Skip to main content

Table 2 Summary of datasets

From: Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data

      Library size (× 106)    
Dataset and reference Replicate size Species Type Number of genes Min. Max. Correlation among replicatesa Sequencing instrument Library type
CRC AZA {3, 3} Human mRNA 16,499 3.3 4.2 (0.99, 0.99) HiSeq 2000 PE, 100, poly(A)
Hammer [39] {2, 2} Rat mRNA 15,908 17.3 23.5 (0.99, 0.99) GAII SR, 50, poly(A)
Bottomly [40] {10, 11} Mouse mRNA 12,784 2.7 7.3 (0.82, 0.99) GAIIx SR, 30, poly(A)
GTEx [41] {28, 30} Human mRNA 18,632 10.2 76.8 (0.45, 0.99) HiSeq 2000 PE, 76, poly(A)
Zhang [36] {81, 91} Human mRNA 19,254 10.8 31.7 (0.29, 0.98) HiSeq 2000 PE, 90, poly(A)
    lncRNA 10,051 0.3 1.0 (0.19, 0.97)   
NGP nutlin {10, 10} Human mRNA 17,489 13.4 18.1 (0.98, 0.99) NextSeq 500 PE, 75, poly(A)
    lncRNA 8929 0.2 0.4 (0.83, 0.99)   
  1. aPearson’s correlation is calculated among replicates within conditions based on read counts
  2. Data include the species, gene biotype, number of genes (annotated genes with at least one count in each condition), number of replicates per condition, library size (minimum, maximum), Pearson correlation among replicates (minimum, maximum), sequencing instrument, library type (SR=single read, PE=paired-end read, read length (nucleotides), sequencing type poly(A)/total).