|
| Status |
Public on Dec 06, 2023 |
| Title |
WT_treated_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cell
|
| Organism |
Bacillus subtilis |
| Characteristics |
strain: 168
cell type: bacterial cell
genotype: WT
treatment: 10 µM dGR24
bacterial growth: OD (600) of 1
|
| Treatment protocol |
Treatment solutions (DMSO and rac-GR24) were added directly to the flasks by manual pipetting at an optical density (OD 600) ranging from 1.0 to 1.1.
|
| Growth protocol |
approximately of 500 µl (1:100) of the starter culture was inoculated into a prewarmed 50 ml liquid LB and grown in a shaker incubator (Innova 42, New Brunswick Scientific) at 185 RPM and 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures were harvested at OD ranging from 1.4 to 1.5 and immediately centrifuged at 10,000xg for 2 minutes using a Heraeus Multifuge X3R Centrifuge. The resulting pellet was then rapidly transferred to liquid nitrogen. RNA was extracted using the Spectrum Plant Total RNA kit (Sigma-Aldrich).
Paired-end libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturers' protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
WT_mock_vs_WT_reated
|
| Data processing |
libraries were generated using the Illumina Stranded TotalRNAwith Ribo-Zero Plus product which is a rRNA depletion workflow as per manufacturers instructions
Adapter trimming, read mapping onto the Bacillus subtilis subsp. subtilis str. 168 (GCA_000009045) reference genome and read counts were carried out with kallisto
Differentially expressed genes (DEGs) analysis was done by DEseq2 using R studio.
Assembly: Bacillus subtilis subsp. subtilis str. 168 (GCA_000009045)
Supplementary files format and content: MS Excel files report log2FoldChange
|
| |
|
| Submission date |
Jul 07, 2023 |
| Last update date |
Dec 06, 2023 |
| Contact name |
Muhammad Kamran |
| E-mail(s) |
pplantscience@gmail.com
|
| Phone |
0472717390
|
| Organization name |
The University of Western Australia
|
| Department |
School of Molecular sciences
|
| Lab |
Waters Lab
|
| Street address |
35 Stirling Hwy, Crawley WA
|
| City |
Perth |
| State/province |
WA |
| ZIP/Postal code |
6009 |
| Country |
Australia |
| |
|
| Platform ID |
GPL30886 |
| Series (1) |
| GSE236759 |
Effects of strigolactone analogue dGR24 on the transcriptome of Bacillus subtillis |
|
| Relations |
| BioSample |
SAMN36347464 |
| SRA |
SRX20930076 |
