SRR5121112	GSE92601	GSM2433293	GPL18956	PMID_29807996	ORF1_2	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	BGI inhouse software “filter_fq” for basecalling and trimming PGCGROWTHCONDITIONS
SRR5121112	GSE92601	GSM2433293	GPL18956	PMID_29807996	ORF1_2	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Read-mapping was done with soap2.21. Mapping towards genes was done by the following parameters -m 0 -x 1000 -s 28 -l 32 -v 5 -r 2 -p 3 PGCGROWTHCONDITIONS
SRR5121112	GSE92601	GSM2433293	GPL18956	PMID_29807996	ORF1_2	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	The gene expression values were calculated as RPKM (reads per kilobase transcriptome per million mapped reads) by the inhouse BGI pipeline. PGCGROWTHCONDITIONS
SRR5121112	GSE92601	GSM2433293	GPL18956	PMID_29807996	ORF1_2	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Genome_build:  NC_000913 PGCGROWTHCONDITIONS
SRR5121112	GSE92601	GSM2433293	GPL18956	PMID_29807996	ORF1_2	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process PGCGROWTHCONDITIONS
SRR5121112	GSE92601	GSM2433293	GPL18956	PMID_29807996	ORF1_2	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	The cells for RNA extraction were immediately mixed with RNA Protect Bacterial reagent® (Qiagen) and processed by the RNAeasy Mini Kit (Qiagen) according to the manufacturers instructions. The cells for whole cell proteomics were chilled in ice-slush, pelleted at 14000 rpm, 4°C and the media was aspirated.  The cells were washed with 3×1.5 mL PBS with pelleting at as above in between. The final pellet was stored at -80°C until being shipped to the Proteomics Core Facility at University of Gothenburg for processing. The RNA was shipped to BGI for total RNA sequencing. PGCGROWTHCONDITIONS
SRR5121112	GSE92601	GSM2433293	GPL18956	PMID_29807996	ORF1_2	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	TruSeq PGCGROWTHCONDITIONS
SRR5121112	GSE92601	GSM2433293	GPL18956	PMID_29807996	ORF1_2	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
SRR5121112	GSE92601	GSM2433293	GPL18956	PMID_29807996	ORF1_2	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	organism	Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
SRR5121112	GSE92601	GSM2433293	GPL18956	PMID_29807996	ORF1_2	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	source_name	E. coli MG1655 / pORF1 PGCGROWTHCONDITIONS
SRR5121112	GSE92601	GSM2433293	GPL18956	PMID_29807996	ORF1_2	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	treatment_protocol	The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
SRR5121112	GSE92601	GSM2433293	GPL18956	PMID_29807996	ORF1_2	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR5121112	GSE92601	GSM2433293	GPL18956	PMID_29807996	ORF1_2	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	characteristics	replicates: ORF1 replicate 2 / not induced PGCGROWTHCONDITIONS
SRR5121112	GSE92601	GSM2433293	GPL18956	PMID_29807996	ORF1_2	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
SRR5121112	GSE92601	GSM2433293	GPL18956	PMID_29807996	ORF1_2	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	organism	Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
SRR5121112	GSE92601	GSM2433293	GPL18956	PMID_29807996	ORF1_2	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	source_name	E. coli MG1655 / pORF1 PGCGROWTHCONDITIONS
SRR5121112	GSE92601	GSM2433293	GPL18956	PMID_29807996	ORF1_2	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	treatment_protocol	The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
SRR5121112	GSE92601	GSM2433293	GPL18956	PMID_29807996	ORF1_2	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	contact_name	Dan,I.,Andersson PGCGROWTHCONDITIONS