|
Status |
Public on Dec 06, 2023 |
Title |
RsbQS96A_mock_rep3 |
Sample type |
SRA |
|
|
Source name |
bacterial cell
|
Organism |
Bacillus subtilis |
Characteristics |
strain: 168 cell type: bacterial cell genotype: RsbQS96A treatment: DMSO 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_RsbQS96A_mock RsbQS96A_mock_vs_RsbQS96A_treated rsbQ_mock_vs_RsbQS96A_mock
|
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 |
SAMN36347453 |
SRA |
SRX20930087 |