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20170715 PV92 Workshop at AZCTE

20170715 PV92 Workshop at AZCTE

Jul 08, 2017

Event Organizer

Molly Cohen (AZED)

CyVerse Trainers

Uwe Hilgert (BIO5)

TAs

Ken Feldman (UA), Nick Taylor (UA)

Date

July 15, 2017

Time

13:00-17:00 (mas o menos)

Location

Loews Ventana Resort

7000 N Resort Dr, Tucson, AZ 85750

Ventana Canyon-Salon L

Required Workshop Prep

1. CyVerse Account

  • Get your free account at http://user.iplantcollaborative.org. (Make sure to REMEMBER your username and password.) Please register with an institutional email account (e.g. '.edu', '.org', 'gov', 'K12').

2. Laptop

Please bring a WiFi enabled laptop to the workshop. Make sure your laptop has the following:

  • Internet Browser: Please have an up-to-date web browser (We strongly recommend Firefox or Safari - Internet Explorer and Chrome have been known to have compatibility issues.)

  • Flash Player and Adobe/Acrobat Reader

4. Pre-Workshop Guide and Homework

  • Download and print this manual to get the most out of the workshop.

  • Complete the Pre-Workshop Survey

Etherpad/Chatroom

We will use the following Etherpad for instant & shared communications during the workshop:  https://etherpad.mozilla.org/eYOfsFktUW

Instructional Materials

Materials are downloadable/accessible from the Resources column in the Workshop Agenda below.

Workshop Agenda

Time

Description

Objectives

Tools

Sources

Resources

Links

7:30

Doors Open / Sign-in / Set up

 

 

 

This workshop in 20 min. or less

Pre-Survey

08:00

Welcome - Self-Introductions

 

 

 

08:30

Overview

Relatedness By Descent

Mobile Genetic Elements (Transposons)

Polymorphism

Allele

 

 

08:45

Wet lab

  • isolate DNA

  • start PCR

Identify personal genotype at PV92 locus

  • Isolate and amplify DNA

MolBio lab equipment

  • Pipets

  • Centrifuge

  • Thermocycler

MolBio lab supplies

  • Chelex

  • Primers & nucleotides

  • Polymerase

  • N. Anderson @ UA

  • Carolina Biologicals

 

10:00

eLab

  • Part A

  • Part B

Identify PV92 locus in data bases

  • Identify and isolate PCR primer sequences

  • Conduct PCR electronically

  • Predict size of PCR amplicon

 

WWW

  • DNALC site

    • Recipes

  • NCBI site

    • BLAST

    • GenBank

 

10:45

Break

 

 

 

 

 

11:00

eLab

  • Part C

Examine PV92 locus in human genome

  • What chromosome is it on?

  • Is it in a gene?

WWW

  • NCBI site

    • Human Genome Viewer (Mapview)

    • BLAST

 

 

11:30

Wet lab

  • Load gel

Identify personal genotype at PV92 locus

  • Analyze amplified DNA

MolBio lab equipment

  • Gel electrophoresis equipment

  • N. Anderson @ UA

  • Carolina Biologicals

  • Invitrogen E-Gels

 

12:00

Lunch

 

 

 

 

 

01:00

Wet lab

  • Analyze gels

Identify personal genotype at PV92 locus

  • Analyze agarose gel

Understand population genetics

  • Hardy-Weinberg equilibrium

  • Genetic Drift versus Selective Pressure

  • Human Migration

MolBio lab equipment

  • Lightbox

WWW

  • Allele Server

  • Simulation Server

  • N. Anderson @ UA

  • Carolina Biologicals

  • IO Rodeo

01:15

eLab

  • Discover Frequencies

 

 

 

 

 

02:00

eLab

  • Part D

Identify and analyze all states of PV92 known to man

WWW

  • NCBI

    • BLAST

  • BioServers

    • SequenceServer

  • DNA Subway

    • Blue Line

    • MUSCLE

  • Mega

 

Human PV92 locus

 

Bioinformatics

05:00 m.o.m.

Dismissal

 

 

 

 

 

Consultations

Still questions?

 

 

 

 

Participants

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Logistics, Accommodations, and other details

Arrival Time

Please arrive at 7:45 AM to avoid delays to the workshop.