Manipulative Experiment

Week	Activity	Resources
1	Lab safety, Introduction to Microbiomes, Introduction to Bean Beetles, Pre-semester Survey	Introduction to microbiomes powerpoint Introduction to bean beetles powerpoint Instructor's notes on introduction to bean beetles Video tutorial on handling and sexing of bean beetles Suggested readings
2	Experimental Design and setup of experimental manipulation
3	Practice culturing of microbes with stock cultures	Instructor’s notes on preparing media & pouring plates Instructor’s notes on culturing microbial communities Student handout on culturing microbial communities [docx] [pdf] Video tutorial on surface sterilization of bean beetles Video tutorial on culturing microbial communities
4	Practice phenotypic assessment of microbes and Introduction to DNA Subway with practice data	Instructor’s notes on culturing microbial communities Student handout on culturing microbial communities [docx] [pdf] Instructor Cyverse Tutorial Student Cyverse Tutorial [docx] [pdf] DNA Subway Tutorial DNA Subway Video Tutorial
5	Introduction to community analysis of sequencing data with practice data	Studying microbiomes powerpoint BeanBeetleMicrobiome app Tutorial [docx] [pdf]
6	DNA extraction for microbial community sequencing	Instructor’s notes on DNA extraction Student handout on DNA extraction [docx] [pdf] Video tutorial on DNA extraction DNAeasy Blood & Tissue Insect Protocol DNAeasy Blood & Tissue Handbook
7	Iteration Day for failed DNA extractions and culturing microbes	Instructor’s notes on preparing media & pouring plates Instructor’s notes on culturing microbial communities Student handout on culturing microbial communities [docx] [pdf] Video tutorial on surface sterilization of bean beetles Video tutorial on culturing microbial communities
8	Phenotypic assessment of microbes & culture-based PCR of selected colonies	Instructor’s notes on culturing microbial communities Student handout on culturing microbial communities [docx] [pdf] Instructor’s notes on colony-based PCR Student handout on colony-based PCR [docx] [pdf] What is PCR? Polymerase Chain Reaction | miniPCR bio™ video Introduction of Sanger Sequencing video Video tutorial on colony-based PCR
9	Electrophoresis and Iteration Day for failed culture-based PCR	Instructor’s notes on electrophoresis Student handout on colony-based PCR [docx] [pdf] What is Gel Electrophoresis? | miniPCR bio™ video Video tutorial on gel electrophoresis
10	Introduction to bioinformatics & analysis of colony sequencing data	Student handout on BLAST analysis of sequencing data [docx] [pdf]
11	Introduction to community analysis, community analysis of phenotype and colony-based PCR data	Studying microbiomes powerpoint Student handout on community analysis of phenotype (class data) [docx] [pdf] Student handout on community analysis of phenotype (database data) [docx] [pdf] Student handout on community analysis of colony-based sequence (class data) [docx] [pdf] Student handout on community analysis of colony-based sequence (database data) [docx] [pdf] Instructor handout on community analysis
12	Analysis of microbial community sequencing data with DNA Subway	DNA Subway Tutorial DNA Subway Video Tutorial
13	Community analysis of sequencing data	BeanBeetleMicrobiome app Tutorial [docx] [pdf]
14	Final presentations, Post-semester survey