|
| Status |
Public on Oct 27, 2020 |
| Title |
BPSM_Cu_Shock Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Bordetella pertussis total RNAseq
|
| Organism |
Bordetella pertussis |
| Characteristics |
strains: BPSM
protocol: RNAseq
culture conditions: strain was cultivated in SS media to OD600 nm = 1.5 and 2 mM CuSO4 was added for 30 min
collected_by: Alex Rivera-Millot
collection_date: November 2018
|
| Treatment protocol |
The bacterial cultures were stopped at mid exponential phase (OD600 =1.5) by adding 2 mL of a mixture of 5:95 phenol:ethanol (v:v) to 8 mL of bacterial suspensions.
|
| Growth protocol |
B. pertussis strains were grown on BG agar plates for 2 days at 37°C and then cultured in modified Stainer Scholte (SS) liquid medium at 37°C under agitation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacteria were pelleted, and total RNA was extracted using TriReagent (Invitrogen) following the manufacturer’s instructions. Genomic DNA was removed by DNase I treatment (Sigma Aldrich).
For each RNAseq sample, DNA-depleted total RNA was treated with the Ribo-Zero rRNA Removal Kit (Illumina) following the manufacturer’s recommendations. The rRNA-depleted RNA was then used to build the Illumina library using the TruSeq RNA Library Preparation Kit, followed by sequencing on an Illumina NextSeq 500 benchtop sequencer on SR150 high output run mode.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
BPSM_Shock.xlsx
|
| Data processing |
The RNAseq data of each sample were analyzed using Rockhopper v2.0.3 with the default parameters to calculate the RPKM value for each coding sequence with the Bordetella pertussis Tohama I NC_002929 or the Bordetella bronchiseptica NC_002927 genome annotations
Genome_build: Bordetella pertussis Tohama I NC_002929 and Bordetella bronchiseptica NC_002927
Supplementary_files_format_and_content: Excel files with RPKM values for each duplicated sample.
|
| |
|
| Submission date |
Feb 10, 2020 |
| Last update date |
Oct 27, 2020 |
| Contact name |
Rudy Antoine |
| E-mail(s) |
rudy.antoine@pasteur-lille.fr
|
| Phone |
+33320871153
|
| Organization name |
CIIL
|
| Street address |
1, rue du Professeur Calmette
|
| City |
Lille |
| ZIP/Postal code |
59021 |
| Country |
France |
| |
|
| Platform ID |
GPL27446 |
| Series (1) |
| GSE145049 |
RNAseq analyses of copper effect on Bordetella pertussis and Bordetella bronchiseptica |
|
| Relations |
| BioSample |
SAMN14079395 |
| SRA |
SRX7703719 |
