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Series GSE49816 Query DataSets for GSE49816
Status Public on Aug 31, 2013
Title Evaluation of quantitative miRNA gene expression platforms in the microRNA Quality Control (miRQC) study
Organisms Homo sapiens; Escherichia phage MS2
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary MiRNAs are important negative regulators of protein coding gene expression, and have been studied intensively over the last few years. Several measurement platforms, designed to determine their relative RNA abundance levels in biological samples, have been developed. In this study, we systematically compared 12 commercially available miRNA 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 miRNA family members with varying homology. We developed novel and robust quality metrics to objectively assess platform performance of very different technologies such as small RNA sequencing, RT-qPCR and (microarray) hybridization. We assessed reproducibility, sensitivity, accuracy, specificity, and concordance of differential expression. The results indicate that each method has its strengths and weaknesses, which helps to guide informed selection of a quantitative miRNA gene expression platform in function of particular study goals.
 
Overall design Sequencing of 20 miRQC samples on Illumina Genome Analyzer IIx System
 
Contributor(s) Schroth G, Narayanan A, Veeramachaneni V
Citation(s) 24973947
Submission date Aug 12, 2013
Last update date May 15, 2019
Contact name Aishwarya Narayanan
Organization name Strand Life Sciences
Street address 5th Floor, KBP, Bellary Road
City Bangalore
ZIP/Postal code 560024
Country India
 
Platforms (2)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL17561 Illumina Genome Analyzer IIx (Enterobacterio phage MS2)
Samples (20)
GSM1207643 miRQC A
GSM1207644 miRQC A repeat
GSM1207645 miRQC B
Relations
BioProject PRJNA214981
SRA SRP028738

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
GSE49816_RAW.tar 280.0 Kb (http)(custom) TAR (of TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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