De novo assembly of bacterial transcriptomes from RNA-seq data

Table 1 Sequencing data sets

Organism	Type	Domain	Class	SRA accession number	Read type	Length of reads (bp)	Number of reads	Number of reference genes
Escherichia coli	DNA-seq	Bacteria	Gammaproteobacteria	SRP049375	Single	100	67,713,365	-
Escherichia coli	RNA-seq	Bacteria	Gammaproteobacteria	SRX254784	Single	100	34,085,732	4,190
Acinetobacter oleivorans	RNA-seq	Bacteria	Gammaproteobacteria	SRX560107	Paired	101	19,140,537	2,934
Deinococcus gobiensis	RNA-seq	Bacteria	Deinococci	SRX061110	Paired	75	18,676,333	610
Mycobacterium tuberculosis	RNA-seq	Bacteria	Actinobacteria	SRX380298	Paired	51	2,364,009	752
Streptococcus pyogenes	RNA-seq	Bacteria	Bacilli	SRX252449	Single	72	7,049,947	372
Bacillus subtilis	RNA-seq	Bacteria	Bacilli	SRX533166	Single	51	14,010,827	1,917
Staphylococcus aureus	RNA-seq	Bacteria	Bacilli	SRX172891	Paired	101	9,067,797	1,720
Propionibacterium acnes	RNA-seq	Bacteria	Actinobacteria	SRX278003	Single	75	195,541,304	1,777
Clostridium acetobutylicum	RNA-seq	Bacteria	Clostridia	SRX316281	Single	50	13,256,052	202
Pyrococcus abyssi	RNA-seq	Archaea	Thermococci	SRX556571	Single	40	51,342,770	133
Methanobrevibacter smithii	RNA-seq	Archaea	Methanobacteria	SRX031877	Single	36	32,744,832	211
Schizosaccharomyces pombe	RNA-seq	Eukarya	Schizosaccharomycetes	NA	Paired	68	4,000,000	3,591

The table summarizes the DNA-seq data set and the 12 RNA-seq data sets used in this study. Information in the table includes the length and number of sequencing reads in each data set. NA, not available.

ISSN: 1474-760X