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EGL Resources


Orientation

All new researchers in the lab should familiarize themselves with the following materials:

EGL pdf introduction (pdf): explains the rights and responsibilities of every lab user.

Guide to the supply sign-out/billing system (pdf)

Thermocycler policies (pdf)

3730 policies (pdf)

 

We are a large lab and we strive to minimize waste and find creative ways to reuse lab products.

Recycle:
The blue bins in all our lab rooms are for paper and cardboard only. Do not put plastics or glass into these bins. Bottle recycling bins are found in 4141.

Reduce energy consumption:
Turn off the lights in a room when you are the last to leave.
Turn off thermocyclers and heat blocks when they are no longer in use.

Sustainable Science initiative (pdf)

Extraction Protocol: Salt Extraction Protocol (M. MacManes)


Forms

3730 templates: Use the templates below to create a plate record for the 3730 for either sequencing or microsatellite runs. Pay careful attentions to the instructions to avoid the most common errors that prevent a plate record from being successfully imported.

Instructions (pdf)

Note: the template files will download as text files. You must open them through a spreadsheet program to edit them:

LongSeq: for runs when one or more samples are expected to have 700 bp or more of sequence data.

FastSeq: for runs when all samples are expected to have less than 700 bp of sequence data.

MSat: for all microsatellite runs.

 

Primers: You may use the primer template spreadsheet for all order requests. However, you must use it for any orders with non-standard conditions. (Standard conditions: unlabeled, synthesis scale = 25 nmoles, purification = desalted)

Invitrogen primer order request (xls)

 

Loans: All loans from the MVZ tissue collection, whether for internal or external researchers, are administered and approved by the MVZ staff and faculty cuartors. See the "Access and Loans" page for contact information and procedures. If you are a part of the MVZ community and would like to use the collection, use this form (doc) to prepare your in-house tissue loan request.


Manuals

Equipment manuals by room:

Cloning room:

Nanodrop spectrophotometer

Electroporator (Eppendorf 2810)

Extraction lab/pre-PCR:

Specialty pipettes: EDP plus electronic, Distriman manual repeater, Rainin E-man hybrid

Centrifuges: Eppendorf 5415D (24-place)

PCR/sequencing lab:

Thermocyclers: MJ PTC-100, MJ PTC-200, Bio-Rad iCycler, ABI 2720

3730: Chemistry Guide, Emergency Guide (i.e. what to do if the red light begins flashing)

Centrifuges: (refrigerated), Sigma 4K15C, Labconco Vacuum centrifuge

Specialty pipettes: EDP plus electronic, Distriman manual repeater, Rainin E-man hybrid

Software

Fragment Analysis
The EGL supports the use of GeneMapper 4.0 (PC only) for scoring microsatellite and other fragment data. It is installed on two lab computers: the PC in the extraction lab on the 4th floor and a PC in the Amphibia web area in the 3rd floor museum. GeneMapper use takes priority on these computers. There is currently no sign up for use of GeneMapper. Please work out any time conflicts among yourselves.

Resources for download:
GeneMapper: GeneMapper for Dummies (powerpoint guide to v. 3.7 by Tom Devitt), Quick Reference Guide (v 4.0), Microsatellite Analysis: Getting Started (v. 4.0), Reference and Troubleshooting Guide (v. 4.0), GeneMapper Software User Guide (v. 3.7)

Sequencing Analysis
The EGL supports three different software packages for the alignment and editing of sequencing files from the 3730. Please note though that currently there is limited intercompatibility between these programs. You should intend to complete your alignment and editing of a project on the software where you began it. Keep in mind too that all of these programs are licensed and the license availability to you may vary.

Sequencher (Mac and PC):
Where to get the software:
Any lab member may install the sequencher software (available from the lab manager; current version is 4.8), but sequencher requires a physical key to save or export data. Without a key, sequencher can still be used to view sequencing traces from the 3730 but edits cannot be saved.

Sequencher: Here is an overview of how to use Sequencher's basic alignment and editing functions. For more advanced applications, check out the tutorials on their website.

License access: The lab maintains four keys (2 Mac and 2 PC) for Sequencher 4.8 and up. Two of these are kept in the 3rd floor museum (mac key in the herp library, PC key in the Amphibia web corner) and two with the 4th floor computers. These may be taken for use on personal or other general use computers within the museum only according to the following rules:
— 3rd floor keys: May be borrowed at any time by lab researchers for use within MVZ property (i.e. the museum and the EGL) only. The key must be signed out on the sheet affixed to the host computer with your name and the room you will be using it in. Return the key immediately after you are done using it and sign it back in.
— 4th floor keys: Must remain with their host computer during museum business hours (M-F 8am - 5pm). These may be borrowed by lab researchers at night or over the weekend, but, again, they may not be taken from the MVZ under any circumstances. The key must be signed out on the sheet affixed to the host computer with your name and the room you will be using it in. Return the key immediately after you are finished editing and sign it back in.
Documentation: Here is an overview (pdf) of how to use Sequencher's basic alignment and editing functions. For more advanced applications, check out the tutorials on their website.

CodonCode Aligner (Mac and PC):
Where to get the software:
The current version of CodonCode Aligner (2.0.6) may be downloaded directly from their website. You receive a free 30-day trial license automatically with your download.
License access: The EGL maintains two networked licenses for CodonCode Aligner which allows concurrent use on two computers. Contact the lab manager for information on how to access the server. Please quit CodonCode Aligner as soon as you are finished editing so that the next person in the queue has access to the license.
Documentation: CodonCode Aligner manual (pdf). CodonCode also offers web-based tutorials for learning the software.

Genious Pro (Mac, PC, and Linux):
Where to get the software:
The current version of Genious (4.0) may be downloaded directly from their website. It comes with a free 14-day trial of Genious Pro, after which the software will maintain only the functionality of Genious Basic unless a license key is entered. (Comparison of Pro vs. Basic features.)
License access: The EGL maintains a single concurrent license for Genious Pro. Contact the lab manager to obtain the license code. Since only one computer may use the Pro features of this program at any given time, please quit the program or revert to the Basic mode as soon as you are finished editing.
Documentation: Geneious manual (pdf). Video demos are also available on their website.


Product Inserts

Product inserts for lab reagents (all pdfs)

Extraction kits:
Qiagen DNeasy blood and tissue kit
PureGene extraction kit

Taq polymerase:
ABI Amplitaq Gold
Invitrogen
NEB
Roche
Sigma Jumpstart Accutaq
Sigma Jumpstart

Gel Visualization:
GelStar

PCR clean-up:
ExoSAP-IT
GelASE
QiaQuick gel extraction spin column

3730 Genetic analysis:
Big Dye v. 3.1
Liz-500

Cloning kits:
Invitrogen TA kit
Invitrogen Topo TA kit

Primer design:

Primer 3

OligoAnalyzer


PCR Troubleshooting:

Sequencing: Troubleshooting advice and help for identifying and improving failed DNA sequencing reactions

Failed DNA Sequencing Reactions

Troubleshooting - Eton Bioscience Inc.

Online Sequence Trouble-shooting Guide

Roswell Park Cancer Institute - Troubleshooting Your Data

ABRF : DNA Sequencing Troubleshooting Resource

UT Austin: Sequencing Troubleshooting

Eurofins DNA Sequencing Trouble Shooting Guide

Iowa State University DNA Facility - DNA Sequencing Troubleshooting Guide

University of Hawaii: Sequencing Troubleshooting Guide

McMaster University: Troubleshooting

Geneservice Ltd - DNA Sequencing Service

Amplicon Express DNA Sequencing Troubleshooting


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