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- Created 18 Aug 2017
NIBLSE Incubator: CpG Islands
Overview
Bioinformatics: CpG Islands
This is an introductory activity used in a sophomore level medium sized genetics course (50 students). The activity is introduced in class but the majority of the work is completed independently, outside of class. Students chose a eukaryotic organism and download all 5kb upstream sequences from the UCSC genome browser database. Students then use free on-line CpG island search tools to analyze a sub set of those sequences for CpG islands. Student have to use their ingenuity to design a figure that displays the frequency and location of CpG islands for the genes they analyzed.
Incubator Details
Statement from the author (Edward Himelblau):
The author identified the following areas of focus during the Incubator:
- Review the technical and scientific content of the activity
- Get feedback from other teachers on how to improve the activity for different student audiences
- Clarifying the learning outcomes and working on assessments that address those goals
- Develop a grading rubric for the activity
Statement from the managing editor (Sam Donovan):
This exercise has a couple of really nice features including giving students choices about which organisms to study, which genes to analyze, and how to represent their findings. With a little work it can be a broadly useful introduction to accessing genomic data, using online analysis tools, and comparing different patterns of CpG island distribution.
I recommend that the Incubator group consider:
- providing a bit more background for teachers who don't have much bioinformatics experience
- connecting the introduction and analysis of CpG islands to biological implications
- identifying different ways that this protocol could be extended to address a variety of learning outcomes
Incubator start and end times:
December 20, 2017 to February 16, 2018.
QUBES Liaison: Hayley Orndorf
Licensing Information
All NIBLSE Incubators are under Creative Commons licensing. The default license for Incubators is the Attribution-ShareAlike 4.0 International license. This license allows for sharing of adaptations of the work, as longs as all adaptations are shared alike. It also allows for commercial use of the work. Learn more at the Creative Commons website.
Authorship Information
During the Learning Resource Incubator process a small group of faculty work on improving and supporting the use of existing bioinformatics lessons. Prior to the start of the incubator, the author addresses their expectations around participant authorship. Below are the author's expectations around contributions and authorship.
- Contributions to the teaching resource:
- I plan to list each of the incubator personnel who actively participate as contributors.
- Authorship of the primary teaching resource:
- I plan to include incubator participants who make a significant intellectual contribution to the primary teaching resource as a co-author.
- Authorship of derivative or customized materials:
- I plan to support others if they are interested in customizing these materials for use in other course contexts or with other student audiences.