E-MTAB-1815 - RNA-seq of non coding RNA from 20 standardized positive and negative control samples, including human universal reference RNA, human brain RNA and titrations thereof, human serum samples, and synthetic spikes from homologous microRNA family members

Status
Released on 1 September 2013, last updated on 2 May 2014
Organism
Homo sapiens
Samples (20)
Protocols (5)
Description
MicroRNAs are important negative regulators of protein coding gene expression, and have been studied intensively over the last few years. To this purpose, different measurement platforms to determine their RNA abundance levels in biological samples have been developed. In this study, we have systematically compared 12 commercially available microRNA expression platforms by measuring an identical set of 20 standardized positive and negative control samples, including human universal reference RNA, human brain RNA and titrations thereof, human serum samples, and synthetic spikes from homologous microRNA family members. We developed novel quality metrics in order to objectively assess platform performance of very different technologies such as small RNA sequencing, RT-qPCR and (microarray) hybridization. We assessed reproducibility, sensitivity, quantitative performance, and specificity. The results indicate that each method has its strengths and weaknesses, which helps guiding informed selection of a quantitative microRNA gene expression platform in function of particular study goals.
Experiment types
RNA-seq of non coding RNA, microRNA profiling by high throughput sequencing, quality control testing design
Contact
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-MTAB-1815.idf.txt
Sample and data relationshipE-MTAB-1815.sdrf.txt
Processed data (2)E-MTAB-1815.processed.1.zip, E-MTAB-1815.processed.2.zip
Links