characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2021-12-06T00:11:47Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2021-12-06T00:11:47Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA10146962
characteristics.characteristic: External Id
characteristics.text: Center for Biotechnology, CeBiTec, University of Bielefeld, Universitatsstrasse 27, 33699 Bielefeld, Germany
characteristics.characteristic: INSDC center name
characteristics.text: 2021-12-06T00:11:47Z
characteristics.characteristic: INSDC first public
characteristics.text: 2021-12-06T00:11:47Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS7803465
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-10949:SAMPLE_12
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: Protocols: 1 mL culture was added to 250 μL pure ethanol supplemented with 5 % phenol, flash-frozen in liquid nitrogen and stored at −80°C . Synechocystis strains were cultivated in BG11 medium with appropriate antibiotics at 30°C and aeration with 0.5% CO2 in all experiments. For the endpoint measurements cultures were grown in Erlenmeyer flask in an Infors HT multitron chamber, shaken at 150 rpm, and light intensity was 80 umol/m2/sec. For the time series 1 L culture was grown in a Lambda Photobioreactor ca. 90 umol/m2/sec per OD (manually adjusted to OD) with pH kept stable at pH 8. Inducers for gyrase knock-down and topoisomerase I overexpression were added at inoculation after pre-culturing without inducer. For the time series experiment the inducer was added at time point t=0 h, 1 h after SAMPLE_10 was taken. Frozen samples were centrifuged ( 10 min , 4°C , maximum speed). The pellet was resuspended in 1 mL PGTX and incubated ( 5 min , 95°C ). After cooling on ice for 2 min , 700 μL chloroform:isoamyl alcohol (24:1) was added and the mixture incubated (10 min , room temperature) while shaking gently. The mixture was centrifuged (10 min , 4°C , maximal speed). The upper phase was transferred to a fresh tube and 1 volume chloroform:isoamyl alcohol was added. After repeating the centrifugation step, the upper phase was transferred and precipitated with 3 volumes of 99.5 % ethanol and 1/2 volume 7.5 M ammonium acetate and (time series only) 1 μL RNA-grade glycogen at −20°C over night. The RNA was pelleted by centrifugation (30 min , 4°C , maximum speed), washed twice with 70 % ethanol and resuspended in 30 μL RNase-free water. Volumes were adjusted to contain 2 μg of nucleic acid (Nanodrop), and DNA was removed by DNaseI (ThermoFisher: EN0525) according to the manufacturer’s specifications but at 2x reaction buffer concentration. RNA was extracted as above but using 1/10 volume of 3 M sodium acetate (pH 5.3) instead of ammonium acetate for precipitation. The Illumina Ribo-Zero Plus rRNA Depletion Kit was used to remove the ribosomal RNA molecules from the isolated total RNA. Removal of rRNA was evaluated with the RNA Pico 6000 kit on the Agilent 2100 Bioanalyzer. RNA was free of detectable rRNA. Preparation of cDNA libraries was performed according to the manufacturer’s instructions for the TruSeq stranded mRNA kit (Illumina, San Diego, CA, United States). Subsequently,
characteristics.characteristic: description
characteristics.text: topA overexpression
characteristics.characteristic: genotype
characteristics.text: Synechocystis sp. PCC 6803
characteristics.characteristic: organism
characteristics.text: Synechocystis sp. PCC 6803
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_1148
characteristics.characteristic: organism
characteristics.text: whole organism
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0000468
characteristics.characteristic: organism part
characteristics.text: Synechocystis sp. PCC 6803
characteristics.characteristic: scientific_name
characteristics.text: topA-OX
characteristics.characteristic: strain
characteristics.text: SAMPLE_12
characteristics.characteristic: title