Molecular Biology 480/580
Laboratory Schedule*
-Fall 2014-
*Note see: http://csmbio. for the complete course expectations.



Dr. Terrie Rife
Office Number: 3028D Biosciences
Phone Number:568-3343
Office Hours: T 3:30 - 4:30 p.m., WF 10:30-11:30 a.m.. and by appointment

Dr. Ray Enke
Office Number: 3016G Biosciences
Phone Number:568-5635
Office Hours: T Th 9:30-10:30 a.m., W 2:30-3:30 and by appointment

* The Best way to reach us is through email communication

Laboratory:  Section 1: Biosciences 3022; Monday - 1:25-5:15 p.m. (Rife) and Section 2: Biosciences 3022: Tuesday- 2:00 - 5:50 p.m. (Enke)
Section Numbers:
Lab Section 1 (#70036); Lab Section 2 (#70037)


Attendance - Reminder that Attendance in Lab is Mandatory- a 10% reduction in grade will be given for each lab day missed unless prior permisson from the instructor is obtained or documentation of an illness or family emergency is turned in within a timely fashion. Prompt arrival will also be expected from students. Failure to arrive to class on time may also result in a grade reduction of up to 2% of the overall lab grade for every 15 minutes that you are late for lab.

Time Expectations for Lab Work Outside of the Class - Molecular biological experiments often involve doing something quickly, and then waiting, and then do something else, thus, time will be required outside of the normal class time to finish several of the experiments. As often as possibe you wil be informed in advance of the expectations outside of class for a given weeks experiments.

Lab Safety - Students are required to wear close-toed shoes at all times in the lab and safety glasses when working on the bench with chemicals. Students should not work alone in the laboratory. Students must fill out a lab safety sheet which indicates their understanding of these and other JMU safety regulations.

Class Preperation - Starting the second week of lab, students are required to familiarize themselves with the protocols ahead of the lab period and to bring a copy of the protcol to lab. Familiar to come to class prepared means that your group will likely need to spend more than four hours in the research lab in order to complete the lab.

Lab Notebook - While lab notebooks will not be graded, maintainence of a quility lab notebook is strongly suggested as lab notebook information will be needed for both the lab take-home exam and lab reports. Suggestions for keeping a quality lab notebook can be found at

Learning Goals (Based on JMU Biology Learning Goals)

1. Formulate a hypothesis and identify relevant variables necessary to test that hypothesis.
2. Design and execute experiments to test hypothesis.
3. Obtain and organize Molecular data.
4. Analyze and interpret Molecular data.
5. Use effective professional communication in posters.
6. Use effective professional communication in oral reports.
7. Use mathematics to understand and analyze biological phenomena
8. Synthesize information and concepts, and apply that knowledge to new situations.
9. Experience working “at the bench” in a controlled environment.
10. Be able to perform several molecular techniques including microarray analysis, real time PCR, Western Blotting, protein, RNA and DNA isolation.


Grading (500 pts)

Date Scheduled

Western Blotting Lab Report

Monday, September 29/ Tuesday, September 30


Microarray Lab Report

Monday, November 17/ Tuesday, September 18


Real-Time Lab Report

Monday, December 5/ Tuesday, December 6


Lab Assignments

Throughout Semester (See Lab Schedule for due dates)


Lab Quizzes

September 15 and December 1



Lab Schedule and Protocol Links

Week of:
Procedures and
August 25


Lab Safety Form Link

The Basic Math of Solution Preparation

September 1

Protein Extraction and Quantification

Western Blot Proposal (15 pts)

Protein Isolation Protocol

September 8

Note: Lab requires time outside of lab, see lab procedure for details.

Western Blot

Western Blot Protocol

Western Report Guidelines

September 16

Note: This is a long lab and make go overtime.

Antibody Detection

Lab Quiz (25 pts)

Antibody Detection


Microarray Proposal Instructions*

September 22

RNA Isolation

Microarray Proposal (15 pts)

September 29

RNA Quality Check

Western Blotting Lab Report (100 pts)

RNA Isolation and Analysis

RNA Quality Guide

Ocober 6

cDNA Synthesis

Probe Construction

October 13

Note: Time out of class is required for this laboratory see lab procedure for details


Lab Participation Points (5 pts)



October 20


Microarray Analysis I - Gridding and Segmenting

Lab Journal Club (20 pts)

Excel Microarray Analysis (15 pts)

Please Print out copies of: Scanalyze Guide

Getting your data ready for R (Updated Feb. 3, 2012)

and before class please watch a video of how to use Scanalyze and a video of how to move your data from Scanalyze to Excel . These videos were put together by a now graduated class member, Lisa Brown for a microarray workshop held for faculty at JMU. Note that the second video refers specifically to arrays used at that workshop so the protocol is slightly different for your data but you will get a good idea of the basic steps that will be required of you this week from watching this video.

Useful Links for Class:

GCAT Information
Analyzing your Array Picture
Magic Tool Information

Ocober 27


Genomic Analysis II- Statistical Analysis and Begining Array Interpretation, RNA Seq Interpretation

Attendance at Statistics Lecture Date TBA (10 pts)

Google Doc on Microarray Analysis (15 pts)

Please Print a copy of the:

R Protocol by now graduated classmate Dallas Joder who put this program together for his Honors Thesis.


November 3


Genomic Analyisis III -Intermediate Array and RNAseq Analysis


November 10

Real-Time PCR Set-Up

RNA seq Results (30 pts)

Real Time PCR Protocol

Standard Curve for Realtime.doc (once you have set up your samples, we will work together as a class to set up a standard curve)

November 17

Real-Time PCR Analysis

Microarray Lab Report (120 pts)

Agarose Gel of Real time
November 24

No Lab- HappyThanksgiving!


December 2

Lab Wrap-Up

Final Quiz (50 pts)

Real-Time Lab Report (80 pts)

August 2014 - copyright (c)- T. Rife