Bio343: Laboratory Methods In Genomics
Spring, 2018
A. Malcolm Campbell

Working Syllabus

Class meets T/R 9:40 - 10:55 pm in Wall B05
Office Hours: M 11-noon; T 3 - 4 pm; or most anytime by appointment

The college welcomes requests for accommodations related to disability and will grant those that are determined to be reasonable and maintain the integrity of a program or curriculum. To make such a request or to begin a conversation about a possible request, please contact the Office of Academic Access and Disability Resources, which is located in the Center for Teaching and Learning in the E.H. Little Library: Beth Bleil, Director, 704-894-2129; or Alysen Beaty, Assistant Director, 704-894-2939.  It is best to submit accommodation requests within the drop/add period; however, requests can be made at any time in the semester.  Please keep in mind that accommodations are not retroactive.

Learning Goals

Learning Objectives

  1. Define terms used in RNA sequencing and assembly. (knowledge)
  2. Describe what a gene is based on in-depth analysis of a genome. (comprehension)
  3. Report your findings to the class verbally and to a wider audience in writing. (comprehension)
  4. Explain how transcriptomes reveal which parts of the genome are activated. (comprehension)
  5. Demonstrate computer skills that are used in modern genomics. (application)
  6. Examine different signaling pathways that lead to cell and tissue growth. (analysis)
  7. Test whether a known pathway is activated in experimental tissue compared to control. (analysis)
  8. Collect and integrate published data with RNAseq data to describe Charcot-Marie-Tooth type 2 disease. (synthesis)
  9. Evaluate data quality and completeness of signaling pathway activation. (evaluation)
  10. Assess the objectivity and subjectivity used in genomic research. (evaluation)

Bio343 is a lab-only course that is primarily data analysis by computer. I am very excited about this course for two main reasons.

  1. We will be working on an inherently interesting question - Charcot-Marie-Tooth (CMT) type 2D disease. We will be looking at the transcriptome of mouse spinal chord. In particular, we will be looking at two different populations of mRNAs. One population will come from wild-type mice and the other will come from CMT mice.
  2. We are also collaborating with Drs. Charlie Wray and Jeff Chuang Jackson Laboratory in Bar Harbor, ME. We are part of an educational pilot experiment to see if it is feasible to offer research experiences to a national network of undergraduates using RNAseq data to answer legitimate research questions. Very few students in the world get to answer an interesting biological question using RNAseq data and you are among the few who will get this experience.

The mouse strain we are working with is called GarsP278KY and it was generated in a ENU mutagenesis project. You can read more at the MGI entry for this allele. The RNAseq was set up as 3 males and 3 females, with both wildtype and mutant animals, so 12 animals in all.  After cervical dislocation, the spinal cords were removed and flash frozen prior to RNA extraction and subsequent library construction. Emily S. is the graduate student working on this animal and CMT2D. More details here.

Because this is a research course, all of us  have to be flexible in the material we learn. It is impossible to know where this course will take us exactly. I have a rough plan, but nothing firm yet until we see how these projects unfold. If you need a highly structured course, this will not be a good fit for you. Each student will need to learn how to edit a wiki site used for this research project.

Student Collaborators

Required Readings

1) Online web sites

2) Research publications on genomes (PDFs gathered during semester)

3) Course wiki site

Tentative Weekly Schedule

Week of Semester
Subject Matter and Assignments Due
Week 1:
Jan 16 & 18
  • Find information about CMT for class discussion
    • Charcot-Marie-Tooth (CMT) type 2 Disease

Week 2:
Jan 23 & 25

Week 3:
Jan 30 & Feb 1

Week 4:
Feb 6 &8

Start working with RNAseq data

  • start with wiki assignment to understand what was done
  • open new history (Bio343 HTSeq Results)
  • do synchronized DESeq2 to confirm process.
What questions to ask? How to answer them?
Week 5:
Feb 13 & 15

Continue working on RNAseq data (Dr. C. out of town, reviewing a Dept.)

Continue working on RNAseq data 
Week 6:
Feb 20 & 22

Continue working on RNAseq data + quick Zotero lesson

Continue working on RNAseq data, start methods & results
Week 7:
Feb 27 & Mar 1
  • Bring hard copy to lab of first draft paper (not graded)
  • exchange papers for peer review
  • submit peer review to Dr. C. graded by Dr. C.
  • Dr. C. distributes comments for revision
  • Finalize first "half-term" paper - Dr. C. available for question
  • email "half-term" paper by 5 pm March 2 graded by Dr. C.

null Week
Mar 6 & 8

Spring Break

Spring Break

Week 8:
Mar 13 & 15

Start new project:
wet lab exploration of worms
read NR5A1 paper

finish NR5A1 paper
NR5A2 paper
experimental design (PPT)
import data on Galaxy
(see wiki for sample ID)

Week 9:
Mar 20 & 22

DESeq2 & GOrilla

Continue working on RNAseq data
Week 10:
Mar 27 & 29

learn some worm resources
continue working on RNAseq data

solo status report of paired research project  graded by Dr. C.
Week 11:
Apr 3 & 5

Easter Break

continue working on RNAseq data

Week 12:
Apr 10 & 12

continue working on RNAseq data

assess Status and Agree on Endgame
start working on "half-term" research paper #2 (solo author)

Week 13:
Apr 17 & 19

work on group oral presentation

finalize group oral presentation

Week 14:
Apr 24 & 26

Group oral Presentation with peer review
(Vivienne + Owen; Itzy and Jonah)

  • peer feedback is graded by Dr. C.
  • presentation is graded by Dr. C.

Group oral Presentation with peer review
(Stephanie; Ky + Jenna + Aiko; Malcolm; Debbie)

  • peer feedback is graded by Dr. C.
  • presentation is graded by Dr. C.
Week 15:
May 1, 3 & 8

submit hard copy draft for peer-review during class

fellowships presentation
course evaluations
Final paper due (as Word file) emailed by noon on Reading Day

No Class Optional Tuesday
Final paper due (as Word file) emailed by noon on Reading Day

Grades will be based on:

The exact nature of the presentations and papers cannot be determined at this point. You will use the course wiki page as an online lab notebook to track your daily progress. Keep in mind that your work will be the foundation that investigators will use for subsequent research so it is important to keep good notes online.

Grading Scale:

Conversion of Percentage to Letter Grade

A = 100 - 94 A- = 93 - 90
B+ = 89 - 87 B = 86 - 83 B- = 82 - 80
C+ = 79 - 77 C = 76 - 73 C - = 72 - 70
D+ = 69 - 66 D = 65 - 60

F = < 59

Genomics Lecture Course

Genomics Minor

Genomics & Bioinformatics Majors

Biology Department

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