Advanced Genetics and Epigenetics Laboratory
Pablo Jenik1*, Thai Dao1†.
Affiliations:
1
Franklin and Marshall College, Department of Biology.
*Correspondence to: Pablo Jenik, 415 Harrisburg Ave, Lancaster, PA, 17603, pjenik@fandm.edu
† Undergraduate student
Type of Manuscript: CourseSource Lesson Manuscript
Funding & Conflict of Interest Statement: Deparment of Biology, Franklin and Marshall College.
List of Tables, Figures and Supplemental Material: N/A
Title and Description of Primary Image: N/A
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conditions IN WHICH THE LESSON WAS
TAUGHT. Modifications to expand the usability of
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Course
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Lesson Length
o Portion of one class period
o One class period
o Multiple class periods
 One term (semester or quarter)
o One year
o Other
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Key Scientific Process Skills
o Reading research papers
 Reviewing prior research
 Asking a question
 Formulating hypotheses
 Designing/conducting experiments
 Predicting outcomes
 Gathering data/making
observations
 Analyzing data
 Interpreting results/data
 Displaying/modeling results/data
 Communicating results
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Pedagogical Approaches
o Think-Pair-Share
o Brainstorming
o Case Study
o Clicker Question
 Collaborative Work
o One Minute Paper
o Reflective Writing
o Concept Maps
o Strip Sequence
o Computer Model
o Physical Model
 Interactive Lecture
o Pre/Post Questions
o Other
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Bloom’s Cognitive Level (based on
learning objectives & assessments)
o Foundational: factual knowledge &
comprehension
 Application & Analysis
 Synthesis/Evaluation/Creation
Biochemistry
Cell Biology
Developmental Biology
Genetics
Microbiology
Molecular Biology
Introductory Biology
Course Level
o Introductory
 Upper Level
o Graduate
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Class Type
o Lecture
 Lab
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Audience
 Life Sciences Major
o Non-Life Science Major
o Non-Traditional Student
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 4-year College
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Class Size
 1 – 50
o 51 – 100
o 101+
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Principles of how people learn
 Motivates student to learn material
 Focuses student on the material to
be learned
 Develops supportive community of
learners
o Leverages differences among
learners
o Reveals prior knowledge
 Requires student to do the bulk of
the work
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Vision and Change Core Concepts
o Evolution
o Structure and Function
 Information flow, exchange and
storage
o Pathways and transformations of
energy and matter
o Systems
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Vision and Change Core Competencies
 Ability to apply the process of
science
 Ability to use quantitative
reasoning
o Ability to use modeling and
simulation
o Ability to tap into the
interdisciplinary nature of science
o Ability to communicate and
collaborate with other disciplines
o Ability to understand the
relationship between science and
society
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Key Words: List 3 – 10 key words that are
relevant for the Lesson (e.g. mitosis;
meiosis; reproduction; egg; etc.)
o Gene expression
o Transcription factor
o Mutants
o Next generation sequencing
o RStudio
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Scientific Teaching Context Page
Learning Goal(s):
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Students will understand the value of next generation sequencing to analyze gene expression.
Students will appreciate the multiple effects of a single mutation on gene expression.
Learning Objective(s):
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Perform the lab techniques related to purification and manipulation of RNA.
Use computational tools (such as R) to process next generation sequencing data.
Make biological sense of the list of differentially expressed genes.
Design follow-up experiments based on the results of the sequencing data and literature research.
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Main Text
1. Introduction:
This lesson is intended for the lab portion of an upper level Genetics course (Advanced Genetics and Epigenetics).
One of the main topics of the course is the regulation of gene expression by transcription factors and chromatin
modification, and the techniques used to understand these processes. One of the primary tools is the characterization
of organisms mutant for a gene of interest (e.g. a transcription factor). One of the most important pieces of data is
the study of how gene expression changes in the mutant, and how those changes can be used to understand the
mutant phenotypes and the roles of the gene of interest in the development or physiology of the organism in
question. In this lesson we want students to explore the changes in gene expression in Arabidopsis seedlings caused
by mutations in a transcription factor, using RNAseq as the primary tool. We also want students to relate those
changes to phenotypes by a more in-depth exploration of a selected subset of misexpressed genes.
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Intended Audience: Upper level students (juniors and seniors) majoring in biology or
biochemistry.
Learning time: 4 hours/week for 12 weeks.
Pre-requisite student knowledge: Have taken the core genetics class and having basic
knowledge of the regulation of gene expression, including transcription. Have basic
understanding of biostatistics. Have familiarity with reading primary literature. Have basic
molecular biology lab skills.
2. Scientific Teaching Themes:
 Active Learning: Students will perform lab work in pairs. Introduction to bioinformatics
tools and practice analysis will be performed in groups so that students can learn from one
another. Subsequent analysis will be done individually but in consultation with other students.
Finally, each student will also choose their own set of differentially expressed genes, and
write a short grant proposal on those genes with extensive feedback from the instructor.
 Assessment: Quizzes on fundamental lab techniques/procedures and the reasoning behind
them will be held throughout the semester. Students will also be asked to write a short paper
presenting their literature research and experimental design to study genes that are expressed
differently between wild type and mutant plants.
 Inclusive Teaching: The lesson incorporates mostly hands-on activities, both lab and
computer-based. There is also a short lecture component in each class, and a significant
amount of written expression. The lesson, therefore, includes different learning modalities.
3. Lesson Plan:
 Growth of wild-type and mutant Arabidopsis seedlings on petri dishes.
 Total RNA extraction using a modified RNeasy plant mini kit.
 Poly-A enrichment using magnetic beads, and RNA fragmentation.
 Reverse transcription and generation of cDNA library to be sequenced.
 Tutorial to bioinformatics tool.
 Practice analysis using a small sequencing data set.
 Full analysis of their own data set: generation of list of differentially expressed genes, GO
term enrichment, clustering, other downstream analyses.
 Selection and validation
(by qRT-PCR) of a small subset of misregulated genes.
 Exploration of the primary literature related to the genes of interest and design of possible
follow-up experiments.
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Week
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3-4
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6-7
8-9
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Activities
Growing seedlings on agarose plates
RNA purification
Reverse transcription and generating library
Introduction to R
Practice RNA analysis on R using a small data set
Analysis of differential expression of sequenced library
Explore selected genes, researching literature
qRT-PCR to validate differential expression
Peer review of paper assignment
4. Teaching Discussion: N/A.
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