|
| Status |
Public on Oct 03, 2022 |
| Title |
V. cholerae Δtgt + tobramycin_replicate 3 [tgttob3_S51] |
| Sample type |
SRA |
| |
|
| Source name |
bacterial culture
|
| Organism |
Vibrio cholerae O1 biovar El Tor str. N16961 |
| Characteristics |
growth phase: exponential phase OD 0.3
treatment: tobramycin 0.4 µg/ml
|
| Treatment protocol |
no treatment or supplemented with tobramycin 0.4 µg/ml or ciprofloxacin 0.0005 µg/ml
|
| Growth protocol |
growth in liquid MH supplemented or not up to OD 0,3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures were centrifuged, and RNA was harvested using Trizol reagent. Illumina TruSeq mRNA Sample Prep Kit (20020595) was used with 7 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols (Krin et al., 2018, PMID: 29783948)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Count data were analyzed using R version 3.2.0 and the Bioconductor package DESeq2 version 1.8.1
Data were normalized with DESeq2 and the “shorth” parameter
The dispersion estimation and statistical test for differential expression were performed with default parameters
The generalized linear model was set with a single covariate corresponding to the biological condition, biological replicates being included into each condition
Raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg procedure and genes with an adjusted p-value lower than 0.001 were considered differentially expressed.
Assembly: V. cholerae N16961 accession numbers AE003852 and AE003853
Supplementary files format and content: number of reads and differencial expression values
|
| |
|
| Submission date |
Sep 30, 2022 |
| Last update date |
Oct 03, 2022 |
| Contact name |
Zeynep Baharoglu |
| E-mail(s) |
baharogl@pasteur.fr
|
| Organization name |
Institut Pasteur
|
| Department |
Génomes et Génétique
|
| Lab |
Plasticité du Génome Bactérien
|
| Street address |
28 Rue du Docteur Roux
|
| City |
Paris |
| ZIP/Postal code |
75015 |
| Country |
France |
| |
|
| Platform ID |
GPL30088 |
| Series (1) |
| GSE214520 |
V. cholerae transcriptome or deleted for the tgt gene in MH, supplemented or not with tobramycin or ciprofloxacin |
|
| Relations |
| BioSample |
SAMN31104804 |
| SRA |
SRX17761044 |
