GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE16000 Query DataSets for GSE16000
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
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.
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).
Contributor(s) Gelfond JA, Chen Y
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date May 06, 2009
Last update date Mar 21, 2012
Contact name Jonathan Adam Gelfond
Phone 210 567 0851
Organization name UT Health Science Ctr San Antonio
Department Epidemiology & Biostatistics
Lab Bioinformatics
Street address Mail Code 7933, 7703 Floyd Curl
City San Antonio
State/province TX
ZIP/Postal code 78229
Country USA
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
Samples (10)
GSM400510 NonAmp1_ArrayB
GSM400513 Day1-RT1-ArrayA
GSM400676 Day1-RT2-ArrayA
BioProject PRJNA115415

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE16000_RAW.tar 200.0 Kb (http)(custom) TAR (of TXT)
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap