characteristics.text: 2025-02-01
characteristics.characteristic: ENA first public
characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: Max-Planck-Institute for Terrestrial Microbiology
characteristics.characteristic: INSDC center name
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS23005807
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-14794:ΔdifE-2
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: not collected
characteristics.characteristic: collection date
characteristics.text: Protocols: M. xanthus cells of the indicated strains were grown exponentially in suspension cultures in 1% CTT broth (1% [wt/vol] Bacto casitone, 10 mM Tris-HCl [pH 8.0], 1 mM K2HPO4/KH2PO4 [pH 7.6], 8 mM MgSO4) at 32°C. 20 mL of these suspension cultures were harvested by centrifugation (6,000 xg for 5 min).   Total RNA was extracted using the Monarch® Total RNA Miniprep Kit (New England Biolabs) according to the manufacturer’s protocol. Next, Turbo DNase (Thermo Fisher Scientific) was added to the RNA following the manufacturer’s protocol and subsequently removed using the Monarch® RNA Cleanup Kit (50 μg; New England Biolabs). For all samples, RNA integrity was analyzed by capillary electrophoresis using the MultiNA microchip electrophoresis system (Shimadzu).  For removal of rRNA, a mixture of in vitro transcribed biotin-labelled RNA probes directed against 5S, 16S and 23S bacterial rRNA were mixed with the total RNA samples. The hybridized rRNA molecules were then removed using streptavidin magnetic beads. The ribodepleted-RNA samples were then fragmented using ultrasound (2 pulses of 30 s at 4°C each). Then, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng µl-1 using a high fidelity DNA polymerase (14 PCR cycles). The cDNA was purified using an Agencourt AMPure XPkit (Beckman Coulter Genomics). At all steps, quality was assessed via the MultiNA microchip electrophoresis system (Shimadzu)
characteristics.characteristic: description
characteristics.text: ΔdifE
characteristics.characteristic: genotype
characteristics.text: not collected
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: exponentially growing in suspension cultures
characteristics.characteristic: growth condition
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Myxococcus xanthus
characteristics.characteristic: organism
characteristics.text: Myxococcus xanthus
characteristics.characteristic: organism
characteristics.text: biological replicate
characteristics.characteristic: replicate
characteristics.text: Myxococcus xanthus
characteristics.characteristic: scientific_name
characteristics.text: SA5649
characteristics.characteristic: strain
characteristics.text: ΔdifE-2
characteristics.characteristic: title