|
| Status |
Public on Feb 20, 2023 |
| Title |
marine-A-moins |
| Sample type |
SRA |
| |
|
| Source name |
Vibrio cholerae N16961 in Marine Broth exponential growth phase
|
| Organism |
Vibrio cholerae O1 biovar El Tor str. N16961 |
| Characteristics |
cell type: bacterial cells
media: Marine Broth
growth phase: exponential
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using protocol published in Krin et al, 2018.
rRNA were depleted with the MICROBExpress™ Bacterial mRNA Enrichment Kit (Fisher scientific, AM1905). RNA libraries for RNA-seq were prepared using the TruSeq Stranded RNA LT prep kit, set A and B (ref 15032611, Illumina). Sequencing was performed on the Illumina Hiseq2000 platform to generate single-end 51 bp reads bearing strand specificity.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were cleaned of adapter sequences and low-quality sequences using an in-house program (https://github.com/baj12/clean_ngs).Only sequences at least 25 nt in length were considered for further analysis.
Bowtie version 1.2.2, with default parameters, was used for alignment on the reference genome
Genes were counted using HTSeq-count version 0.6.1
Assembly: Vibrio cholerae N16961 reference genome (accession numbers AE003852 andAE003853)
Supplementary files format and content: matrix table from DESeq2 analysis
|
| |
|
| Submission date |
Oct 04, 2022 |
| Last update date |
Feb 20, 2023 |
| Contact name |
Rachel Legendre |
| E-mail(s) |
rachel.legendre@pasteur.fr
|
| Organization name |
Institut Pasteur
|
| Department |
Research and Resource Center for Scientific Informatics
|
| Lab |
Hub of Bioinformatics and Biostatistics
|
| Street address |
28, rue du docteur Roux
|
| City |
Paris |
| ZIP/Postal code |
75724 |
| Country |
France |
| |
|
| Platform ID |
GPL30088 |
| Series (1) |
| GSE214813 |
Gene expression profile of Vibrio cholerae N16961 grown in various conditions of culture |
|
| Relations |
| BioSample |
SAMN31155059 |
| SRA |
SRX17797309 |
