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Series GSE189930 Query DataSets for GSE189930
Status Public on Jan 20, 2022
Title A MicroRNA Next-Generation-Sequencing Discovery Assay (miND) For Genome-Scale and Absolute Quantitation of Circulating MicroRNA Biomarkers
Organisms Homo sapiens; synthetic construct
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary The plasma levels of tissue-specific microRNAs can be used as prognostic and diagnostic biomarkers for chronic and acute diseases. Thereby, the combination of diverse miRNAs into biomarker signatures using multivariate statistics seems especially powerful in view to tissue and condition specific miRNA shedding into the plasma. Although Next-Generation Sequencing (NGS) technology enables to analyse circulating microRNAs on a genome-scale level, it suffers from potential biases (e.g. adapter ligation bias) and lacks absolute transcript quantitation. In order to develop a robust NGS discovery assay for genome-scale quantitation of circulating microRNAs we first evaluated the sensitivity, repeatability and ligation bias of four commercially available small RNA library preparation protocols. The protocol from RealSeq Biosciences was selected based on its performance and usability, and coupled with a novel panel of exogenous small RNA spike-in controls to enable absolute quantitation and ensure comparability of data across independent NGS experiments. The established MicroRNA Next-Generation-Sequencing Discovery Assay (miND) was validated for its relative accuracy, precision, analytical measurement range and sequencing bias and was considered fit-for-purpose for microRNA biomarker discovery. Summarized, all these criteria were met and thus our analytical platform is considered fit-for-purpose for microRNA biomarker discovery from plasma, serum, cerebrospinal fluid (CSF), synovial fluid (SF), or extracellular vesicles (EV) extracted from cell culture medium in the setting of any diagnostic, prognostic or patient stratification need.
 
Overall design A comprehensive comparison of four commersially available small RNA sequencing protocols followed by the assay development and validation for the MicroRNA Next-Generation Discovery Assay (miND)
 
Contributor(s) Khamina K, Diendorfer AB, Skalicky S, Weigl M, Pultar M, Krammer T, Fournier CA, Schofield AL, Otto C, Smith AT, Buchtele N, Schoergenhofer C, Jilma B, Frank BJ, Hofstaetter JG, Grillari R, Grillari J, Ruprecht K, Goldring CE, Rehrauer H, Glaab WE, Hackl M
Citation(s) 35163149
Submission date Dec 01, 2021
Last update date Mar 31, 2022
Contact name Andreas B Diendorfer
E-mail(s) service@tamirna.com
Organization name TAmiRNA GmbH
Street address Leberstra├če 20
City Wien
ZIP/Postal code 1110
Country Austria
 
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL19604 Illumina HiSeq 2500 (synthetic construct)
Samples (81)
GSM5710065 Qiaseq_miRXplore_Rep01
GSM5710066 Qiaseq_miRXplore_Rep02
GSM5710067 Qiaseq_miRXplore_Rep03
Relations
BioProject PRJNA785168

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
GSE189930_RAW.tar 1.4 Mb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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