characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2017-03-16T17:02:03Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-03-06T17:14:19Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA103892638
characteristics.characteristic: External Id
characteristics.text: Bielefeld University CeBiTec
characteristics.characteristic: INSDC center name
characteristics.text: 2017-03-16T17:02:03Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-03-06T17:14:19Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1581806
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-4362:Biofilm2
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: Protocols: B. amyloliquefaciens FZB42 was grown in three test tubes for each of the two replicates containing 10 ml biofilm inducing MgSS medium (5 mM K2HPO4 (pH 7), 100 mM MOPS (pH 7), 2 mM MgCl2, 700 µM MnCl2, 50 µM FeCl2, 1 µM ZnCl2, 2 µM thiamine, 0.5 % glycerol, 50 µg/ml tryptophan, 50 µg/ml phenylalanine) with an inoculation density of 0.01 OD600. After 22.5 h, cell growth reached the early stationary phase and six of the test tubes were transferred from the shaker to a test tube rack to induce biofilm formation on the surface of the medium. Remaining test tubes were kept rotating to sustain the planktonic growth state. Cultivations were stopped 24 h after induction of biofilm formation. For the isolation of RNA from cells in biofilm formation the biofilm of three test tubes was combined in 1.5 ml RLT buffer (provided in RNeasy Mini Kit; Qiagen) per replicate. Biofilm was harvested by holding a pipette tip on the biofilm on the surface and fishing the whole biofilm out before resuspending it in RLT buffer. For the isolation of RNA from planktonic cells, 1.5 ml cell culture of three test tubes per replicate were centrifuged and the resulting pellet was resuspended in 1.5 ml RLT buffer. Resuspended cells were disrupted by ribolysation (30s; speed 6.5, repeated after 1 min on ice) in 2 ml tubes with Lysing Matrix B (MPbiomedical). Subsequently, the RNA was isolated according to the published protocol by Rüberg et al. (2003) using the RNeasy Mini Kit (Qiagen, Hilden, Germany). Enrichment of the mRNA (depletion of rRNA) was performed applying the RiboZero rRNA Removal Kit for Bacteria according to the manufacture’s protocol using 3 µg of RNA per sample. Library preparations for paired-end sequencing on the Illumina HiSeq 1500 platform were performed according to protocols provided by Illumina
characteristics.characteristic: description
characteristics.text: biofilm formation
characteristics.characteristic: developmental stage
characteristics.text: Bacillus amyloliquefaciens
characteristics.characteristic: organism
characteristics.text: Bacillus amyloliquefaciens
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_1390
characteristics.characteristic: organism
characteristics.text: Bacillus amyloliquefaciens
characteristics.characteristic: scientific_name
characteristics.text: Biofilm2
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/BTO_0002690
characteristics.characteristic: title