Comparative Transcriptomics of Diverse Microbes

Escherichia coli strain MG1655 was used in three biological replicate DNA-seq experiments (Cari Vanderpool, personal communication). Library construction and sequencing on an Illumina HiSeq 2500 were performed at the WM Keck Center for Comparative and Functional Genomics at the University of Illinois at Urbana-Champaign. The DNA libraries were prepared with the KAPA Library Preparation Kits (KAPA Biosystems (Wilmington, MA, USA)). The libraries were quantified by quantitative PCR , pooled in equimolar concentration, and sequenced on one lane for 101 cycles from one end of the fragments using a TruSeq SBS version 3 sequencing kit (Illumina (San Diego, CA, USA)). The fastq files were generated with Casava 1.8.2 (Illumina).
RNA-seq data from E. coli, Streptococcus pyogenes, Mycobacterium tuberculosis, Bacillus subtilis, Staphylococcus aureus, Pyrococcus abyssi, Acinetobacter oleivorans, Propionibacterium acnes, Methanobrevibacter smithii, Clostridium acetobutylicum, and Deinococcus gobiensis were downloaded from the Sequence Read Archive (SRA) [23 (link)]. Details on each RNA-seq data set, including accession number in the SRA, length of the reads, whether the reads are single-end or paired-end, and the number of reads, is provided in Table 1. The Schizosaccharomyces pombe RNA-seq data [24 (link)] were downloaded from the Trinity tutorial [25 (link)].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.