|
| Status |
Public on Mar 15, 2006 |
| Title |
Gene expression profiling of the four human tissues by two microarray platforms and TaqMan real-time PCR |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
Expression profiling by RT-PCR
|
| Summary |
This study provides one of the largest “reference” data set of gene expression measurements using TaqMan® Gene Expression Assay based real-time PCR technology. This data set allowed us to use an orthogonal gene expression technology to evaluate the performance of different microarray platforms. We conclude that microarrays are indeed invaluable discovery tools with acceptable reliability for genome-wide gene expression screening, though validation of putative changes in gene expression remains advisable. Our study also characterizes the limitations of microarrays; understanding these limitations will enable researchers to more effectively evaluate microarray results in a more cautious and appropriate manner
Keywords: cross-platform comparison of gene expression measurements
|
| |
|
| Overall design |
In this study, we analyzed the gene expression profiles of three human tissues: brain, lung, liver and one universal human reference sample (UHR) using two representative commercial long-oligonucleotide microarray platforms: (1) Applied Biosystems Human Genome Survey Microarrays (based on single-color detection); (2) Agilent Whole Human Genome Oligo Microarrays (based on two-color detection). 1,375 genes represented by both microarray platforms and spanning a wide dynamic range in gene expression levels, were selected for TaqMan® Gene Expression Assay based real-time PCR validation. For each platform, four technical replicates were performed on the same total RNA samples according to each manufacturer’s standard protocols. For Agilent arrays, comparative hybridization was performed using incorporation of Cy5 for brain/lung/liver RNA and Cy3 for UHR RNA (common reference). Using the TaqMan® Gene Expression Assay based real-time PCR data set as the reference set
|
| |
|
| Contributor(s) |
Wang Y |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Feb 08, 2006 |
| Last update date |
Jan 18, 2013 |
| Contact name |
Yulei Wang |
| E-mail(s) |
wangyy@appliedbiosystems.com
|
| Organization name |
Applied Biosystems
|
| Street address |
850 Lincoln Centre Dr
|
| City |
Foster City |
| State/province |
CA |
| ZIP/Postal code |
94404 |
| Country |
USA |
| |
|
| Platforms (3) |
| GPL1426 |
ABI Human Genome Survey Microarray Version 1 |
| GPL1708 |
Agilent-012391 Whole Human Genome Oligo Microarray G4112A (Feature Number version) |
| GPL2845 |
Applied Biosystems TaqMan Gene Expression Assays (human) |
|
| Samples (44)
|
|
| Relations |
| BioProject |
PRJNA95071 |
Less...
More...