characteristics.text: 2024-01-01
characteristics.characteristic: ENA first public
characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: Bielefeld University, Center for Biotechnology (CeBiTec), Universitätsstraße 27,  33615, Bielefeld, Germany Bielefeld University, Medical Faculty OWL Universitätsstraße 27,  33615, Bielefeld, Germany
characteristics.characteristic: INSDC center name
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS20817661
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-14293:3_MW00G_0.2_D-xylose_TB2-T1
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: not collected
characteristics.characteristic: collection date
characteristics.text: Protocols: 400 mL main cultures (four replicates) for poly-omic analysis with the respective carbon sources were inoculated to a starting OD600 of 0.05 and grown to exponential phase (OD600 of 0.8). Cells were cooled down with liquid nitrogen and harvested at 9,000xg, 15 min, 4°C. Cell pellets were stored at -70°C and used for RNA-seq Growth experiments with the glycerol-adapted S. acidocaldarius MW00G werewas performed in 4 replicatesat 76°C and 120 rpm under constant shaking using (Innova®44,  (New Brunswick, Germany) in the presence 10 mM glycerol, 20 mM glycerol or 40 mM glycerol as sole carbon and energy source. For comparison the same strain was cultivated with 0.2 % (w/v) D-xylose. Cells were inoculated into Brock’s basal salt medium containing the respective carbon source to an OD600 of 0.05 and growth was monitored as increase in OD600 over time.  The paired-end cDNA reads were mapped to the Sulfolobus acidocaldarius DSM 639/MW001 genome sequence (accession number CP000077.1) using bowtie2 v2.2.7. with default settings for paired-end read mapping. All mapped sequence data were converted from SAM to BAM format with SAMtools v1.3  and imported to the software ReadXplorer v.2.2. RNA was isolated using Zymo Direct-zol RNA Miniprep kit following manufactures instructions. The RNA quality was checked by Trinean Xpose (Gentbrugge, Belgium) and the Agilent RNA Nano 6000 kit using an Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany).  Pan-Archaea riboPOOL kit from siTOOLs Biotech was used to remove the rRNA. TruSeq Stranded mRNA Library Prep Kit from Illumina was applied to prepare the cDNA libraries.
characteristics.characteristic: description
characteristics.text: not collected
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: 0.2 % (w/v) D-xylose
characteristics.characteristic: growth condition
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Sulfolobus acidocaldarius
characteristics.characteristic: organism
characteristics.text: Sulfolobus acidocaldarius
characteristics.characteristic: organism
characteristics.text: whole organism
characteristics.characteristic: organism part
characteristics.text: Sulfolobus acidocaldarius
characteristics.characteristic: scientific_name
characteristics.text: 3_MW00G_0.2_D-xylose_TB2-T1
characteristics.characteristic: title