Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

34 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MiRQC PGM data

ABSTRACT: 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.

INSTRUMENT(S): Ion Torrent PGM

ORGANISM(S): Homo sapiens

SUBMITTER: Brian Sanderson

PROVIDER: E-MTAB-1815 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Performance Evaluation of Commercial miRNA Expression Array Platforms

Project description:This data is part of a miRNA platform comparison study. We compared the performance characteristics of four commercial miRNA array technologies and found that all platforms performed well in separate measures of performance. The Ambion and Agilent platforms were more accurate, whereas the Illumina and Exiqon platforms were more specific. Furthermore, the data analysis approach had a large impact on the performance, predominantly by improving precision. Performance of four (4) commercially available miRNA platforms was evaluated using 7 placenta samples spiked with synthetic microRNA spikes (in Latin-square design) absent in placenta. Platforms were primarily evaluated for accuracy and specificity.

2010-06-23 | E-GEOD-19248 | biostudies-arrayexpress

Evaluation of quantitative miRNA gene expression platforms - custom microRNA GeneChip

Project description:MicroRNA microarray expression dataset used to develop novel and robust quality metrics to objectively assess platform performance of very different technologies. The HsMir v1s520779F custom array is primarly based on the commercially available Affymetrix microRNA microarray version 2.0 (Affymetrix GeneChip miRNA 2.0 Array datasheet P/N EXP00180 Rev 1) with i) microRNA probe sequences updated using miRBase version 17 ii) all human pre-microRNAs removed iii) all non-human sequences removed iv) all viral target sequences removed. In summary, the array contains 1738 mature microRNAs and 2333 other small RNAs (such as small nucleolar RNAs or small cajal body-specific RNAs) probe sequences plus the Affymetrix hybridization and normalization control probesets.

2013-08-09 | E-GEOD-49661 | biostudies-arrayexpress

A cross-comparison of technologies for the detection of microRNAs from FFPE samples of hepatoblastoma patients [NanoString]

Project description:This work highlights similarities and differences between three platforms (next-generation sequencing, microarray and NanoString) for detecting miRNAs and compares their strengths and weaknesses. miRNA expression profiles were determined in Hepatoblastoma FFPE samples using a NanoString platform.

2015-05-03 | E-GEOD-62017 | biostudies-arrayexpress

Evaluation of quantitative miRNA gene expression platforms in the microRNA Quality Control (miRQC) study

Project description: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. Sequencing of 20 miRQC samples on Illumina Genome Analyzer IIx System

2013-08-31 | E-GEOD-49816 | biostudies-arrayexpress

MicroRNA sequencing of mouse soleus muscle

Project description:MicroRNA sequencing using Ion Torrent Proton platform Single run of a pool of m.soleus from 5 male mice

2015-03-31 | E-GEOD-63342 | biostudies-arrayexpress

Serum microRNA profiles from the Malmö Diet and Cancer Study - Cardiovascular Cohort

Project description:This data set pertains to expression levels of 750 mature human microRNA in the serum samples from the Malmö Diet and Cancer Study - Cardiovascular cohort to determine consistently expressed microRNAs in the pilot study of N=12 samples.

2018-11-08 | E-MTAB-7246 | biostudies-arrayexpress

A cross-comparison of technologies for the detection of microRNAs from FFPE samples of hepatoblastoma patients [sequencing]

Project description:This work highlights similarities and differences between three platforms (next-generation sequencing, microarray and NanoString) for detecting miRNAs and compares their strengths and weaknesses. miRNA expression profiles were determined in 6 Hepatoblastoma FFPE samples using a next-generation sequencing platform.

2015-05-03 | E-GEOD-62010 | biostudies-arrayexpress

microRNA epxression patterns can discriminate between patients with oligometastatic and polymetastatic progression

Project description:This SuperSeries is composed of the following subset Series: GSE25552: microRNA epxression patterns can discriminate between patients with oligometastatic and polymetastatic progression: tissues GSE25967: microRNA epxression patterns can discriminate between patients with oligometastatic and polymetastatic progression: cell lines Refer to individual Series

2010-12-09 | E-GEOD-25968 | biostudies-arrayexpress