This lab is the beginning of a 12-week project during which students will clone a gene from the ciliate Tetrahymena thermophila, fuse it to the gene encoding GFP, put the engineered gene back into Tetrahymena, and induce its expression. The gene will be cloned by PCR, so the first step is to design primers to allow the amplification of the desired gene. This lab will take students through the steps to do that, and will also demonstrate the use of other bioinformatics tools.

• Bioinformatics I
• Bioinformatics I - Instructor's Guide

This lab is the beginning of a 13-week project in which students will engineer a construct to knockout a gene from the ciliate Tetrahymena thermophila. The first step is to identify an appropriate gene homolog in Tetrahymena using the databases. Students will then design primers to amplify the gene by PCR and clone it into a plasmid vector.

• Bioinformatics II
• Bioinformatics II - Instructor's Guide

In this module, students assess the relative amount of expression of a gene of interest throughout different stages in the Tetrahymena life cycle. The life cycle is complex and involves a number of physiological changes and DNA processing events (see Tetrahymena Facts). Gene expression is evaluated through assessing the relative production of gene transcripts at different time points in the life cycle by reverse transcriptase PCR, yielding an "expression profile". (Estimated time: 5 x 4-hour laboratory periods.)

This module was developed by Douglas Chalker, Washington University, MO. Students engineer genetic constructs for the tagging and expression of a Tetrahymena protein of interest. Fluorescence microscopy is used to determine localization of the tagged protein. (Estimated time: 9 x 4 hour laboratory periods.)

In this module, students engineer genetic constructs to delete individual genes from the Tetrahymena genome. (Estimated time: 10 x 4 hour laboratory periods.)

The Student / Unpublished Results database (SUPRDB) provides a workspace where researchers can share unpublished experimental results with each other. Many of the results in the database are produced by student researchers, and the results are linked to the Tetrahymena Genome Database to enable sharing of the results with the larger Tetrahymena research community.

The Tetrahymena Genome Database (TGD) is a wiki for the Tetrahymena research community. It provides a BLAST service, GBrowse genome browsers, and information on Tetrahymena genes and proteins.

Developed by Dr. Mark Peterson, this module provides an overview of the different types of RNA-Seq data analyses. It describes how to assess the quality of RNA-Seq data with FastQC, trim adapters and low quality data with Trimmomatic, read mapping with RSEM, differential expression analysis with DESeq, variant detection with VarScan, and de novo assembly with Trinity.

CourseSource Publication

Peterson, M.P., Malloy, J.T., Buonaccorsi, V.P., and Marden, J.H. 2015. Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching. CourseSource. https://doi.org/10.24918/cs.2015.14

Developed by Dr. Vince Buonaccorsi at Juniata College, the GCAT-SEEK Eukaryotic Genomics Workshop Manual consists of seven chapters that cover genome assembly, gene annotations, and variant calling:

1. Genome assembly I: Quality control with FastQC and Trimmomatic
2. Genome assembly II: Assembly size estimation and k-mer graphs
3. Genome assembly III: Assembly algorithms
4. Genome annotation with Maker I: Overview and repeat finding
5. Genome annotation with Maker II: Whole genome analysis
6. Whole genome annotation: Miscellaneous methods
7. SNP calling and interpretation

CourseSource Publication

Buonaccorsi, V.P., Hamlin, D., Fowler, B., Sullivan, C., and Sickler, A. 2017. An Introduction to Eukaryotic Genome Analysis in Non-model Species for Undergraduates: A tutorial from the Genome Consortium for Active Teaching. CourseSource. https://doi.org/10.24918/cs.2017.1

by Melanie Frazier

Report on outcomes of NSF INCLUDES program. NSF INCLUDES (Inclusion across the Nation of Communities of Learners of Underrepresented Discoverers in Engineering and Science) is a comprehensive national initiative designed to enhance U.S. leadership in science, technology, engineering and mathematics (STEM) discoveries and innovations by focusing on diversity, inclusion and broadening participation in these fields at scale. The vision of NSF INCLUDES is to catalyze the STEM enterprise to collaboratively work for inclusive change, which will result in a STEM workforce that reflects the diversity of the Nation. 

A report summarizing a series of webinars and workshops to garner community input into pathways for keeping data science education broadly inclusive by bridging the digital and data divide among higher education institution types.

https://www.thermofisher.com/us/en/home/life-science/cell-analysis/cellular-imaging/high-content-screening/hca-q-and-a.html