|
| Status |
Public on Oct 01, 2023 |
| Title |
Apatite_2 |
| Sample type |
SRA |
| |
|
| Source name |
not applicable
|
| Organism |
Cupriavidus basilensis |
| Characteristics |
strain: SRS
cell line: not applicable
cell type: not applicable
genotype: WT
treatment: Apatite
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using a phenol-chlorform method. Briefly, 500 µL culture and 1 ml PBS are centrifuged at 5000 g for 5 min. Lysozyme and Superase-IN RNase inhibitor are used. This is followed by bead-beating with RNASolv reagent (Omega Bio-tek). Chloroform is added and the samples sit at room temperature for 3 min. The samples are then centrifuged at >12000 g for 15 min at 4 ºC. The top aqueous layer is removed and an equal volume of 70% ethanol is added. The samples are then processed using the EZNA Total RNA Kit according to the manufacturer's instructions (Omega Bio-Tek).
5 µl of each sample (concentration 2-10 ng/µl) was used for library preparation with the NEBNext Ultra II Directional RNA library Prep kit following the manufacturer's instructions.
NovaSeq platform for paired-end 150bp
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
https://github.com/twbattaglia/RNAseq-workflow
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore/0.6.5-GCCcore-8.3.0-Java-11-Python-3.7.4
Trimmed sequence reads were mapped to the genome of Cupriavidus using STAR/2.7.10a-GCC-8.3.0
Feature counts were performed using HTSeq/0.13.5-foss-2019b-Python-3.7.4
Supplementary files format and content: tab-delimited text files include transcript count values for each Sample
|
| |
|
| Submission date |
Oct 28, 2022 |
| Last update date |
Oct 01, 2023 |
| Contact name |
He Fu |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Georgia
|
| Department |
Microbiology
|
| Street address |
120 Cedar St
|
| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
| |
|
| Platform ID |
GPL32789 |
| Series (1) |
| GSE216827 |
Effects of metals on the gene expression of Cupriavidus basilensis SRS |
|
| Relations |
| BioSample |
SAMN31510105 |
| SRA |
SRX18065612 |
