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| Status |
Public on May 13, 2009 |
| Title |
Reproducibility of Quantitative RT-PCR Array in miRNA Expression Profiling and Comparison with Microarray Analysis |
| Organism |
Mus musculus |
| Experiment type |
Other
Non-coding RNA profiling by array
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| Summary |
High reproducibility with TaqMan microRNA array (qPCR-array) was demonstrated by comparing replicate results from the same RNA sample. Pre-amplification of the miRNA cDNA improved sensitivity of the qPCR-array and increased the number of detectable miRNAs. Furthermore, the relative expression levels of miRNAs were maintained after pre-amplification. When the performance of qPCR-array and microarrays were compared using different aliquots of the same RNA, a low correlation between the two methods (r = -0.443) indicated considerable variability between the two assay platforms. Higher variation between replicates was observed in miRNAs with low expression in both assays. Finally, a higher false positive rate of differential miRNA expression was observed using the microarray compared to the qPCR-array.
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| Overall design |
Replicate preparations (n =4) using different aliquots of a single C2C12 RNA sample (500 ng) were used to determine the reproducibility of the reverse transcription process as well as the results of the same reverse transcription products performed on different days. TaqMan microRNA Array A was used for this purpose.
To assess the reliability of pre-amplification, miRNA expression profiles obtained with and without pre-amplification using MiRNA TaqMan Array B were performed.
Independent miRNA expression profiling studies using uParaflo microfluidic biochips were performed by an independent company to determine the relationship between results obtained with qPCR-array and microarrays. Aliquots of the same C2C12 RNA were used in both the qPCR-array (500 ng) and microarrays (8 µg).
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| Contributor(s) |
Gelfond JA, Chen Y |
| Citation missing |
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| Submission date |
May 06, 2009 |
| Last update date |
Mar 21, 2012 |
| Contact name |
Jonathan Adam Gelfond |
| E-mail(s) |
gelfondjal@uthscsa.edu
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| Phone |
210 567 0851
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| Organization name |
UT Health Science Ctr San Antonio
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| Department |
Epidemiology & Biostatistics
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| Lab |
Bioinformatics
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| Street address |
Mail Code 7933, 7703 Floyd Curl
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| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
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| Platforms (3) |
| GPL8526 |
Applied_Biosystems_Taqman_miRNA_Expression Assays_B (Mouse) |
| GPL8527 |
Applied_Biosystems_Taqman_miRNA_Expression Assays_A (Mouse) |
| GPL8529 |
LC_MRA-1002_miRMouse_12.0_080901 |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA115415 |
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