qPCR-kurs

Senast ändrad: 04 april 2018

Real Time Quantitative PCR

 (7 credits)

October 1st-29th, 2014

 

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 .pptx, AssignmentMinitab 17 

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

Seminar 3 (Normalisation), Alyona Minina, Daniel Uddenberg

Homework 5

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

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

Homework 3

Lecture 6 (Normalisation), Daniel Uddenberg, 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

web tool to verify your reference genes (find M-stability value)

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)

RTPrimerDB

 

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

 

 

Your data:

            CFX connect                                                   IQ5

                     

                  CFX short manual                               IQ5 short manual

                                        dilution factor for efficiency curves

                       Tina        6-fold                                          Anna

                       Zaenab                                        10-fold  Kiran    

                       Jun                                                            Jule

                       Shiran                                         10-fold   Reza

                       Enid                                               4-fold  Martin      

                       Enrique     5-fold                                        Maite

                       Anders      2-fold                                       Mohammad

 

sample A and sample B preparation:

plasmid concentration was measured with NanoDrop = 177ng/ml

- > diluted 17.7 times to the  concentration 10 ng/ul

->concentration was confirmed with Nanodrop = 9.8 ng/ul

->this dilution was aliquoted as sample A for students

->an extra aliquote of sample A was diluted additionally 1:5, 1:10, 1:25, 1:60

->these dilutions were aliquoted as samples B and signed with students names

 

Sample B

Sample B concentration ng/ul

Student

sample A 1:5

2

Tina

sample A 1:5

2

Jule

sample A 1:5

2

Anna

sample A 1:5

2

Enrique

sample A 1:10

1

Martin

sample A 1:10

1

Zaenab

sample A 1:10

1

Maite

sample A 1:10

1

Anders

sample A 1:25

0,4

Enid

sample A 1:25

0,4

Mohammad

sample A 1:60

0,17

Reza

sample A 1:60

0,17

Jun

sample A 1:60

0,17

Kiran

sample A 1:60

0,17

Shirin

 

 

 

 

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.

Daniel Uddenberg, Department of Physiological Botany, UU

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

Kontaktinformation
Sidansvarig: alena.minina@slu.se