Table 3

Unique reference genes shared between and unique to DNA and RNA datasets

Reference genes present ina


Depth (m)

DNA+RNAb

DNA onlyc

RNA only


OMZ

50

11,374

113,747

21,445

85

5801

172,055

6766

110

17,843

109,924

31,697

200

12,688

126,574

17,408

BATS 216

20

29,841

90,866

60,287

50

26,954

110,131

38,145

100

31,416

119,795

36,871

HOT 186

25

28,459

135,390

44,243

75

18,098

142,892

21,800

110

12,148

125,882

12,315

500

14,345

248,534

13,573

Soil

Surface

104,453

283,180

107,475


aNumber of unique NCBI-nr reference genes (accession numbers) identified as top matches to query reads via BLASTX (bit score > 50); in instances when a read matched multiple genes with equal bit scores, all genes were counted. bGenes present in both DNA and RNA datasets, that is, 'expressed' genes. cGenes present only in the DNA dataset, that is, 'non-expressed' genes. BATS, Bermuda Atlantic Time Series; BLAST, Basic Local Alignment Search Tool; HOT, Hawaii Ocean Time Series; NCBI-nr, National Center for Biotechnology Information non-redundant protein database; OMZ, oxygen minimum zone.

Stewart et al. Genome Biology 2011 12:R26   doi:10.1186/gb-2011-12-3-r26

Open Data