psora_plusNB_input_b
Cereibacter sphaeroides
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
ENA first public
2025-10-30
INSDC center name
Institute for Microbiology and Infection, University of Birmingham
INSDC status
public
Submitter Id
E-MTAB-15087:psora_plusNB_input_b
broker name
ArrayExpress
collection date
not collected
geographic location (country and/or sea)
not collected
growth condition
M22+ media. 30 degrees Celsius
isolate
not applicable
replicate
biological replicate b
response to treatment
2 μg/ml novobiocin
sample name
E-MTAB-15087:psora_plusNB_input_b
scientific_name
Cereibacter sphaeroides
strain
Rhodobacter sphaeroides 2.4.1