Course Identification

Real Time PCR Theory

Lecturers and Teaching Assistants

Dr. Dan Michael, Dr. Aldema Sas-Chen, Dr. Ester Feldmesser, Dr. Ron Rotkopf
Dr. Hagai Marmor-Kollet

Course Schedule and Location

Second Semester
June 14-18 14:00-16:00 , June 21-25 14:00-16:00,

Field of Study, Course Type and Credit Points

Life Sciences: Laboratory; Elective; Regular; 0.50 points
Life Sciences (Molecular and Cellular Neuroscience Track): Laboratory; Elective; Regular; 0.50 points
Life Sciences (Computational and Systems Biology Track): Laboratory; Elective; Regular; 0.50 points


Will be taught on line via ZOOM.
Schedule: June 14-18 14:00-16:00
June 21-25 14:00-16:00





Language of Instruction


Registration by


Attendance and participation


Grade Type

Pass / Fail

Grade Breakdown (in %)

2 assignments

Evaluation Type


Scheduled date 1


Estimated Weekly Independent Workload (in hours)



Real-time PCR has become a robust and routine method for detecting and quantifying nucleic acids. Thus, real-time PCR is used for measuring the expression of genes, validating the results from microarray experiments, genotyping, analyzing DNA variations (such as DNA SNPs) as well as for monitoring various biomarkers in microbiology and oncology.


Owing to the unfortunate COVID-19 pandemic, we have revised a well-established laboratory course and turned it into a “practical theory course”. Thus, lectures will be given online through Zoom sessions and practical sessions will be omitted at this stage.  In this revised course, we will discuss the fundamentals of real-time PCR and review many of its applications. Participants will have an opportunity to learn about the quantification of gene expression, among other relevant topics. In particular, we will discuss the preparation of RNA for mRNA expression analysis and for micro-RNA (miR) expression analysis. Then, two different technologies will be introduced. The first utilizes the dsDNA binding fluorescent probe SYBR and the other utilizes a target-specific probe that fluoresces upon hybridization and hydrolysis (TaqMan being one commercially available product).  Importantly, we will learn about the importance of primer design, and we will practice extensively (online) strategies for data analysis (the standard curve-based approach versus other approaches). In addition, we will discuss various aspects of adequate experimental design and the requirements for reporting results according to the recently established MIQE guidelines, which ensure proper practice and the reproducibility of scientific results. This will be followed by an introduction to statistical analysis of the data.


Given the use of DNA amplification in order to detect various pathogens and viruses, in particular, we will explain how real-time PCR is used to detect the SARS-CoV-2 by using a real-time PCR-based assay that requires hydrolysis probes. Finally, we will discuss a novel instrument-less approach to amplify viral sequences as an alternative to real-time PCR approaches.

Learning Outcomes

Upon successful completion of this course students should be able to:

  1. Discuss the use of real-time PCR as a reliable and sensitive method for quantifying nucleic acids and its applications.

  2. Discuss algorithms for primer design.
  3. Learn about relative quantification of selected cellular mRNAs and miRs.
  4. Differentiate between the various methods of analysis.
  5. Discuss the need for suitable standards to guide proper practice and data communication. In this regard, appreciate the need to adhere to the well-defined MIQE (Minimum standard for publication of qPCR Experiments) criteria.
  6. Obtain and appreciate tools for statistical analysis.
  7. Translate the acquired the knowledge. Thus, allow to adapt, in one’s own systems of choice, proper technical and analytical methodologies that are reliably used in real-time PCR.

Reading List