OneArrayPLUS Gene Expression Profiling

 
 
Whole genome expression profiling with the OneArray line of microarrays has been vastly improved with the launch of our OneArrayPLUS protocol. The OneArrayPLUS workflow utilizes Agilent Extended Dynamic Range (XDR) technology for improved output of raw intensity signals. The dynamic range produced using OneArrayPLUS is 10 times greater than our previous protocol.


   OneArrayPLUS vs. our old protocol
In a series of tests comparing OneArrayPLUS to our previous protocol, OneArrayPLUS repeatedly led to the detection of nearly 10,000 more probes and 2-fold greater signal intensities. Overall, OneArrayPLUS increases the dynamic range and enhances the sensitivity of OneArray whole genome microarrays.
OneArrayPLUS Improvements
Performance Metrics
OneArray
OneArrayPLUS
Probes detected
18,409
28,782
Average probe intensity
1,810
4,025
Control probe intensity
49,665
127,238
 
   qPCR validation
We measured gene expression differences between a human reference RNA sample and a human brain RNA sample. Differences were measured using OneArrayPLUS and our previous protocol, and both microarray data sets were compared to TaqMan qPCR expression data. The correlation between the microarray data and the qPCR data is very high for both OneArray protocols; however the correlation between OneArrayPLUS and qPCR (0.913) was higher than the correlation between our previous protocol and qPCR (0.893). The higher correlation in the OneArrayPLUS data is due to more accurate gene expression measurements and a greater number of differentially expressed genes.
   Repeatability and Reproducibility
To measure repeatability, we hybridized the same HeLa RNA sample to 3 OneArray microarrays (H001, H002, and H003). We repeated this same test with another HeLa RNA sample (H004, H005, and H006). The correlation between technical replicates are highlighted in red, indicating a very high level of repeatability. The correlation between the separate RNA samples is represented in white area of the table, indicating a very high level of reproducibility.
   Sensitivity and Dynamic Range
The OneArrayPLUS service protocol utilizes the latest in microarray scanner technology from Agilent. The Extended Dynamic Range (XDR) settings allow the dynamic range of our OneArray microarrays to go beyond the constraints set by typical 16-bit microarray scanners. This greater dynamic range allows us to better detect genes expressing at low levels, and to better quantify genes that are highly expressed to the point of saturation.
   OneArray Plus FAQ
  Q1. What are the advantages and disadvantages of using the OneArrayPLUS protocol?  

 
 
Q2. Phalanx Biotech performed OneArray service for me in the past. Can I compare new OneArrayPLUS data to older data?  

 
 
Q3. The OneArrayPLUS protocol seems very good at detecting and quantifying genes expressed at low levels. Do you have qPCR data that validates the microarray data for such genes?  

 
 
Q4. Does the OneArrayPLUS protocol also apply to OneArray microRNA expression profiling services?