|
| Status |
Public on Feb 16, 2022 |
| Title |
V. cholerae hapR+ ravAviA+ glucose 0.4_replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial culture
|
| Organism |
Vibrio cholerae O1 biovar El Tor str. N16961 |
| Characteristics |
genotype: hapR+ ravAviA+
growth phase: exponential phase OD 0.3
treatment: glucose 0,4%
|
| Treatment protocol |
no treatment or supplemented with glucose 0.4% or maltose 0.4%
|
| 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 |
| |
|
| Description |
M145_GLUC_2
|
| Data processing |
The RNA-seq analysis was performed with Sequana 0.9.2. In particular, we used the RNA-seq pipeline 0.9.6 built on top of Snakemake 5.31.1.
Briefly, reads were trimmed from adapters using cutadapt 2.10 then mapped to the Vibrio cholerae reference genome GCF_000006745.1 from NCBI using Bowtie 2.3.5.1.
Clustering of transcriptomic profiles were assessed using a Principal Component Analysis (PCA).
Differential expression testing was conducted using DESeq2 library 1.24.0 scripts indicating the significance (Benjamini-Hochberg adjusted p-values, false discovery rate FDR < 0.05) and the effect size (fold-change) for each comparison.
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 |
Feb 13, 2022 |
| Last update date |
Feb 16, 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) |
| GSE196651 |
V. cholerae transcriptome in MH, supplemented or not with glucose 0.4% or maltose 0.4% |
|
| Relations |
| BioSample |
SAMN25891952 |
| SRA |
SRX14164077 |
