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Table 1 Main methods to detect and quantify noncoding RNAs

From: Long non-coding RNAs in Oral squamous cell carcinoma: biologic function, mechanisms and clinical implications

  Method Advantages Limitations Reference (PMID)
ncRNA Northern blot Gold standard;
Specificity
Limited sensitivity;
Low throughput;
Time consuming;
Limited for quantification
([42], 11679671);
([43], 18025253)
ncRNA SPR Sensitivity Expensive read-out system;
High background signal;
Limited throughput
([44], 17061884);
([45], 21284927)
ncRNA In situ hybridization Locates miRNA in tissue and cell compartments Low throughput;
Invasive sample collection;
Limited sensitivity;
Limited quantification
([46], 16369549);
([47], 22482439)
ncRNA Microarray High throughput Fair specificity;
Medium sensitivity;
Limited quantification
([48], 17675362);
([49], 22593088)
ncRNA Bioluminescence Sensitivity High costs;
Difficult to standardize
([50], 18302417)
ncRNA Electrochemical detection Cost-effective sensitive sensors Verified background signal;
Special nanoparticle labels
([51], 19367400);
([52], 21207998)
ncRNA RNA sequencing High throughput;
Sensitivity;
Specificity
Complex data analysis;
High costs
([53], 20473869);
([54], 22298638)
ncRNA Nanopore-based RNA detection Single-molecule detection;
Contractible;
Possibilities for high throughput;
Rapid
Requiring sophisticated detection instruments;
Complex data analysis
([55], 20972437);
([56], 21892163)
ncRNA qRT-PCR Semi-high throughput;
Good quantification;
Amplification enables;
Sensitivity
Difficult to distinguish single-nucleotide differences;
Not for ncRNA discovery
([57], 21867561);
([58], 22332658)
ncRNA Flow cytometry-FISH High throughput detection of in situ hybridization No quantification;
No location of the ncRNA
([59], 22057868)
ncRNA Nanoresonator chip Quantitative sensitivity;
Specificity
Limited reproducibility;
Complex production process for nanoresonators
([60], 22115599)
ncRNA Base stacking hybridization coupling with time-resolved fluorescence technology Rapid,
Universal label;
Sensitivity
Needs fluorescent tag ([61], 22365748)
ncRNA Scanometric miRNA array Sensitivity High background signal ([62], 22489825)
ncRNA Fluorescence quenching on graphene oxide Amplification process;
Sensitivity
High costs ([63], 22510208)
  1. LNA Locked nucleic acid, ncRNA Noncoding RNA, qRT-PCR Quantitative reverse transcription PCR, LOD Limit of detection, SPR Surface plasmon resonance