characteristics.text: 2025-02-03
characteristics.characteristic: ENA first public
characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: UOM-BCF
characteristics.characteristic: INSDC center name
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS18297043
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-13795:Sample 18
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: not collected
characteristics.characteristic: collection date
characteristics.text: Protocols: 20 mL of cells were sampled from the bioreactor and immediately mixed in pre-chilled tubes containing 2 mL ice-cold stop solution (95% ethanol, 4% phenol, 1% chloroform). Cells were pelleted at 8000 x g for 5 min at 4 °C. The supernatant was removed, the pellet resuspended in 3 mL of RNA later and split into 3 x 1 mL aliquots. Cells were incubated at room temperature for 5 min, followed by centrifugation at 10,000 x g for 5 min at 4 °C. Supernatants were removed and the pellets frozen in liquid nitrogen and stored at -80 °C. A fresh colony of a doubly-tagged fluorescent strain of Rba. sphaeroides (fbcC-CFP, puhA-YFP) was inoculated into 10 mL of M22+ liquid medium supplemented with 0.1% Cas-amino acids and grown semi-aerobically in the dark. This culture was used to inoculate 50 mL of M22+ liquid medium in a 250 mL baffled conical flask. This culture was grown overnight at high aeration (250 RPM at 30 °C) and subsequently used as the starter culture for the induction experiment.  The fermentor apparatus (Infors HT Labfors 3 system) was set to a culture volume of 1.4 L, with a gas inflow rate of 1.5 L/min-1; stirring speed of 450 RPM; and temperature of 30 °C. Gas provision was via separate high pressure cylinders of oxygen-free nitrogen and compressed air set to 1 Bar of output. The Labfors 3 system gas mix parameter was initially set to 100% compressed air (21% O2) to enable fully aerobic growth. The fermentor was equilibrated to aerobic conditions for at least 30 minutes prior to inoculation. Cells and vitamin mix were added to the vessel via syringe through a sterile septum port. Optical density at 680 nm was monitored periodically throughout the aerobic growth phase from a starting OD of 0.2. Once the culture reached an OD of ~1.0, the T0 sample was taken The switch to oxygen limitation was achieved by altering the gas mix parameters to 14% compressed air and 86% oxygen-free nitrogen (3% O2). Oxygen concentration of the vessel gas out flow (reflecting the headspace concentration) was monitored periodically throughout the experiment and during the switch (where the headspace oxygen concentration reduced from ~20.6% to ~3% within 90 seconds) by a GOX 100T oxymeter and GOEL-370 oxygen sensor (Greisinger) calibrated against compressed air. Light conditions in the room were constant and the vessel was covered between sampling to prevent any significant light exposure. Further samples were taken at +5, +30, +60, +120 and +180 min after switching to oxygen limitation. RNA isolation from frozen cell pellets of R. sphaeroides was performed by Azenta UK PolyA selection and transcript library preparations were performed by Azenta UK
characteristics.characteristic: description
characteristics.text: not collected
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: anaerobic
characteristics.characteristic: growth condition
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Rhodobacter sphaeroides 2.4.1
characteristics.characteristic: organism
characteristics.text: Cereibacter sphaeroides 2.4.1
characteristics.characteristic: organism
characteristics.text: 3
characteristics.characteristic: replicate
characteristics.text: Cereibacter sphaeroides 2.4.1
characteristics.characteristic: scientific_name
characteristics.text: Sample 18
characteristics.characteristic: title