Comparison of microarray platforms for measuring differential microRNA expression
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA156595PRJNA156593PRJNA149349PRJNA156589PRJNA156587PRJNA156591
ORGANISM(S): synthetic construct Homo sapiens
PROVIDER: GSE33127 | GEO | 2012/11/26
SECONDARY ACCESSION(S): PRJNA149349
REPOSITORIES: GEO
Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2013-10-22 | E-GEOD-51508 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2013-10-22 | GSE51508 | GEO
Project description:BackgroundMicroarray technology applied to microRNA (miRNA) profiling is a promising tool in many research fields; nevertheless, independent studies characterizing the same pathology have often reported poorly overlapping results. miRNA analysis methods have only recently been systematically compared but only in few cases using clinical samples.Methodology/principal findingsWe investigated the inter-platform reproducibility of four miRNA microarray platforms (Agilent, Exiqon, Illumina, and Miltenyi), comparing nine paired tumor/normal colon tissues. The most concordant and selected discordant miRNAs were further studied by quantitative RT-PCR. Globally, a poor overlap among differentially expressed miRNAs identified by each platform was found. Nevertheless, for eight miRNAs high agreement in differential expression among the four platforms and comparability to qRT-PCR was observed. Furthermore, most of the miRNA sets identified by each platform are coherently enriched in data from the other platforms and the great majority of colon cancer associated miRNA sets derived from the literature were validated in our data, independently from the platform. Computational integration of miRNA and gene expression profiles suggested that anti-correlated predicted target genes of differentially expressed miRNAs are commonly enriched in cancer-related pathways and in genes involved in glycolysis and nutrient transport.ConclusionsTechnical and analytical challenges in measuring miRNAs still remain and further research is required in order to increase consistency between different microarray-based methodologies. However, a better inter-platform agreement was found by looking at miRNA sets instead of single miRNAs and through a miRNAs - gene expression integration approach.
| S-EPMC3441572 | biostudies-literature
Project description:Microarray technology applied to miRNA profiling is a promising tool in many research fields. At present, only few studies have addressed intra- and inter-platform reproducibility by using tissues/cell-lines of different origin to maximize differences in miRNA content. Although the approach might provide an useful system to address technical issues since, for sure, a huge modulation can be evaluated, it does not reflect the common experimental practice in laboratory. As a matter of fact, from all these studies it is not know how concordant can be expected the results obtained by different platforms starting from biological meaningful specimens. We investigated the issue of inter-platform reproducibility using four miRNA microarray platforms and nine paired tumor/normal colon tissues. The tumor and the normal counter-part samples were prospectively collected from 9 patients who underwent surgical resection at the INT-MI. Neoplastic samples were obtained from the central area of the neoplasia, avoiding to select necrotic material or transition zones with healthy mucosa. Samples of colonic healthy mucosa were resected at least 20 centimeters far from the neoplasia and distant from the surgical resection margins. Tissue samples were stored in liquid nitrogen until RNA extraction. Total RNA was extracted from 10–20 mg of tumor samples and from 30–40 mg of normal samples.
2012-11-26 | GSE33125 | GEO
Project description:Microarray technology applied to miRNA profiling is a promising tool in many research fields. At present, only few studies have addressed intra- and inter-platform reproducibility by using tissues/cell-lines of different origin to maximize differences in miRNA content. Although the approach might provide an useful system to address technical issues since, for sure, a huge modulation can be evaluated, it does not reflect the common experimental practice in laboratory. As a matter of fact, from all these studies it is not know how concordant can be expected the results obtained by different platforms starting from biological meaningful specimens. We investigated the issue of inter-platform reproducibility using four miRNA microarray platforms and nine paired tumor/normal colon tissues. The tumor and the normal counter-part samples were prospectively collected from 9 patients who underwent surgical resection at the INT-MI. Neoplastic samples were obtained from the central area of the neoplasia, avoiding to select necrotic material or transition zones with healthy mucosa. Samples of colonic healthy mucosa were resected at least 20 centimeters far from the neoplasia and distant from the surgical resection margins. Tissue samples were stored in liquid nitrogen until RNA extraction. Total RNA was extracted from 10–20 mg of tumor samples and from 30–40 mg of normal samples.
2012-11-26 | GSE33123 | GEO
Project description:Microarray technology applied to miRNA profiling is a promising tool in many research fields. At present, only few studies have addressed intra- and inter-platform reproducibility by using tissues/cell-lines of different origin to maximize differences in miRNA content. Although the approach might provide an useful system to address technical issues since, for sure, a huge modulation can be evaluated, it does not reflect the common experimental practice in laboratory. As a matter of fact, from all these studies it is not know how concordant can be expected the results obtained by different platforms starting from biological meaningful specimens. We investigated the issue of inter-platform reproducibility using four miRNA microarray platforms and nine paired tumor/normal colon tissues. The tumor and the normal counter-part samples were prospectively collected from 9 patients who underwent surgical resection at the INT-MI. Neoplastic samples were obtained from the central area of the neoplasia, avoiding to select necrotic material or transition zones with healthy mucosa. Samples of colonic healthy mucosa were resected at least 20 centimeters far from the neoplasia and distant from the surgical resection margins. Tissue samples were stored in liquid nitrogen until RNA extraction. Total RNA was extracted from 10–20 mg of tumor samples and from 30–40 mg of normal samples.
