differentially expressed genes, followed by a whole day hands-on RNA-Seq analysis pipeline: TUXEDO protocol.


    Participant Requirements

    • Admittance to the course is limited to 10 participants.
    • A basic knowledge of biochemistry and molecular biology, a basic familiarity with computer usage and a need for RNA sequence analysis for current ongoing research are recommended pre-requisites.
    • Participants will be required to complete an online module prior to workshop.
    • Participants will need to have their own laptop to access the USF research Computing  infrastructure for hands-on sessions.
    • Prior sequence analysis or command line experience are not required. 


    Workshop Structure

    Day 1 (Monday Morning): Illumina Sequencing Introduction & Computer and Software Check (open to non-registered participants)

    Day 2 (Friday): Illumina Sequencing Refresher & Linux for Bioinformatics

    Day 3 (Monday): Introduction to RNA sequencing & RNA-seq Alignment and Visualization

    Day 4 (Tuesday): Introduction to R and Bioconductor & Expression and Differential Expression

    Day 5 (Wednesday): RNA-seq - TUXEDO Pipeline Hands-on Workshop Structure

  • RNA-seq Workshop Registration

    Click here for Online Registration 

    If you have questions regarding the USF Genomics Workshops, email genomics@health.usf.edu. 

    Due to enrollment caps, there is a waitlist for the USF Genomics Workshops. You will be contacted after registering about the next available workshop.

  • Microbiome Analysis Training

    Goal

    This 3-Day in-depth course will instruct participants on theoretical and practical concepts related to microbiome sequencing analysis, enabling them to perform these analyses independently. 

     

    Topics Covered

    • Microbiome: A rapidly-evolving field driving emerging analytic technologies: Overview of marker-sequencing (16S, 18S, & ITS)
    • Best-practices in microbiome experimental design from the bench to the computer: How many samples do I need? Which technology is best to answer my biological question?
    • Brief introduction to R for microbiome data-analysisHands-on 16S rRNA data-analysis using DADA2 (R Package)
    • Visualizing data with the R Microbiome-package

     

    Workshop Structure

    Day 1: Introduction to Microbiome Data Analysis and Introduction to R and Data-Plotting

    Day 2: Metataxonomic analysis Experimental Design and Metataxonomic analysis OTU/ASV Generation

    Day 3: Metataxonomic analysis Visualization

     

    Participant Requirements

    A basic knowledge of biochemistry and molecular biology, a basic familiarity with computer usage, and a need for microbiome sequence analysis for current ongoing research projects are recommended prerequisites.

    Participants should bring laptops with a minimum of the following configuration: Mac - OS X 10.12 (64-bit) or Windows - 7 (64-bit)

     

  • Microbiome Analysis Training Registration

    The first Microbiome Analysis Training will be held on November 6-8, 2019 (Wednesday-Friday).

    The deadline for the November 2019 training is October 24, 2019. Admittance to the course is limited and requires registration.

    Click here for Online Registration

    Questions regarding the USF Genomics Training can be sent to genomics@usf.edu