Real Time Quantitative PCR

 (7 credits)

October 1st-29th, 2014

Lectures and Seminars files 

Seminar 5 (Reports), Alyona Minina, Department of Plant Biology, SLU

Homework 7

2014.10.24 9:00-12:00 Seminar 4 (Statistical analysis),Alyona/ Maartje Klapwijk

Homework 6 pdf or .pptxAssignment,  Minitab 17 

Lecture 7 (Statistical analysis), Maartje Klapwijk, Department of Ecology, SLU

Seminar 3 (Normalisation), Alyona Minina,

Homework 5

Homework 4Excel example of RT-qPCR design,  guideline for design calculation

Seminar 2 (RT-qPCR), Alyona Minina, Department of Plant Biology, SLU 

Homework 3

Lecture 6 (Normalisation), Department of Physiological Botany, UU  

Lecture 5 (Microarray), Pauliina Munne, FuGU, Helsinki University 

Lecture 4 (qPCR in forensics), Johannes Hedman, Lund University/SKL polisen

Lecture 3 (Next gen seq), Olga Vinnere Pettersson, NGI Uppsala  

Homework 3: design primers for the experimental part of the course

Seminar 1 (qPCR), Alyona Minina, Department of Plant Biology, SLU  

Homework 2

Lecture 2 (qPCR), Alyona Minina, Department of Plant Biology, SLU  

Homework  1

Lecture 1 (PCR), Alyona Minina, Department of Plant Biology, SLU

 

 

Useful stuff

Manual for run setup and data analysis

MIQE guidelines

How to find linear regression in Excel

Efficiency calculation

Short guide for qPCR data analsysis

 

Selecting reference genes

GENEVESTIGATOR (make sure JAVA is of the latest version and is enabled in your internet browser)

 

Primer design

Guidelines for primer design

Primer3Plus

Primer-BLAST

 

Softwares for data analylis (for Windows only, sorry)

 

CFX Manager, to install:

  1. download the file

  2. unzip CFX Manager 3.1.zip

  3. open the folder CFX_Manager

  4. run the Setup file

 

IQ5, to install:

  1. download the file

  2. unzip the IQ5.zip

  3. run the dotnetfx file

 

Short manuals for qPCR machines softwares:

  CFX short manual                          

  IQ5 short manual

 

Here you can find the syllabus  and  schedule

 

Real-time quantitative PCR is a very popular method broadly used and missused in molecular biology. The aim of this course is not only to teach the very basics of the qPCR theory and practice, but also to introduce students to the MIQE guidelines essential for designing performing and interpreting quantitative experiments in a reliable way.

Another aim of this course is to familiarize students with more adavanced techonologies alternative to qPCR which are gradually becoming more and more available. Students will have an opportunity to meet with experts from SciLifeLab and Functional Genomics Unit of Helsinki University and also learn how qPCR is applied in forensic science.

 

 

To register for the course send an e-mail to: alena.minina @ slu.se

Deadline for registration: September 19th 2014

All lectures are open, registration is required only to attend the practical part of the course

 

 

 

Lecturers

Alyona Minina, Department of Plant Biology, SLU

Olga Vinnere Pettersson, UU. NGI Uppsala.

Maartje Klapwijk, Department of Ecology, SLU

Johannes Hedman, Applied Microbiology, Lund University. SKL

Pauliina Munne, FuGU, Helsinki University

 

Participants (max. 16 students)

 

  1. Salim Hossain Reza, Department of Plant Biology, SLU

  2. Konstantia Gkarmiri, Department of Forest Mycology and Plant Pathology, SLU

  3. Enid Ming Zhao,Department of Plant Biology, SLU

  4. Martin Palmqvist, Department of Chemistry and Biotechnology, SLU

  5. Jun Yi, Department of Plant Biology, SLU

  6. Zaenab Al-Azzawi,Department of forest mycology and plant pathology, SLU

  7. Jule Brandenburg, Department of Chemistry and Biotechnology, SLU

  8. Kiran Kumar Jagarlamudi, Department of Anatomy, Physiology and Biochemistry, SLU

  9. Anna Carlson, Department of Plant Biology, SLU

  10. Enrique Del Olmo de Medina, Castilla-La mancha University/SLU

  11. Maite Urbano, Cordoba University/SLU

  12.  Shirin Akhter, Department of Plant Biology, SLU

  13. Anders Johannisson, Department of Anatomy, Physiology and Biochemistry, SLU

  14. Mohammad Jaber Alipour, SLU