2012-11-26 | GSE33122 | GEO
Project description:Microarray technology applied to miRNA profiling is a promising tool in many research fields. At present, only few studies have addressed intra- and inter-platform reproducibility by using tissues/cell-lines of different origin to maximize differences in miRNA content. Although the approach might provide an useful system to address technical issues since, for sure, a huge modulation can be evaluated, it does not reflect the common experimental practice in laboratory. As a matter of fact, from all these studies it is not know how concordant can be expected the results obtained by different platforms starting from biological meaningful specimens. We investigated the issue of inter-platform reproducibility using four miRNA microarray platforms and nine paired tumor/normal colon tissues. The tumor and the normal counter-part samples were prospectively collected from 9 patients who underwent surgical resection at the INT-MI. Neoplastic samples were obtained from the central area of the neoplasia, avoiding to select necrotic material or transition zones with healthy mucosa. Samples of colonic healthy mucosa were resected at least 20 centimeters far from the neoplasia and distant from the surgical resection margins. Tissue samples were stored in liquid nitrogen until RNA extraction. Total RNA was extracted from 10–20 mg of tumor samples and from 30–40 mg of normal samples.
2012-11-26 | GSE33124 | GEO
Project description:Microarray technology applied to miRNA profiling is a promising tool in many research fields. At present, only few studies have addressed intra- and inter-platform reproducibility by using tissues/cell-lines of different origin to maximize differences in miRNA content. Although the approach might provide an useful system to address technical issues since, for sure, a huge modulation can be evaluated, it does not reflect the common experimental practice in laboratory. As a matter of fact, from all these studies it is not know how concordant can be expected the results obtained by different platforms starting from biological meaningful specimens. We investigated the issue of inter-platform reproducibility using four miRNA microarray platforms and nine paired tumor/normal colon tissues. The tumor and the normal counter-part samples were prospectively collected from 9 patients who underwent surgical resection at the INT-MI. Neoplastic samples were obtained from the central area of the neoplasia, avoiding to select necrotic material or transition zones with healthy mucosa. Samples of colonic healthy mucosa were resected at least 20 centimeters far from the neoplasia and distant from the surgical resection margins. Tissue samples were stored in liquid nitrogen until RNA extraction. Total RNA was extracted from 10–20 mg of tumor samples and from 30–40 mg of normal samples.
2012-11-26 | GSE33126 | GEO
Project description:Microarray technology applied to miRNA profiling is a promising tool in many research fields. At present, only few studies have addressed intra- and inter-platform reproducibility by using tissues/cell-lines of different origin to maximize differences in miRNA content. Although the approach might provide an useful system to address technical issues since, for sure, a huge modulation can be evaluated, it does not reflect the common experimental practice in laboratory. As a matter of fact, from all these studies it is not know how concordant can be expected the results obtained by different platforms starting from biological meaningful specimens. We investigated the issue of inter-platform reproducibility using four miRNA microarray platforms and nine paired tumor/normal colon tissues. The tumor and the normal counter-part samples were prospectively collected from 9 patients who underwent surgical resection at the INT-MI. Neoplastic samples were obtained from the central area of the neoplasia, avoiding to select necrotic material or transition zones with healthy mucosa. Samples of colonic healthy mucosa were resected at least 20 centimeters far from the neoplasia and distant from the surgical resection margins. Tissue samples were stored in liquid nitrogen until RNA extraction. Total RNA was extracted from 10–20 mg of tumor samples and from 30–40 mg of normal samples. Nine paired tumor/normal colon tissues on Agilent human miRNA Microarray.
2012-11-26 | E-GEOD-33124 | biostudies-arrayexpress
Project description:Microarray technology applied to miRNA profiling is a promising tool in many research fields. At present, only few studies have addressed intra- and inter-platform reproducibility by using tissues/cell-lines of different origin to maximize differences in miRNA content. Although the approach might provide an useful system to address technical issues since, for sure, a huge modulation can be evaluated, it does not reflect the common experimental practice in laboratory. As a matter of fact, from all these studies it is not know how concordant can be expected the results obtained by different platforms starting from biological meaningful specimens. We investigated the issue of inter-platform reproducibility using four miRNA microarray platforms and nine paired tumor/normal colon tissues. The tumor and the normal counter-part samples were prospectively collected from 9 patients who underwent surgical resection at the INT-MI. Neoplastic samples were obtained from the central area of the neoplasia, avoiding to select necrotic material or transition zones with healthy mucosa. Samples of colonic healthy mucosa were resected at least 20 centimeters far from the neoplasia and distant from the surgical resection margins. Tissue samples were stored in liquid nitrogen until RNA extraction. Total RNA was extracted from 10–20 mg of tumor samples and from 30–40 mg of normal samples. Nine paired tumor/normal colon tissues on Miltenyi miRXplore Microarray.
2012-11-26 | E-GEOD-33123 | biostudies-arrayexpress