Bio343: Laboratory Methods In Genomics
Spring, 2017
A. Malcolm Campbell


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 - Down Syndrome. We will be looking at the transcriptome of mouse embryonic stem cells (ES) that have an extra copy of the mouse ortholog of chromosome #21 which causes Down Syndrome. In particualr, we will be looking at two different populations of cells. One population will have the father's extra copy of "chromosome #21". The other popuation wil have the mother's extra chromosome. Will we see any differences in the transcriptomes of these two different sources of ES?
  2. We will be collaborating with a class from Colby College in Maine; Dr. Andrea Tilden will be offering a parallel course for her students. We will benefit from collaborating with her students as we conduct our research because both classes will exchange information that could be of interest to everyone. This collaboration mirrors modern research in the post-genomics era.
  3. We are also collaborating with Drs. Charlie Wray and Laura Reinholdt at 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 legitmate 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 17 & 19

Week 2:
Jan 24 & 26

  • Find and Read ES Papers for class discussion
  • Find and Read Down Syndrome Papers for class discussion

Week 3:
Jan 31 & Feb 2

  • Find and Read ES Papers for class discussion
  • Find and Read Down Syndrome Papers for class discussion
Week 4:
Feb 7 &9

Start working with RNAseq data

Name Genotype
CB122_P8_TM Trisomic_maternal
CB121_P8_TM Trisomic_maternal
CB125_P8_TM Trisomic_maternal
CB117_P8_M maternal
CB126_P8_M maternal
CB131_P8_M maternal
CB087_P8_P paternal
CB089_P9_P paternal
CB091_P9_P paternal
CB093_P8_TP Trisomic_paternal
CB100_P9_TP Trisomic_paternal
CB103_P8_TP Trisomic_paternal

What questions to ask? How to answer them?
ExAC Database with CNV and SNP data for humans
Week 5:
Feb 14 & 16

Continue working on RNAseq data 

Continue working on RNAseq data 
Week 6:
Feb 21 & 23

Continue working on RNAseq data 

Continue working on RNAseq data

Week 7:
Feb 28 & Mar 2

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 7 & 9

Spring Break

Spring Break

Week 8:
Mar 14 & 16

Continue working on RNAseq data

Continue working on RNAseq data - finalize plans

Week 9:
Mar 21 & 23

Continue working on RNAseq data

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

Papers on: imprinted genes & ESC transcriptome
Week 10:
Mar 28 & 30

Continue working on RNAseq data

Continue working on RNAseq data
Week 11:
Apr 4
& 6

Continue working on RNAseq data

Continue working on RNAseq data

Week 12:
Apr 11 & 13

Continue working on RNAseq data

Assess Status and Agree on Endgame
start working on term research paper (solo author)

Week 13:
Apr 18 & 20

Easter Break

Finalize Oral Presentation #2

Week 14:
Apr 25 & 27

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 2 & 4 & 9

Keep working on term paper

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


© Copyright 2017 Department of Biology, Davidson College, Davidson, NC 28035
Send comments, questions, and suggestions to: macampbell@davidson.edu