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Table 2 Comparison between expression and transcript assemblies for sample 2

From: Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues

 

Cytoplasmic

PolyA+

Total

Nuclear

Number expressed exons

241704

203924

187836

168962

N50 size

428

354

308

-

Bases in transcripts > 500 nt (M)

14.7

13.3

1.9

-

Bases in transcripts > 1000 nt (M)

4.5

3.5

0.5

-

ORFs > 100aa

6,323

6,028

883

-

  1. Shown are the N50 sizes (half of the bases in the assembly resides in contigs this size or larger), the total bases contained in contigs larger than 500 and 1000 nucleotides and the number of transcripts with open reading frames (ORF) larger than 100 amino acids. In all cases, the cytoplasmic assembly outperforms polyA+ selection, as well as Total RNA. Trinity could not assemble the nuclear fraction due to long run times and we terminated the process after taking up 2.5 CPU years.