Experimental Methods in Systems Biology

About this course: 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.

Created by:  Icahn School of Medicine at Mount Sinai

• Taught by:  Marc Birtwistle, PhD, Assistant Professor

  Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY)

Basic Info Course 2 of 6 in the Systems Biology and Biotechnology Specialization Commitment 6-8 hours/week Language English How To Pass Pass all graded assignments to complete the course. User Ratings 4.6 stars Average User Rating 4.6See what learners said Trabajo del curso

Cada curso es como un libro de texto interactivo, con videos pregrabados, cuestionarios y proyectos.

Ayuda de tus compañeros

Conéctate con miles de estudiantes y debate ideas y materiales del curso, y obtén ayuda para dominar los conceptos.

Certificados

Obtén reconocimiento oficial por tu trabajo y comparte tu éxito con amigos, compañeros y empleadores.

Icahn School of Medicine at Mount Sinai The Icahn School of Medicine at Mount Sinai, in New York City is a leader in medical and scientific training and education, biomedical research and patient care.

Syllabus


WEEK 1


Introduction
Description goes here


5 videos, 6 readings expand

1. Video: Lecture 1 -Scope and Overview
2. Leyendo: Lecture Slides
3. Video: Lecture 2 - Biological Model Systems
4. Leyendo: Lecture Slides
5. Video: Lecture 3 - Experimental Perturbations
6. Leyendo: Lecture Slide
7. Video: Lecture 4 - Measuring Nucleic Acids
8. Leyendo: Lecture Slides
9. Video: Lecture 5 - Measuring Protein and Protein States
10. Leyendo: Lecture Slides
11. Leyendo: Reading List

Graded: Quiz 1

WEEK 2


Deep mRNA Sequencing
Description goes here


5 videos, 4 readings expand

1. Video: Lecture 1 - History of Sequencing
2. Video: Lecture 2 - 2nd and 3rd Generation Sequencing
3. Leyendo: Lecture Slides
4. Video: Lecture 3 - Illumina-Based mRNA Sequencing
5. Leyendo: Lecture Slides
6. Video: Lecture 4 - Lab-Based Video
7. Video: Lecture 5 - mRNA Sequencing Data Analysis
8. Leyendo: Lecture Slides
9. Leyendo: Reading List

Graded: Quiz 2

WEEK 3


Mass Spectrometry-Based Proteomics
Description goes here


6 videos, 3 readings expand

1. Video: Lecture 1 - Basics of Mass Spectrometry 1
2. Video: Lecture 2 - Basics of Mass Spectrometry 2
3. Leyendo: Lecture Slides
4. Video: Lecture 3 - Quantification in Proteomics
5. Leyendo: Lecture Slides
6. Video: Lecture 4 - Lab-Based Video - Proteomics Day 1
7. Video: Lecture 5 - Lab-Based Video - Proteomics Day 2
8. Video: Lecture 6 - Lab-Based Video - Analysis
9. Leyendo: Reading List

Graded: Quiz 3

WEEK 4


Midterm Exam
Description goes here

Graded: Midterm Exam

WEEK 5


Flow and Mass Cytometry for Single Cell Protein Levels and Cell Fate
Description goes here


7 videos, 4 readings expand

1. Video: Lecture 1 - Flow Cytometry 1
2. Video: Lecture 2 - Flow Cytometry 2
3. Leyendo: Lecture Slides
4. Video: Lecture 3 - Mass Cytometry
5. Leyendo: Lecture Slides
6. Video: Lecture 4 - Cytometry Data Analysis
7. Leyendo: Lecture Slides
8. Video: Lecture 5 - Lab-Based Video - Flow Cytometry - Acquisition
9. Video: Lecture 6 - Lab-Based Video - Flow Cytometry - Analysis
10. Video: Lecture 7 - Lab-Based Video - Mass Cytometry
11. Leyendo: Reading List

Graded: Quiz 4

WEEK 6


Live-cell Imaging for Single Cell Protein Dynamics
Description goes here


5 videos, 4 readings expand

1. Video: Lecture 1 - Fluorescence Microscopy
2. Video: Lecture 2 - Types of Imaging
3. Leyendo: Lecture Slides
4. Video: Lecture 3 - Visualizing Molecules in Living Cells: Fluorescent Tools
5. Leyendo: Lecture Slides
6. Video: Lecture 4 - Quantification
7. Video: Lecture 5 - Lab-Based Video
8. Leyendo: Lecture Slides
9. Leyendo: Reading List

Graded: Quiz 5

WEEK 7


Integrating and Interpreting Datasets with Network Models and Dynamical Models
Description goes here


3 videos, 4 readings expand

1. Video: Lecture 1 - Omics data and Network Model Analyses
2. Leyendo: Lecture Slides
3. Video: Lecture 2 - Single Cell Time Course Data and Dynamical Model Analyses
4. Leyendo: Lecture Slides
5. Video: Lecture 3 - Dynamical Model Case Study
6. Leyendo: Lecture Slides
7. Leyendo: Reading List

Graded: Quiz 6

WEEK 8


Final Exam

Graded: Final Exam