"strain: JM83"	"characteristics_ch1.1"
"genotype/variation: wild type"	"characteristics_ch1.2"
"treated with: none (untreated control)"	"characteristics_ch1.3"
"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. DNA was isolated using the Wizard Genomic DNA Purification Kit (Promega)."	"extract_protocol_ch1.1"
"Library preparation was performed by vertis Biotechnologie AG, according to the following protocol: the DNA samples were treated with ultrasound (3-5 pulses of 30 sec at 4°C). After end-repair, TruSeq sequencing adapters were ligated to the DNA fragments. Finally, the DNA was PCR-amplified to about 20-30 ng/μl using a high fidelity DNA polymerase (9-11 cycles, depending on the sample). Aliquots of the PCR amplified libraries were examined 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_DNA"	"title.1"
"OTHER"	"library_strategy.1"
"strain: JM83"	"characteristics_ch1.1"
"genotype/variation: wild type"	"characteristics_ch1.2"
"treated with: none (untreated control)"	"characteristics_ch1.3"
"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"