SRR3033280SRR3033281SRR3033282SRR3033283	GSE76167	GSM1975604	GPL18133	PMID_27375130PMID_27668277	Rodrigue_6-WT-phiNi-2	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Basecalls performed using HCS 2.0.5 and RTA 1.17.20 PGCGROWTHCONDITIONS
SRR3033280SRR3033281SRR3033282SRR3033283	GSE76167	GSM1975604	GPL18133	PMID_27375130PMID_27668277	Rodrigue_6-WT-phiNi-2	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	RNA-seq reads were aligned to the W3110 genome  using CASAVA 1.8.2 PGCGROWTHCONDITIONS
SRR3033280SRR3033281SRR3033282SRR3033283	GSE76167	GSM1975604	GPL18133	PMID_27375130PMID_27668277	Rodrigue_6-WT-phiNi-2	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Gene expression (based on known genes) was determined using Cufflinks 2.0.2, only PF reads were retained PGCGROWTHCONDITIONS
SRR3033280SRR3033281SRR3033282SRR3033283	GSE76167	GSM1975604	GPL18133	PMID_27375130PMID_27668277	Rodrigue_6-WT-phiNi-2	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Genome_build: W3110  (NC_007779) PGCGROWTHCONDITIONS
SRR3033280SRR3033281SRR3033282SRR3033283	GSE76167	GSM1975604	GPL18133	PMID_27375130PMID_27668277	Rodrigue_6-WT-phiNi-2	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Supplementary_files_format_and_content: excel file with coverage and FPKM measurements PGCGROWTHCONDITIONS
SRR3033280SRR3033281SRR3033282SRR3033283	GSE76167	GSM1975604	GPL18133	PMID_27375130PMID_27668277	Rodrigue_6-WT-phiNi-2	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	extract_protocol	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). PGCGROWTHCONDITIONS
SRR3033280SRR3033281SRR3033282SRR3033283	GSE76167	GSM1975604	GPL18133	PMID_27375130PMID_27668277	Rodrigue_6-WT-phiNi-2	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	extract_protocol	Library preparation were performed with Epicentre ScriptseqTM v2 RNA-Seq Library preparation kit with 50 ng of depleted RNA; Strand orientated RNA-Seq PGCGROWTHCONDITIONS
SRR3033280SRR3033281SRR3033282SRR3033283	GSE76167	GSM1975604	GPL18133	PMID_27375130PMID_27668277	Rodrigue_6-WT-phiNi-2	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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. PGCGROWTHCONDITIONS
SRR3033280SRR3033281SRR3033282SRR3033283	GSE76167	GSM1975604	GPL18133	PMID_27375130PMID_27668277	Rodrigue_6-WT-phiNi-2	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR3033280SRR3033281SRR3033282SRR3033283	GSE76167	GSM1975604	GPL18133	PMID_27375130PMID_27668277	Rodrigue_6-WT-phiNi-2	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	source_name	Escherichia coli_control condition PGCGROWTHCONDITIONS
SRR3033280SRR3033281SRR3033282SRR3033283	GSE76167	GSM1975604	GPL18133	PMID_27375130PMID_27668277	Rodrigue_6-WT-phiNi-2	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR3033280SRR3033281SRR3033282SRR3033283	GSE76167	GSM1975604	GPL18133	PMID_27375130PMID_27668277	Rodrigue_6-WT-phiNi-2	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	strain: W3110 PGCGROWTHCONDITIONS
SRR3033280SRR3033281SRR3033282SRR3033283	GSE76167	GSM1975604	GPL18133	PMID_27375130PMID_27668277	Rodrigue_6-WT-phiNi-2	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	growth phase: log phase PGCGROWTHCONDITIONS
SRR3033280SRR3033281SRR3033282SRR3033283	GSE76167	GSM1975604	GPL18133	PMID_27375130PMID_27668277	Rodrigue_6-WT-phiNi-2	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	genotype: wild type PGCGROWTHCONDITIONS
SRR3033280SRR3033281SRR3033282SRR3033283	GSE76167	GSM1975604	GPL18133	PMID_27375130PMID_27668277	Rodrigue_6-WT-phiNi-2	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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. PGCGROWTHCONDITIONS
SRR3033280SRR3033281SRR3033282SRR3033283	GSE76167	GSM1975604	GPL18133	PMID_27375130PMID_27668277	Rodrigue_6-WT-phiNi-2	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR3033280SRR3033281SRR3033282SRR3033283	GSE76167	GSM1975604	GPL18133	PMID_27375130PMID_27668277	Rodrigue_6-WT-phiNi-2	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	source_name	Escherichia coli_control condition PGCGROWTHCONDITIONS
SRR3033280SRR3033281SRR3033282SRR3033283	GSE76167	GSM1975604	GPL18133	PMID_27375130PMID_27668277	Rodrigue_6-WT-phiNi-2	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	contact_name	Agnès,,Rodrigue PGCGROWTHCONDITIONS