|
| Status |
Public on May 01, 2020 |
| Title |
RNAseq of Bordetella pertussis BPSM DBvgA 2 |
| Sample type |
SRA |
| |
|
| Source name |
delta bvgA
|
| Organism |
Bordetella pertussis |
| Characteristics |
strain: BPSM
genotype/variation: delta bvgA
culture conditions: strain were cultivated in SS media to OD600 nm = 2.
collected_by: Loic Coutte
collection_date: Jun-16
|
| Treatment protocol |
The bacterial cultures were stopped at mid exponential phase (OD600 =1.5-2) 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 supplemented when indicated with 50 mM MgSO4 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 |
| |
|
| 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 B. pertussis Tohama I BX470248 genome annotation.
To avoid false positive and to increase clarity, RNAseq results were considered with LogFC<-2 or LogFC>2.
Genome_build: B. pertussis Tohama I BX470248
Supplementary_files_format_and_content: excel file with gene, Product, Synonym, Log FC BPSM Mg vs BPSM, Log FC BPSM DBvgA vs BPSM, qValue BPSM vs BPSM Mg, qValue BPSM vs BPSM BvgA, RPKM BPSM, RPKM BPSM Mg, RPKM BPSM DBvgA
|
| |
|
| Submission date |
Sep 10, 2019 |
| Last update date |
May 01, 2020 |
| Contact name |
loic coutte |
| E-mail(s) |
[email protected]
|
| Phone |
33320871146
|
| Organization name |
INSERM
|
| Department |
microbiology
|
| Street address |
1 rue du Pr Calmette, U1019 INSERM
|
| City |
Lille |
| ZIP/Postal code |
59021 |
| Country |
France |
| |
|
| Platform ID |
GPL27446 |
| Series (1) |
| GSE137180 |
RNAseq analyses of BvgA in Bordetella pertussis |
|
| Relations |
| BioSample |
SAMN12721824 |
| SRA |
SRX6825797 |
