Experimental Methods in Systems Biology

Icahn School of Medicine at Mount Sinai

Learn about the technologies underlying experimentation used in systems biology, with particular focus on RNA sequencing, mass spec-based proteomics, flow/mass cytometry and live-cell imaging.

A key driver of the systems biology field is the technology allowing us to delve deeper and wider into how cells respond to experimental perturbations. This in turns allows us to build more detailed quantitative models of cellular function, which can give important insight into applications ranging from biotechnology to human disease. This course gives a broad overview of a variety of current experimental techniques used in modern systems biology, with focus on obtaining the quantitative data needed for computational modeling purposes in downstream analyses. We dive deeply into four technologies in particular, mRNA sequencing, mass spectrometry-based proteomics, flow/mass cytometry, and live-cell imaging. These techniques are often used in systems biology and range from genome-wide coverage to single molecule coverage, millions of cells to single cells, and single time points to frequently sampled time courses. We present not only the theoretical background upon which these technologies work, but also enter real wet lab environments to provide instruction on how these techniques are performed in practice, and how resultant data are analyzed for quality and content. 

Syllabus

Week 1:  Introduction (5 ~20 min presentations)

1.      Scope and Overview

2.      Biological Model Systems

3.      Experimental Perturbations

4.      Measuring Nucleic Acids

5.      Measuring Protein and Protein States

Week 2:  Deep mRNA Sequencing (4 ~20 min presentations)

1.      Underlying Principles

2.      Sample Preparation

3.      Data Acquisition

4.      Data Analysis

Week 3:  Mass Spectrometry-Based Proteomics (4 ~20 min presentations)

1.      Underlying Principles

2.      Sample Preparation

3.      Data Acquisition

4.      Data Analysis

Week 4:  Mid-term Exam

Week 5:  Flow and Mass Cytometry for Single Cell Protein Levels and Cell Fate (4 ~20 min presentations)

1.      Underlying Principles

2.      Sample Preparation

3.      Data Acquisition

4.      Data Analysis

Week 6:  Live-cell Imaging for Single Cell Protein Dynamics (4 ~20 min presentations)

1.      Underlying Principles

2.      Sample Preparation

3.      Data Acquisition

4.      Data Analysis

Week 7a:  Integrating and Interpreting Datasets with Network Models and Dynamical Models (2 ~20 min presentations)

1.      What are Network and Dynamical Models?

2.      Why Network and Dynamical Models?

Week 7b:  Overview and Conclusions (2 ~20 min presentations)

Week 8:  Final Exam

Recommended Background

Freshman or sophomore level cell biology, chemistry, biochemistry, and basic statistics.

Suggested Readings

Review articles and selected original research articles are discussed in the lectures. A set of review articles will be required reading. Reading primary articles is not required to complete the course, but can be quite useful. All materials will be from open access journals or will be provided as links to e-reprints, so there will be no cost to the student.

Course Format

Each class session will consist of video lectures, divided into multiple shorter segments. For evaluation, students will be given a mid-term exam and a final exam.

FAQ

  • Will I get a Statement of Accomplishment after completing this class?

    Yes. Students who successfully complete the class will receive a Statement of Accomplishment signed by the Course Director.

Dates:
  • 27 October 2014, 8 weeks
Course properties:
  • Free:
  • Paid:
  • Certificate:
  • MOOC:
  • Video:
  • Audio:
  • Email-course:
  • Language: English Gb

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