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ExProfile™ Gene qPCR Arrays

Introduction

For high-throughput profiling of gene expression

The ExProfile™ Gene qPCR Arrays are designed for profiling the expressions of pre-made or customized sets of coding-genes in various tissues or cells. The resulting differential expressions of profiled genes help researchers to identify those that are biologically significant and relevant to their research. In each 96-well plate, there are up to 84 pairs of qPCR primers and 12 wells of controls which are used to monitor the efficiency of the entire experimental process – from reverse transcription to qPCR reaction.

Each pair of primers used in the qPCR arrays has been experimentally validated to yield a single dissociation curve peak and to generate a single amplification of the correct size for the targeted mRNA. A cDNA pool, containing reverse transcript products from total RNA of 10 different tissues, was used as the qPCR validation template.

A universal real-time PCR condition was developed for easy profiling and analysis of  the gene expression in a high-throughput fashion. The All-in-One™ First-Strand cDNA Synthesis Kits and qPCR Mix Kits are the recommended and supported RT-PCR reagents for use with the ExProfile™ gene qPCR arrays. These reagents have been optimized to produce high sensitivity, efficiency, and specificity.

Key advantages

Validated mRNA primers

  • Each primer pair is designed using a proprietary algorithm and has been experimentally validated

Robust performance

  • Sensitive – Detects as low as 4 copies of RNA using ExProfile gene qPCR array and recommended reagents/conditions
  • Broad linearity – Simultaneously detects mRNAs at different expression levels
  • Reproducible – High reproducibility (R2> 0.99) for inter-array and intra-array replicates

Pre-arranged groups, or customized groups

  • Pre-arranged cancer-related groups
  • Pre-arranged pathway-related groups
  • Customized gene arrays for focused study

Gene qPCR array experimental work flow

Figure 1. Gene qPCR array experimental work flow.

 

Performance Data

Linear Range and Sensitivity (spike-in control RNA)  
Broad linear range and high sensitivity

Figure 2. Broad linear range and high sensitivity

Mouse total RNA with serially diluted Spike-in control RNA were reverse-transcribed using All-in-One first strand cDNA synthesis kit. The reverse-transcribed cDNA samples were detected using All-in-One qPCR mix and spike-in control specific primers deposited in a 96-well plate. The resulting Ct values were plotted against the log5 of the amounts of spike-in control RNA. The data demonstrated a broad linear dynamic range from 4 to 1.6*106 copies of input RNA as well as high sensitivity.

Positive calls with a range of total RNA  
High positive calls with as little as 15.36 ng of total RNA

Figure 3. High positive calls with as little as 15.36 ng of total RNA

Different amounts of MCF_7 total RNA (1000, 200, 40, 8, 1.6ng) were analyzed with the Human Breast Cancer Gene qPCR Array (PAG-HGBE96-01).The percentage of positive calls (Ct < 35) is plotted against the input amount of total RNA in each qPCR reaction.

Inter-Array Reproducibility  
High inter-array reproducibility

Figure 4. High inter-array reproducibility
Two ExProfile™ qPCR gene array replicates (plate A and B) were analyzed using human total RNA (10-tissue mix) on the Bio-Rad iQ5. The Ct values of the replicate plates were plotted against each other. R2 > 0.99 was observed for high inter-array reproducibility. R2 > 0.99 was also observed for intra-array reproducibility (data not shown).

   

 

Catalog Arrays

ExProfile™ Catalog Gene qPCR Arrays

ExProfile™ catalog gene qPCR arrays profile the expression of a group of pre-selected genes, such as pathway-related, cancer-related, disease-relate genes. These genes are carefully chosen for their close correlation to a specific pathway, cancer, or disease, based on a thorough literature search of peer-reviewed publications. 

