Skip to main content

Table 1 Summary of Results

From: Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods

Representative Figure(s) Assessment Clontech Illumina NEB NEXTflex Deduped Fivepercent
Method information
 Figure 1 Designed for adapter ligation mitigation? Adapter Ligation free None PEG PEG and Randomized adapters PEG and Randomized adapters PEG and Randomized adapters
 Figure 1 Designed for reverse transcription and PCR bias mitigation? None None None None UMI None
Performance metrics
 Figure 2 How similar are the quantifications of the same brain sample? lowest correlations with other methods Intermediate Intermediate Intermediate Intermediate Intermediate
 Figure 3 Accuracy - similar detection of different sequences Intermediate Worst Worst Intermediate Best Intermediate
Detection Diversity
 Figure 4a-b Mapping rate to miRNA Worst Best Best Best Besta Besta
 Figure 4c Detection of miRNA across triplicates at 1000 ng Intermediate Intermediate Intermediate Intermediate Best Worst
 Figure 4d Consistency of miRNA detection at 1000 ng Worst Intermediate Best Intermediate Intermediate Intermediate
 Figure 4e Diversity of detection of isomiRs across triplicates at 1000 ng Best Intermediate Intermediate Worst Intermediate Worst
 Figure 4f Consistency of isomiR detection at 1000 ng Intermediate Worst Best Intermediate Intermediate Intermediate
 Figure 4i False isomiR detection per synthetic sequence Worst Intermediate Intermediate Best Best Best
 Figure 4j False IsomiR expression Intermediate Intermediate Worst Best Best Best
 Figure 5a Consistency across batch Intermediate Worst Best Best Best Intermediate
 Figure 5b-c Consistency across triplicates Intermediate Worst Best Intermediate Best Worst
Overall conclusions
   Poor mapping rate, more accurate miRNA quantification, poor isomiR accuracy Not as accurate, less detection, and less consistency Good mapping, not as accurate, quite consistent, poor isomiR accuracy Good mapping, more accurate miRNA quantification, more accurate isomiR quantification Best performance overall, more accurate miRNA quantification Deduping improves performance, not just an effect of reducing number of reads
  1. The table depicts the results of the various assessments performed on the 6 small RNA sequencing methods. aThe mapping rate of the raw NEXTflex data should reflect the quality for the data used for the Deduped and Fivepercent methods as these are derived from the raw NEXTflex data