|
| Status |
Public on Mar 01, 2023 |
| Title |
Escherichia coli MG1655 WT + tobramycin, biol rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
strain: MG1655
cell type: bacteria
genotype: wt
treatment: tobramycin
|
| Treatment protocol |
Cultures were supplemented or not with 0.25 ug/ml of tobramycin.
|
| Growth protocol |
Overnight cultures were diluted 1000X in MH medium. Cells were grown until OD600nm of 0.4.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures were centrifuged, and RNA was purified using using the RNAeasy kit (Thermofischer Scientific), according to the manufacturer instruction (protocole 2 and 4). 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 |
NextSeq 2000 |
| |
|
| Description |
Ectob2_S8
|
| 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 0.01 were considered differentially expressed.
Assembly: Escherichia coli K12 accession numbers U00096.2
Supplementary files format and content: Excel files containing number of reads and differencial expression for all the conditions
Supplementary files format and content: MH vs tob (Escherichia coli MG1655 WT non treated vs treated with tobramycin. NCM MH vc tob (Escherichia coli NCM3416 non treated vs treated with tobramycin) and MH vs NCM MH (Escherichia coli K12 WT non treated vs NCM3416 non treated)
|
| |
|
| Submission date |
Feb 01, 2023 |
| Last update date |
Mar 01, 2023 |
| 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 |
GPL33080 |
| Series (1) |
| GSE224240 |
Effect of sub-MIC tobramycin treatment on E. coli MG1655 WT and NCM3416 |
|
| Relations |
| BioSample |
SAMN33006345 |
| SRA |
SRX19245605 |
