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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).