Bio343: Laboratory Methods In Genomics
Spring, 2018
A. Malcolm Campbell
(he/him/his)


Tentative 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

Learning Goals

Learning Objectives

  1. Define terms used in RNA sequencing and assembly. (knowledge)
  2. Describe a gene 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 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 Down Syndrome. (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 three 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.

Because this is a research course, we will all 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 and Read Papers about CMT for class discussion
    • Charcot-Marie-Tooth (CMT) Disease

Week 2:
Jan 23 & 25

  • Find and Read Papers for class discussion
  • Find and Read CMT Papers for class discussion
  • Find and Read CMT Papers for class discussion

Week 3:
Jan 30 & Feb 1

  • Find and Read CMT Papers for class discussion
  • Find and Read CMT Papers for class discussion
Week 4:
Feb 6 &8

Start working with RNAseq data

What questions to ask? How to answer them?
ExAC Database with CNV and SNP data for humans
Week 5:
Feb 13 & 15

Continue working on RNAseq data 

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

Continue working on RNAseq data 

Continue working on RNAseq data

Week 7:
Feb 27 & Mar 1

Continue working on RNAseq data

Group oral Presentation #1 with peer review

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

null Week
Mar 6 & 8

Spring Break

Spring Break

Week 8:
Mar 13 & 15

Continue working on RNAseq data

Continue working on RNAseq data - finalize plans

Week 9:
Mar 20 & 22

Continue working on RNAseq data

Individual status report on RNAseq projects
graded by Dr. C.

Papers on: imprinted genes & ESC transcriptome
Week 10:
Mar 27 & 29

Continue working on RNAseq data

Continue working on RNAseq data
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 term research paper (solo author)

Week 13:
Apr 17 & 19

Work on Oral Presentation #2

Finalize Oral Presentation #2

Week 14:
Apr 24 & 26

Group oral Presentation #2 with peer review
(first 3 presentations)

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

Group oral Presentation #2 with peer review
(second 3 presentations)

  • 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

Grading
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

Biology Department


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Send comments, questions, and suggestions to: macampbell@davidson.edu