"Illumina Casava 1.8 software was used for basecalling."	"data_processing.1"
"S. pneumoniae reads were mapped to the D39 whole genome with Rockhopper version 1.21, using default parameters. E. coli reads were mapped to the K-12, substr. MG1655 whole genome with Bowtie 2, using parameters --mixed --discordant -D 10 -R 2 -N 0 -L 22 -i S,0,2.50."	"data_processing.2"
"Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. For the S. pneumoniae samples this was done internally by Rockhopper version 1.21 after aligning reads."	"data_processing.3"
"Genome_build: Streptococcus pneumoniae D39 (assembly ASM1436v1)"	"data_processing.4"
"Genome_build: Escherichia coli K-12, substr. MG1655 (assembly ASM584v2)"	"data_processing.5"
"Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample."	"data_processing.6"
"For all the samples; when 1/3 of the maximum OD600 was reached, cells were harvested by centrifugation (7,500 rcf for 5 min) and frozen. For RNA isolation, cells were lysed by bead beating and RNA was purified using phenol-chloroform extractions and ethanol precipitations. DNA was removed from the sample with RNase-free DNase I (Fermentas) treatment for 45 min. Ribolock (Fermentas) was added to avoid RNA degradation."	"extract_protocol_ch1.1"
"Library preparation was performed by vertis Biotechnologie AG, according to the following protocol: RNA samples were first treated with rDNase. From the total RNA samples, ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit (Bacteria, Epicentre). the rRNA depleted RNA samples were fragmented with ultrasound (2 pulses of 30 sec at 4°C). Firststrand cDNA synthesis was primed with a N6 randomized primer. Then, Illumina TruSeq sequencing adapters were ligated to the 5' and 3' ends of the cDNA. The cDNA was finally amplified with PCR (16-18 cycles, depending on sample) using a proof reading enzyme. Aliquots of each library were analyzed by capillary electrophoresis."	"extract_protocol_ch1.2"
"Overnight cultures of strain JM83 were diluted 1/100 in LB medium and grown in microtiter plates. To study the effects of trimethoprim, cells grown without antibiotics were compared to cells grown with 0.5 μg/ml trimethoprim."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Untreated E. coli cells"	"source_name_ch1.1"
"EC_Cont1_RNA"	"title.1"
"RNA-Seq"	"library_strategy.1"
"strain: JM83"	"characteristics_ch1.1"
"genotype/variation: wild type"	"characteristics_ch1.2"
"treated with: none (untreated control)"	"characteristics_ch1.3"
"molecule subtype: total RNA, rRNA depleted"	"characteristics_ch1.4"
"Overnight cultures of strain JM83 were diluted 1/100 in LB medium and grown in microtiter plates. To study the effects of trimethoprim, cells grown without antibiotics were compared to cells grown with 0.5 μg/ml trimethoprim."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Untreated E. coli cells"	"source_name_ch1.1"