characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-09-23T16:59:16Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-09-23T16:59:16Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA113550812
characteristics.characteristic: External Id
characteristics.text: Department of Microbiology Hirszfeld Institute of Immunology and Experimental Therapy Polish Academy of Sciences
characteristics.characteristic: INSDC center name
characteristics.text: 2023-09-23T16:59:16Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-09-23T16:59:16Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS15547231
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-13025:ΔHP1021_3
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: Protocols: Bacterial cultures (12 ml BB-FBS) of Helicobacter pylori N6 wild-type and ΔHP1021 strains were grown under microaerobic conditions to OD600 of 0.8-1.0. Immediately after opening the jar, 1 ml of the non-stressed culture was added to 1 ml of the RNAprotect Bacteria Reagent (Qiagen), vortexed and incubated for 5 min at room temperature. In parallel, the cultures were moved to aerobic conditions for 25 min (air atmosphere, 37 °C, 140 rpm orbital shaking). After oxidative stress, samples were collected similarly to non-stressed cells. After 5 min incubation with RNAprotect Bacteria Reagent, bacteria were collected by centrifugation (7000 × g, 5 min, RT). RNA was isolated by GeneJET RNA Purification Kit (Thermo Fisher Scientific; K0731) according to the manufacturer’s protocol and treated with RNase-free DNase I (Thermo Fisher Scientific). Next, the subsequent purification by the GeneJET RNA Purification Kit was performed to remove DNase I. A NanoDrop Lite spectrophotometer, agarose gel electrophoresis and Agilent 4200 TapeStation System were used to determine the RNA quality and quantity. RNA was isolated immediately after bacteria collection, stored at -80 °C for up to one month and used for RNA sequencing. RNA was isolated from three independent cultures. RNA was isolated by GeneJET RNA Purification Kit (Thermo Fisher Scientific; K0731) according to the manufacturer’s protocol and treated with RNase-free DNase I (Thermo Fisher Scientific). Next, the subsequent purification by the GeneJET RNA Purification Kit was performed to remove DNase I. A NanoDrop Lite spectrophotometer, agarose gel electrophoresis and Agilent 4200 TapeStation System were used to determine the RNA quality and quantity. RNA was isolated immediately after bacteria collection, stored at -80 °C for up to one month and used for RNA sequencing. RNA was isolated from three independent cultures (three biological replication). The prokaryotic directional mRNA library preparation was performed at the Novogene Bioinformatics Technology Co. Ltd. (Cambridge, UK). The ribosomal RNA was removed from the total RNA, followed by ethanol precipitation. After fragmentation, the first strand of cDNA was synthesised using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit, RT-qPCR for quantification and a bioanalyser for size distribution detection.
characteristics.characteristic: description
characteristics.text: no stress (5% O2)
characteristics.characteristic: environmental stress
characteristics.text: ΔHP1021::aphA-3
characteristics.characteristic: genotype
characteristics.text: Helicobacter pylori
characteristics.characteristic: organism
characteristics.text: Helicobacter pylori
characteristics.characteristic: organism
characteristics.text: whole organism
characteristics.characteristic: organism part
characteristics.text: 3
characteristics.characteristic: replicate
characteristics.text: Helicobacter pylori
characteristics.characteristic: scientific_name
characteristics.text: N6
characteristics.characteristic: strain
characteristics.text: ΔHP1021_3
characteristics.characteristic: title