title: Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues.
abstract: MicroRNAs play a role in regulating diverse biological processes and have considerable utility as molecular markers for diagnosis and monitoring of human disease. Several technologies are available commercially for measuring microRNA expression. However, cross-platform comparisons do not necessarily correlate well, making it difficult to determine which platform most closely represents the true microRNA expression level in a tissue. To address this issue, we have analyzed RNA derived from cell lines, as well as fresh frozen and formalin-fixed paraffin embedded tissues, using Affymetrix, Agilent, and Illumina microRNA arrays, NanoString counting, and Illumina Next Generation Sequencing. We compared the performance within- and between the different platforms, and then verified these results with those of quantitative PCR data. Our results demonstrate that the within-platform reproducibility for each method is consistently high and although the gene expression profiles from each platform show unique traits, comparison of genes that were commonly detectable showed that detection of microRNA transcripts was similar across multiple platforms.
authors: Medical Genome Facility Gene Expression Core, Mayo Clinic, Rochester, Minnesota, United States of America. Kolbert.christopher@mayo.edu
authors: Christopher P
authors: CP
authors: Kolbert
authors: Rod M
authors: RM
authors: Feddersen
authors: Fariborz
authors: F
authors: Rakhshan
authors: Diane E
authors: DE
authors: Grill
authors: Gyorgy
authors: G
authors: Simon
authors: Sumit
authors: S
authors: Middha
authors: Jin Sung
authors: JS
authors: Jang
authors: Vernadette
authors: V
authors: Simon
authors: Debra A
authors: DA
authors: Schultz
authors: Michael
authors: M
authors: Zschunke
authors: Wilma
authors: W
authors: Lingle
authors: Jennifer M
authors: JM
authors: Carr
authors: E Aubrey
authors: EA
authors: Thompson
authors: Ann L
authors: AL
authors: Oberg
authors: Bruce W
authors: BW
authors: Eckloff
authors: Eric D
authors: ED
authors: Wieben
authors: Peter
authors: P
authors: Li
authors: Ping
authors: P
authors: Yang
authors: Jin
authors: J
authors: Jen
mesh_terms: D002460:Cell Line; D005557:Formaldehyde; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D016612:Paraffin Embedding; D015203:Reproducibility of Results; D016707:Tissue Fixation
chemical_list: D035683:MicroRNAs; D005557:Formaldehyde
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