|
| Status |
Public on Jul 01, 2016 |
| Title |
Rodrigue_2-WT-Ni-1 |
| Sample type |
SRA |
| |
|
| Source name |
Escherichia coli_nickel condition
|
| Organism |
Escherichia coli |
| Characteristics |
strain: W3110
growth phase: log phase
genotype: wild type
|
| 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.
|
| Extracted molecule |
total RNA |
| Extraction 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).
Library preparation were performed with Epicentre ScriptseqTM v2 RNA-Seq Library preparation kit with 50 ng of depleted RNA; Strand orientated RNA-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
growth in M63 minimal media plus 0.4% glucose plus 50 µM NiCl2
|
| Data processing |
Basecalls performed using HCS 2.0.5 and RTA 1.17.20
RNA-seq reads were aligned to the W3110 genome using CASAVA 1.8.2
Gene expression (based on known genes) was determined using Cufflinks 2.0.2, only PF reads were retained
Genome_build: W3110 (NC_007779)
Supplementary_files_format_and_content: excel file with coverage and FPKM measurements
|
| |
|
| Submission date |
Dec 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Agnès Rodrigue |
| E-mail(s) |
agnes.rodrigue@insa-lyon.fr
|
| Organization name |
INSA Lyon CNRS
|
| Lab |
MAP UMR 5240
|
| Street address |
10 rue Dubois
|
| City |
Villeurbanne |
| ZIP/Postal code |
69621 |
| Country |
France |
| |
|
| Platform ID |
GPL18133 |
| Series (1) |
| GSE76167 |
Mechanisms of nickel toxicity in bacteria |
|
| Relations |
| BioSample |
SAMN04351199 |
| SRA |
SRX1492017 |
