"Basecalls performed using HCS 2.0.5 and RTA 1.17.20"	"data_processing.1"
"RNA-seq reads were aligned to the W3110 genome  using CASAVA 1.8.2"	"data_processing.2"
"Gene expression (based on known genes) was determined using Cufflinks 2.0.2, only PF reads were retained"	"data_processing.3"
"Genome_build: W3110  (NC_007779)"	"data_processing.4"
"Supplementary_files_format_and_content: excel file with coverage and FPKM measurements"	"data_processing.5"
"Total RNA was extracted using the frozen acid-phenol method described by Maes and Messens (Maes and Messens, 1992) and then treated with RNase-free DNaseI according to the manufacturer’s recommendations (Ambion, USA)."	"extract_protocol_ch1.1"
"Library preparation were performed with Epicentre ScriptseqTM v2 RNA-Seq Library preparation kit with 50 ng of depleted RNA; Strand orientated RNA-Seq"	"extract_protocol_ch1.2"
"Transcriptomic analyses were carried out after growing bacteria in minimal media supplemented with glucose. Several Ni concentrations and exposure times were assayed. rcnA gene expression was taken as an internal control to arbitrate between the different conditions. rcnA is induced by Ni when cells are overloaded with this ion and must detoxify the cytoplasm by extruding excess metal via the RcnAB efflux system. rcnA induction was maximised after culture incubation for 10 min, and longer periods of incubation lead to a decline in rcnA expression (Fig. S1). For the RNA-Seq experiments, bacteria were grown until O.D600nm = 0.3, were treated with 50 µM NiCl2 for 10 min and were frozen prior to RNA extraction."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli_control condition"	"source_name_ch1.1"
"Rodrigue_6-WT-phiNi-2"	"title.1"
"RNA-Seq"	"library_strategy.1"
"strain: W3110"	"characteristics_ch1.1"
"growth phase: log phase"	"characteristics_ch1.2"
"genotype: wild type"	"characteristics_ch1.3"
"Transcriptomic analyses were carried out after growing bacteria in minimal media supplemented with glucose. Several Ni concentrations and exposure times were assayed. rcnA gene expression was taken as an internal control to arbitrate between the different conditions. rcnA is induced by Ni when cells are overloaded with this ion and must detoxify the cytoplasm by extruding excess metal via the RcnAB efflux system. rcnA induction was maximised after culture incubation for 10 min, and longer periods of incubation lead to a decline in rcnA expression (Fig. S1). For the RNA-Seq experiments, bacteria were grown until O.D600nm = 0.3, were treated with 50 µM NiCl2 for 10 min and were frozen prior to RNA extraction."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli_control condition"	"source_name_ch1.1"