Plant Molecular Biology

Control Primers for Arabidopsis


Three primer sets designed for use as internal controls in PCR-based Arabidopsis gene expression analysis. All three primer sets have been functionally validated and optimized by RT-PCR analysis against major Arabidopsis tissues for constitutive expression and specific amplification (see Figures 1 & 2). Further confirmation of those primers, as internal control for data normalization, was conducted in quantitative RT-PCR reactions for pathogen-inducible Arabidopsis genes.
These control primers provide Arabidopsis researchers a simple solution for selecting internal control(s) in gene expression analysis:
  • Sensitive, efficient and cost-effective in a ready-to-use format.
  • Represent different expression levels to match target expression level.
  • Choice of three housekeeping genes to meet customers' specific needs.

Each set contains forward and reverse primers for housekeeping genes:
Product Code Product Name
C3115 Control Primer Set for Arabidopsis CBP20 Gene
Gene Locus: At5g44200
Amplicon Size: 409 bp
C3615 Control Primer Set for Arabidopsis Actin-2 Gene
Gene Locus: At3g18780
Amplicon Size: 257 bp
C3240 Control Primer Set for Arabidopsis UBC Gene
Gene Locus: At5g25760
Amplicon Size: 217 bp
Each primer set (forward and reverse) is suitable for 100 PCR/RT-PCR reactions (for 50 µL reaction volume).

Data Analysis
Figure 1. Gel image of end-point Q-RT-PCR amplification of three housekeeping genes in five Arabidopsis tissues.
Lanes 1: Leaf
Lanes 2: Root
Lanes 3: Stem
Lanes 4: Flower
Lanes 5: Silique
  Total RNA was isolated from five tested tissues and treated with DNase I to reduce genomic DNA background. RT-PCR was performed against control primers with 160 ng RNA for each reaction. Amplicons from each RT-PCR reaction were resolved on 2% agarose gel.
 
Figure 2. Quantitative comparison of housekeeping gene expression in different tissues of Arabidopsis.
Panel A. Experimental setup and CT value
Panel B. Real-Time Q-RT-PCR with control primers
Well# Dye Type Label CT
A1 SBG1 Leaf CBP20 28.015
A2 SBG1 Root CBP20 29.078
A3 SBG1 Stem CBP20 28.199
A4 SBG1 Flower CBP20 26.846
A5 SBG1 Silique CBP20 30.692
Well# Dye Type Label CT
B1 SBG1 Leaf Actin-2 24.921
B2 SBG1 Root Actin-2 23.184
B3 SBG1 Stem Actin-2 24.811
B4 SBG1 Flower Actin-2 24.533
B5 SBG1 Silique Actin-2 26.753
Well# Dye Type Label CT
C1 SBG1 Leaf Ubiquitin 29.631
C2 SBG1 Root Ubiquitin 29.866
C3 SBG1 Stem Ubiquitin 30.801
C4 SBG1 Flower Ubiquitin 28.283
C5 SBG1 Silique Ubiquitin 29.276

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