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Table 2 Summary of transcriptome analysesa

From: Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses

Transcriptome analyses

W5 cDNA

Roche 454 GS FLX

 

Run cycles

Total number of reads

Total read length, Mb

1

526,516

111

   Average read length, bp

210.2

Illumina GA II Paired-End

 

   Read length, bp

40 + 40

   Run lanes

1

Total number of reads

Total read length, Mb

14,802,234

1,184

   GC content

37.1%

Contig assembly

 

   Contig numbers

20,232

   Total contig lengths, Mb

9.0

   Average contig length, bp

447.2

   Largest contig length, bp

4,397

Gene prediction, length > 500 bp

 

   Number of ORFs

2,284

   Number of domains predicted in ORFs

9,720

   Average ORF length, bp

846.9

   Maximum RPKMb value

31,647.2

   Number of GH-like contigs

219

  1. aGC: the nucleotide G+C % ; GH: glycosyl hydrolase; ORF: open reading frame; RPKM: Reads Per Kilobase of exon model per Million mapped reads. bRPKM is a method for estimating relative expression levels of a transcriptome by normalizing short-read expressed tags from deep sequencing over ORF length and total reads (RPKM) [35].