QPCR analysis using qbase+

qbase+ introduction
2 Topics
Installation and Licence
Training Material
Experiment Design Exercises
7 Topics
Exercise 1: Simple Gene Expression Study
Exercise 2: A Large Study
Exercise 3: How to Fill Plates?
Exercise 4: A Growing Study
Exercise 5: A Diagnostic Copy Number Screen
Exercise 6: Fix Experiments with Bad or Missing Data
Exercise 7: Dilution Series for Calculating Amplification Efficiencies
Primer Design Exercises
5 Topics
Criteria for qPCR Primers
Fruit Fly Tap Gene: Designing qPCR Primers using PrimerBLAST
Fruit Fly Tap Gene: Analyzing primer characteristics using OligoAnalyzer
Human F9 Gene: Designing qPCR Primers using PrimerBLAST
Human F9 Gene: In Silico PCR in the UCSC Browser
Gene Expression Analysis
10 Topics
Loading Data
Adding Annotation to Data
Specifying the Aim of the Experiment
Checking the Quality of Technical Replicates and Controls
Considering Amplification Efficiencies
Normalization
Scaling
Visualizing the Results
Statistical Analysis
Run7
Analyzing Data from Different qPCR Experiments over Time
2 Topics
Creating a New Experiment
Analyzing the data
Selecting reference genes: exercises
8 Topics
About RefGenes
Starting the RefGenes Tool
The Genevestigator User Interface
Using the RefGenes Tool to Find Reference Genes
Finding Candidate Reference Genes in the Free Version of Genevestigator
Finding Candidate Reference Genes in the Commercial Version of Genevestigator
Exercise 1: Reference Genes for Mouse Liver
Exercise 2: Reference Genes for Human Heart
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About RefGenes

Since normalization of qPCR data is based on the assumption that the reference targets have the same expression level in all samples it is crucial that the expression of the chosen reference genes is stable. However, none of the so-called housekeeping genes is universally stably expressed.

Genevestigator, both the commercial and the free version, contains a tool, called RefGenes, that allows to identify candidate reference genes that display very stable expression in the context that you are working in, typically a certain tissue of a certain organism.

Genevestigator is a platform that contains curated public microarray data from thousands of experiments/conditions.

RefGenes allows you to select the conditions that are relevant for you, e.g. mouse liver, human fibroblasts, or Arabidopsis thaliana leaves. In a next step, RefGenes identifies the genes with the most stable expression in the selected conditions.