2025-10-30
ENA first public
ERC000011
ENA-CHECKLIST
Institute for Microbiology and Infection, University of Birmingham
INSDC center name
public
INSDC status
ERS24142606
SRA accession
E-MTAB-15087:psora_minusNB_a
Submitter Id
ArrayExpress
broker name
not collected
collection date
Protocols: All cells were harvested by high speed centrifugation (approx 5000 xG). Pellets were flash froze in liquid nitrogen before storage at -80 oC. For each biological replicate, a single colony was inoculated into 10 ml M22+ media and grown at 30 degrees Celsius with vigorous shaking for 2-3 days. This 10 ml culture was used to start a larger culture, typically 100 - 200 ml. The larger culture had a starting OD600 of 0.05, and was grown throughout the day at 30 degrees Celsius with shaking until exponential phase, approx 0.5 OD600. At which point novobiocin was added for 20 minutes if required.  When stated, novobiocin was added to a exponentially growing cells (OD600 0.5) to a final concentation of 2 μg/ml Experiments were done as described by Visser et al with the following changes 28. CTAB purified genomic DNA was resuspended in 225 μl of water. Genomic DNA was sheared to a size of 400 – 500 bp in a Biorupter (Diaganode). 50 μl of sheared genomic DNA was kept as an input sample and the remainder was immobilised on streptavidin T1 dynabeads (ThermoFisher). After washing, and reverse crosslinking as per Visser et al, eluted DNA was precipitated and resuspended in 20 μl water  Visser, B. J., Sharma, S., Chen, P. J., McMullin, A. B., Bates, M. L. & Bates, D. Psoralen mapping reveals a bacterial genome supercoiling landscape dominated by transcription. Nucleic Acids Res. 50, 4436–4449 (2022) DNA was sent to Gene wiz (Azenta) for sequencing, with samples treated as ChIP-seq samples
description
not collected
geographic location (country and/or sea)
M22+ media. 30 degrees Celsius
growth condition
not applicable
isolate
Cereibacter sphaeroides
organism
Cereibacter sphaeroides
organism
biological replicate a
replicate
N/A
response to treatment
Cereibacter sphaeroides
scientific_name
Rhodobacter sphaeroides 2.4.1
strain
psora_minusNB_a
title