GeneCopoeia offers the following catalog arrays:

ExProfile™ Pathway qPCR arrays 

ExProfile™ Cancer Gene qPCR arrays

ExProfile™ Disease and gene group qPCR arrays

Custom Arrays

ExProfile™ Custom Gene qPCR Arrays

ExProfile™ Custom Gene qPCR Arrays profile the expression of customer specified genes. Each primer is designed using a proprietary algorithm and has been experimentally validated. Depending on the number of genes and replicates to be analyzed, GeneCopoeia offers 14 layouts to choose from, including 6 types with 96-well plate and 8 types with 384-well plate. Different controls can also be included in the arrays to help monitor the sample quality, RT and PCR reaction efficiencies and replicates reproducibility:

  • Genomic DNA control (GDC): detects genomic DNA contamination.
  • Spike-in reverse transcription control (RT): monitors the efficiency of the RT reaction.
  • Positive PCR control (PCR): verifies the PCR efficiency.
  • Housekeeping genes (HK): can be used as endogenous positive controls and for array normalization.

For the best performance, All-in-One™ First Strand cDNA Synthesis Kit and All-in-One™ qPCR Mix are the recommended and supported reagents for use with these arrays.

 

Key advantages

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Validated primers

  • Each primer is designed using a proprietary algorithm and has been experimentally  validated

Flexible array design

  • GeneCopoeia offers 14 layouts to choose from, including 6 types with 96-well plate and 8 types with 384-well plate.

Robust performance

  • Sensitive – Detects as low as 4 copies of RNA using ExProfile  Gene qPCR Array and recommended reagents/conditions
  • Broad linearity – Simultaneously detects mRNAs at different expression levels
  • Reproducible -High reproducibility (R2> 0.99) for inter-array and intra-array replicates

 

Cat. No. Product name Species Number of genes Number of plates Document
PAG-CS Exprofile™ Gene qPCR Arrays Custom Services N/A N/A Variable Variable

Analysis Tool

GeneCopoeia offers convenient analysis tool for gene qPCR arrays, as well as custom services. According to the product name and catalog number, download the matched analysis tools from following table.

Analysis Tool for Catalog Arrays

Please download an example for catalog array to see how to fill in the experimental data

Cat. No. Product name Analysis Tool
QG061 Exprofile™ Human Adenocarcinoma Gene qPCR Array
QG062 Exprofile™ Human Brain Cancer Gene qPCR Array
QG063 Exprofile™ Human Breast Cancer Gene qPCR Array
QG064 Exprofile™ Human Bladder Cancer Gene qPCR Array
QG065 Exprofile™ Human Colorectal Cancer Gene qPCR Arrays
QG066 Exprofile™ Human Cervical Cancer Gene qPCR Arrays
QG067 Exprofile™ Human Endometrial Cancer Gene qPCR Arrays
QG068 Exprofile™ Human Head and Neck Cancer Gene qPCR Arrays
QG069 Exprofile™ Human Kidney Cancer Gene qPCR Arrays
QG070 Exprofile™ Human Leukemia Gene qPCR Arrays
QG071 Exprofile™ Human Lung Cancer Gene qPCR Arrays
QG072 Exprofile™ Human Liver Cancer Gene qPCR Arrays
QG073 Exprofile™ Human Lymphoma Gene qPCR Arrays
QG074 Exprofile™ Human Myeloma Gene qPCR Arrays
QG075 Exprofile™ Human Ovarian Cancer Gene qPCR Arrays
QG076 Exprofile™ Human Pancreatic Cancer Gene qPCR Arrays
QG077 Exprofile™ Human Prostate Cancer Gene qPCR Arrays
QG078 Exprofile™ Human Skin Cancer Gene qPCR Arrays
QG079 Exprofile™ Human Stomach Cancer Gene qPCR Arrays
QG080 Exprofile™ Human Thyroid Cancer Gene qPCR Arrays
QG081 Exprofile™ Human Testicular Cancer Gene qPCR Arrays

 

Analysis Tool for Custom Arrays

Operation guidance

 

Please upload your EXCEL file:







Download Datasheet template: Control Data.xls    Sample Data.xls