|
| Status |
Public on Aug 29, 2016 |
| Title |
Thermus at oven 14 hours, biological rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
ATCC 700910
|
| Organism |
Thermus scotoductus SA-01 |
| Characteristics |
growth: log phase
sample type: no elongation
|
| Growth protocol |
Frozen 200 µl stocks of T. scotoductus were cultured aerobically in 10 mL of Castenholz-TYE medium at 65°C to an OD600nm of 1.0 (approx. 24 hr.). A 1% inoculation of this culture was added to Teflon vessels (MARS5 accessory) containing 60 mL of Castenholz-TYE medium pre-warmed to 65°C. Triplicate biological experiments were performed in parallel by placing these vessels either into a convective incubator or a MARS 5 microwave digestor (2.45 GHz, 300W) with an internal IR probe to maintain the temperature at 65 ± 1°C throughout the experiment. Three aliquots of 3 mL were removed at 8, 14, and 24 hours after inoculation from each vessel.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the RNeasy Mini Kit followed the manufacturer’s protocol with the following modification. 180 µL of lysozyme (15 mg/mL) re-suspended in TE Buffer (30 mM Tris-HCl, 1 mM EDTA, pH 8) plus 20 µL Proteinase K (Qiagen) was added to each cell pellet and samples incubated with agitation (125 rpm) for 25 min at room temperature. The optional on-column DNase digestion was extended to 1 hr.
Ribosomal RNA were depleted from RNA samples using Ribo-Zero rRNA Removal Kit for Bacteria (Illumina, San Diego, CA) according to manufacture recommend protocol prior to RNA library preparation. RNA library preparation was carried out using NEBNext® Ultra™ RNA Library Prep Kit for Illumina (New England Biolabs, Inc., Ipswich, MA) according to manufacture recommend protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
RNAseq data from Thermus scotoductus SA-01 cultured at convective incubator for 14 hours
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Read quality trimming trimmomatic .33 using parameters “HEADCROP:8 LEADING:20 SLIDINGWINDOW:5:20 MINLEN:50”
mapped reads to T. scotoductus SA-01, CP001962.1 and plasmid CP001963.1 using Bowtie2 parameter "–very-sensitive"
htseq-count used to count reads that mapped to T. scotoductus SA-01, CP001962.1 and plasmid CP001963.1 gene features
Supplementary_files_format_and_content: comma separated text file containing the raw read counts of all samples
|
| |
|
| Submission date |
Mar 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Baochuan Lin |
| E-mail(s) |
baochuan.lin@nrl.navy.mil
|
| Phone |
202-767-0289
|
| Organization name |
US Naval Research Laboratory
|
| Department |
Center for Bio/Molecular Science & Engineering
|
| Street address |
4555 Overlook Avenue, S. W.
|
| City |
Washington |
| State/province |
DC |
| ZIP/Postal code |
20375 |
| Country |
USA |
| |
|
| Platform ID |
GPL21591 |
| Series (1) |
| GSE79201 |
Molecular Mechanisms Contributing to the Growth and Physiology of an Extremophile Cultured with Dielectric Heating |
|
| Relations |
| SRA |
SRX1631064 |
| BioSample |
SAMN04557013 |
