Transformation of a teaching module to enable a deeper understanding of NGS technologies

Author: sla

Created: 2020-02-17 08:52am

Edited: 2020-02-18 07:12pm

Description:

The purpose of this learning design is to transform an existing quite heavy and passive module consisting of a lecture and an exercise about NGS (Next Generation Sequencing) technologies and their usage to study RNA into a much more active, almost-hands-on learning experience. The course is 10 ECTS and dealing with the most recent advances in the field of RNA molecular biology. Most contemporary scientific articles concerning RNA contain some variant of an NGS experiment, and thus it is necessary to conduct a crash course on NGS at an early stage.

To facilitate active learning, the design is based on the STREAM model (Godsk, 2013). The design is build up as follows:
(1) Most curriculum acquisition takes place out of class before the lecture by reading review articles and watching videos supported by various activities including multiple choice quizzes on Blackboard.
(2) The classroom session falls in three parts: First, there is a short classical lecture including a thorough follow-up on the aforementioned quizzes. Next, there are group discussions related to a specific set of questions and finally the session is wrapped up by the groups producing a ‘pencast' that describes a widely used procedure for RNA sample preparation for NGS.
(3) After the lecture, there is a brief follow-up on the pencasts, and, subsequently, submission of group assignments that are first evaluated by peers and since by the lecturer.

The original module is organised as follows:
(1) Lecture incl. Q&A session 2x45min
(2) Theoretical exercises 2x45 min
(3) Student presentation 1x45 min

According to the SAMR model, which is embedded in STREAM, the re-design leads to a modification of the module. In the transformed version, lecture and theoretical exercises are merged into one module as presented here, whereas the student presentation is kept as is. The total in- and out-of-class workload is similar between the traditional and transformed designs.

Intended Learning Outcomes:

Describe and explain the underlying technologies behind the three main NGS platforms (SOLO taxonomy level 3)
Design a strategy for construction of a DNA library, based on RNA as the starting material, that is compatible with sequencing on the Illumina NGS platform(s) (SOLO taxonomy level 4)
Design and discuss an RNA enrichment strategy based on the most common physico-chemical features of various RNA types (SOLO taxonomy level 5)

Resources		Tasks		Supports
(A) Out-of-Class (before lecture)
Review about topic	→	(A.1) Read review and get superficially acquainted with topic before pre-class videos and exercises (30 min to 2 hrs) ↓
Videos from three main NGS platform manufacturers	→	(A.2) Watch videos and compare the three main NGS platforms by filling out a table on Blackboard (approximately 30 min) ↓	←	Blackboard: Support forum (primarily peer-to-peer at this stage)
Explain-Everything video about NGS library preparation and enrichment of RNA samples for NGS	→	(A.3) Watch videos and answer multiple choice quizzes on Blackboard about NGS library preparation and enrichment of RNA samples for NGS (approximately 30 min) ↓

(B) In-Class (3x45 min)
Summarised data from platform comparisons and multiple choice quizzes (tasks A.2 and A.3 from out-of-class before lecture)		(B.1) Listen to lecture and participate in discussion (approximately 10+20 min) ↓	←	Lecturer briefly introduces the topic and the reasoning for teaching it at this stage and level Lecturer presents and moderates a discussion of comparison of platforms and answers from multiple choice quizzes (tasks A.2 and A.3 from out-of-class before lecture)
Set of questions on Blackboard		(B.2) Work in groups (4-6 people/group): Answer a set of questions related to topic Submit answers online (approximately 60 min) ↓	←	After on-line submission of the answer for each question, the lecturer's suggested answer will be made available on-line Lecturer is present and willing to discuss and explain
Excerpt from review describing the most widely used NGS library preparation protocol Magic pens??		(B.3) Work in groups (4-6 people/group): Submit a 5 min pencast illustrating and explaining the details of selected steps in a widely used NGS sample preparation protocol (approximately 45 min) ↓	←	Lecturer present and can help with production of a pencast
(C) Out-of-Class (after lecture)
All material from (A) and (B) and own notes		(C.1) Watch lecturer's pencast and read comments to your own pencast (approximately 30 min) ↓	←	Blackboard: Lecturer submits a version of the corresponding pencast (task B.3) and comments on submitted versions
		(C.2) Work in groups (4-6 people/group): Each group gets one unique assignment to suggest a procedure consisting of less then 10 steps to enrich for and sequence a specific type of RNA. Procedure submitted online. (approximately 2x30 min)	←	Blackboard: Peer-to-peer reviewing over 2 days followed by review by lecturer Lecturer summarises the suggestions and reviews in a round-up letter

Additional information

Reference:

Godsk, M. (2013). STREAM: a Flexible Model for Transforming Higher Science Education into Blended and Online Learning. In T. Bastiaens & G. Marks (eds.), Proceedings of World Conference on E-Learning in Corporate, Government, Healthcare, and Higher Education 2013, (pp. 722-728). Chesapeake, VA: AACE.