|
| Status |
Public on Oct 26, 2022 |
| Title |
T. maritima, 80, stationary, biol rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cell
|
| Organism |
Thermotoga maritima |
| Characteristics |
strain: MSB8
cell type: bacterial cell
growth phase: stationary
growth temperature: 80° C
|
| Growth protocol |
Thermotoga maritima (strain MSB8, DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, DSM 3109) was cultivated in basal media under anaerobic conditions in 120-ml batch cultures in 250 ml serum bottles. Cultures were incubated either at optimal (80°C) or lower (55°C) growth temperatures. Growth was monitored by measuring the optical density (OD) at 600 nm and by fluorescent microscopy
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets were defrosted on ice and washed with 500 µL of DNase/RNase free water (New England Biolabs). Cells were resuspended in 700 µL of RLT buffer, and 50 mg of acid-washed glass beads (0.1 µm diameter) were added to a safe-lock tube containing the cell suspension. Cell disruption was performed with the OMNI bead mill Homogenizer (6.3 m/s) 2x. RNA was extracted with the RNeasy® Mini Kit (QIAGEN). The cells were harvested at early exponential, exponential, and stationary phases by centrifugation at 3500 rpm for 10 min at 4°C. The supernatant was discarded, and the remaining pellet was immediately frozen at -20°C for RNA extraction. 18 µl (2 µg) of total RNA was hybridized with the Pan-Prokaryote riboPOOL 3’-biotinylated probe (siTOOLs Biotech). The rRNA was subsequently depleted with Hydrophilic streptavidin magnetic beads (New England Biolabs). The depleted rRNA sample was purified before library preparation with RNA clean and concentration (Zymo research) and eluted in 15 µl of DNase-/RNase- Free Water. Samples were QC analyzed with the Agilent RNA 6000 Nano Chips and the Agilent 2100 Bioanalyzer system and stored at -80oC until library preparation
RNA libraries for RNA-seq were prepared using TruSeq RNA stranded kit following manufacturer's protocols and sequenced at the Utrecht Sequencing facility (USeq, The Netherlands)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
T80-03-R1
|
| Data processing |
Adapter sequences and poor quality reads were removed with Trimmomatic v0.36 (parameter settings: Illuminaclip: TruSeq3-SE.fa:2:30:10, leading: 20, trailing: 20, sliding window: 5: 20 min length: 40);
Poly-G tails were removed using cutadapt v1.16 with the --nextseq-trim parameter set to 20
Gene counts were calculated using Salmon v1.1.0 with the mapping-based mode against the reference genome of T. maritima MSB8 (NCBI Reference Sequence: NC_021214.1)
Quantification estimates were imported into R/Bioconductor with tximport and differential gene expression between growth phases and temperatures was assessed with DESeq2 v1.26.0 using the default values
Assembly: NCBI Reference Sequence: NC_021214.1
Supplementary files format and content: tab-delimited text files include raw counts and TPM values for each sample
|
| |
|
| Submission date |
Aug 18, 2022 |
| Last update date |
Oct 26, 2022 |
| Contact name |
Diana X. Sahonero-Canavesi |
| E-mail(s) |
diana.sahonero@nioz.nl
|
| Organization name |
NIOZ
|
| Street address |
Landsdiep 4
|
| City |
't Horntje (Texel) |
| ZIP/Postal code |
1797 SZ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL32581 |
| Series (2) |
| GSE211547 |
Biosynthesis of membrane-spanning ether lipids in Thermotoga maritima |
| GSE211548 |
Biosynthesis of membrane-spanning lipids in Thermoanaerobacter ethanolicus and Thermotoga maritima |
|
| Relations |
| BioSample |
SAMN30385725 |
| SRA |
SRX17133624 |
