|
| Status |
Public on Aug 26, 2021 |
| Title |
V. cholerae hapR+ indole_ replicate3 [IC] |
| Sample type |
SRA |
| |
|
| Source name |
bacterial culture
|
| Organism |
Vibrio cholerae O1 biovar El Tor str. N16961 |
| Characteristics |
genotype/variation: N16961 hapR+
growth phase: exponential phase OD 0.4
treatment: indole 350µM
|
| Treatment protocol |
no treatment or indole 350µM or tobramycin 0,02µg/ml (2% of MIC)
|
| Growth protocol |
growth in liquid MH up to OD 0,4
|
| 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 |
| |
|
| Description |
Zeynep-IC_GTGAAA_L003
processed data file: SLX090-01-vibcol3-indol.IvsMH.complete.txt
|
| 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.
Genome_build: V. cholerae N16961 accession numbers AE003852 and AE003853
Supplementary_files_format_and_content: excel files containing number of reads and differencial expression values
|
| |
|
| Submission date |
Aug 23, 2021 |
| Last update date |
Aug 26, 2021 |
| 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) |
| GSE182561 |
V. cholerae transcriptome without treatment and with indole or sub-MIC tobramycin |
|
| Relations |
| BioSample |
SAMN20929775 |
| SRA |
SRX11862645 |
