|
| Status |
Public on Jun 02, 2021 |
| Title |
R14_t15min_50mM |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria
|
| Organism |
Bacillus cereus |
| Characteristics |
strain: Bc407
time: 15min
concentration no (um): 50
biological replicate: 2
|
| Growth protocol |
Bc407 was grown in LB medium at 37°C with agitation (200rpm) until the end of the exponential growth phase (OD600= 2). Then bacteria were diluted 1/100 in RPMI 1640 Medium GlutaMAXTM (SKU 61870-010, Thermofisher), and exposed to diverse stresses for 15min or 60min at 37°C without agitation. NOC5 (146724-82-5, Calbiochem) was used as NO donor at a final concentration of 10 and 50µM. Sodium nitrite (7632-00-0 Sigma-Aldrich) was used at 2.5 mM, Potassium nitrate (7757-79-1, Merck) at 20 mM and hydrogen peroxide solution (7722-84-1, Sigma-Aldrich) at 0.03% (V/V)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacterial pellets were frozen in liquid nitrogen. The pellet introduce in Lysing Matrix B tubes (MP Biomedicals) and high-speed homogenized in FastPrep-24™ 5G Instrument in presence of phenol. Then impurities were extracted from the aqueous phase in three stages: one step with trizol and two with chloroform. The RNAs in the aqueous phase are then precipitated with isopropanol and dissolved in purified water.
Transcriptome library preparation and sequencing was performed by I2BC Paris-Saclay platform on the Illumina NextSeq sequencer to generate paired-end 40 bp reads bearing strand specificity
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
R14_15C_S11
R14_15C_S11
|
| Data processing |
Low quality triming with sickle (version 1.33, options: -t sanger -x -n -q 20 -l 20)
Read mapping using bowtie2 (version 2.2.6, options: -N 1 -L 16 -R 4)
Read counts on each allelic variant were obtained using HTSeq-count (version 0.10.0)
Genome_build: Bc407 reference genome assembly (NC_018877.1)
|
| |
|
| Submission date |
Mar 10, 2021 |
| Last update date |
Jun 02, 2021 |
| Contact name |
Cyprien Guérin |
| E-mail(s) |
cyprien.guerin@inrae.fr
|
| Phone |
+33-1-3465-2896
|
| Organization name |
INRAE
|
| Lab |
MaIAGE
|
| Street address |
INRAE - Domaine de Vilvert
|
| City |
Jouy-en-Josas |
| ZIP/Postal code |
F-78350 |
| Country |
France |
| |
|
| Platform ID |
GPL29834 |
| Series (1) |
| GSE168681 |
Characterization of a key region involved in the NO stress response of Bacillus cereus |
|
| Relations |
| BioSample |
SAMN18250191 |
| SRA |
SRX10310809 |
