SRR1124840	GSE54199	GSM1310003	GPL14548-GPL18183	PMID_24725406	EC_Cont1_RNA	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	data_processing	Illumina Casava 1.8 software was used for basecalling. PGCGROWTHCONDITIONS
SRR1124840	GSE54199	GSM1310003	GPL14548-GPL18183	PMID_24725406	EC_Cont1_RNA	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	data_processing	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. PGCGROWTHCONDITIONS
SRR1124840	GSE54199	GSM1310003	GPL14548-GPL18183	PMID_24725406	EC_Cont1_RNA	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	data_processing	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. PGCGROWTHCONDITIONS
SRR1124840	GSE54199	GSM1310003	GPL14548-GPL18183	PMID_24725406	EC_Cont1_RNA	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	data_processing	Genome_build: Streptococcus pneumoniae D39 (assembly ASM1436v1) PGCGROWTHCONDITIONS
SRR1124840	GSE54199	GSM1310003	GPL14548-GPL18183	PMID_24725406	EC_Cont1_RNA	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	data_processing	Genome_build: Escherichia coli K-12, substr. MG1655 (assembly ASM584v2) PGCGROWTHCONDITIONS
SRR1124840	GSE54199	GSM1310003	GPL14548-GPL18183	PMID_24725406	EC_Cont1_RNA	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	data_processing	Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample. PGCGROWTHCONDITIONS
SRR1124840	GSE54199	GSM1310003	GPL14548-GPL18183	PMID_24725406	EC_Cont1_RNA	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	extract_protocol	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. PGCGROWTHCONDITIONS
SRR1124840	GSE54199	GSM1310003	GPL14548-GPL18183	PMID_24725406	EC_Cont1_RNA	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	extract_protocol	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[linebreak] and 3[linebreak] 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. PGCGROWTHCONDITIONS
SRR1124840	GSE54199	GSM1310003	GPL14548-GPL18183	PMID_24725406	EC_Cont1_RNA	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	growth_protocol	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. PGCGROWTHCONDITIONS
SRR1124840	GSE54199	GSM1310003	GPL14548-GPL18183	PMID_24725406	EC_Cont1_RNA	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR1124840	GSE54199	GSM1310003	GPL14548-GPL18183	PMID_24725406	EC_Cont1_RNA	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	source_name	Untreated E. coli cells PGCGROWTHCONDITIONS
SRR1124840	GSE54199	GSM1310003	GPL14548-GPL18183	PMID_24725406	EC_Cont1_RNA	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR1124840	GSE54199	GSM1310003	GPL14548-GPL18183	PMID_24725406	EC_Cont1_RNA	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	characteristics	strain: JM83 PGCGROWTHCONDITIONS
SRR1124840	GSE54199	GSM1310003	GPL14548-GPL18183	PMID_24725406	EC_Cont1_RNA	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	characteristics	genotype/variation: wild type PGCGROWTHCONDITIONS
SRR1124840	GSE54199	GSM1310003	GPL14548-GPL18183	PMID_24725406	EC_Cont1_RNA	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	characteristics	treated with: none (untreated control) PGCGROWTHCONDITIONS
SRR1124840	GSE54199	GSM1310003	GPL14548-GPL18183	PMID_24725406	EC_Cont1_RNA	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	characteristics	molecule subtype: total RNA, rRNA depleted PGCGROWTHCONDITIONS
SRR1124840	GSE54199	GSM1310003	GPL14548-GPL18183	PMID_24725406	EC_Cont1_RNA	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	growth_protocol	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. PGCGROWTHCONDITIONS
SRR1124840	GSE54199	GSM1310003	GPL14548-GPL18183	PMID_24725406	EC_Cont1_RNA	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR1124840	GSE54199	GSM1310003	GPL14548-GPL18183	PMID_24725406	EC_Cont1_RNA	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	source_name	Untreated E. coli cells PGCGROWTHCONDITIONS
SRR1124840	GSE54199	GSM1310003	GPL14548-GPL18183	PMID_24725406	EC_Cont1_RNA	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	contact_name	Jelle,,Slager PGCGROWTHCONDITIONS