2025-06-30
ENA first public
ERC000011
ENA-CHECKLIST
SAMEA114501062
External Id
Cardiff University
INSDC center name
2023-10-16T15:10:42Z
INSDC last update
public
INSDC status
ERS16482714
SRA accession
E-MTAB-13439:Sample 14
Submitter Id
ArrayExpress
broker name
not collected
collection date
Protocols: To determine differential expression of genes in response to preservatives, Pluralibacter gergoviae strain ECO77 was cultured in a liquid growth medium without antimicrobial (control condition) and with 0.25x the MIC (test condition). Three to four biological replicates (each with 4 technical replicates) were obtained, and the test results compared to that of the control. After exposure to the control and test condition for 8.5 and 24 hours respectively, the culture samples were rapidly cooled using liquid nitrogen and cells pelleted by centrifugation at 20,000 xg at 4°C for 1 minute. The culture supernatant was removed, and the pelleted cells were snap-frozen in a RNA cryoprotectant and stored at -80°C. Total RNA was extracted within 7 days of harvesting the cells using the Invitogen RiboPure RNA Purification Bacteria Kit (Ambion, Life Technologies Ltd, UK) according to manufacturers’ guidelines. Post elution, in a low ionic strength solution, the contaminating genomic DNA was removed from the RNA samples by DNase 1 treatment (provided in kit). The DNase I and divalent cations in the buffer, were then removed using DNase Inactivation Reagent (provided in kit). RNA was stored at -80 °C. Complimentary DNA (cDNA) libraries were prepared according to the manufacturer’s instructions, using the Illumina Ribo-Zero Plus rRNA Depletion Kit and NEBNext® Ultra™ Directional RNA Library Prep Kit.
description
wild type genotype
genotype
not collected
geographic location (country and/or sea)
liquid growth medium with potassium sorbate
growth condition
not applicable
isolate
Pluralibacter gergoviae
organism
Pluralibacter gergoviae
organism
whole organism
organism part
3
replicate
Pluralibacter gergoviae
scientific_name
ECO77
strain
Sample 14
title