Systems analysis of Halobacterium NRC-1 responses to metal stress

The laboratory exercise is designed to introduce participants at all levels of experience in biology and computation (of course, with some basic intelligence) to one style of systems biology practiced at ISB. The overarching question being addressed here is "How do cells respond to copper stress?" We will take you through initial experiment design, laboratory culturing and sampling, RNA preparation, labeling, microarray hybridization, slide scanning, spot finding, raw data processing, data analysis with Gaggle, and hypothesis formulation and testing. It will be initially guided by prior biological knowledge and later become data-driven. The entire exercise represents a full iteration of systems analysis. Further, we have attempted to leave one extra day (Day 5) to explore other data analysis approaches using additional software tools and algorithms.

BioFlo 110 Modular Benchtop Fermentor (New Brunswick Scientific) (Fermentor will be setup in advance)

Halobacterium cells are grown in 1.5L of CM in batch format to mid log phase (OD ~ 0.6-0.7) using the fermentor.

The following parameters are kept constant:

At mid log phase, the culturing is shifted to continuous mode by pumping fresh media in and taking out spent media at same rate to keep culture volume at 1.5L

Protocol:

Gaggle Demo (time permitting)