|
| Status |
Public on Jan 05, 2022 |
| Title |
manR mutant grown on M9+Fru |
| Sample type |
SRA |
| |
|
| Source name |
Fru-d1825
|
| Organism |
Vibrio cholerae O1 biovar El Tor str. N16961 |
| Characteristics |
genotype: VC1825 gene deletion mutant
culture condition: M9 minimal medium + 0.2% fructose
|
| Treatment protocol |
The cell pellets were rinsed twice with M9 medium lacking a carbon source. Each culture was divided into several aliquots and supplemented with 0.2% indicated sugar. These samples were cultured for 30 min at 37°C.
|
| Growth protocol |
V. cholerae WT or mutant cells cultured overnight were diluted 100-fold in 10 mL of fresh LB medium and cultured at 37°C until OD600 reached 0.5.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After fixing the cells with the same volume of 100% methanol for 1 h at -20°C, total RNA was isolated using the TaKaRa MiniBEST Universal RNA Extraction Kit (#9767A, Takara Bio) according to the manufacturer’s instructions.
Library was constructed using NEBNext® rRNA Depletion Kit (Bacteria) (#E7850) and NEBNext Ultra II RNA library Prep kit for Illumina (#E7770) following manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with default parameter.
Cleaned reads were mapped to reference genome using bowtie2 v.2.3.5 with '--very-sensitive' option.
For counting reads which mapped to each CDS, featureCounts in Subread package was used.
Finally, TPM (transcript per million) normalization of retrieved counts and fold change calculation between groups were performed by R.
Genome_build: Vibrio cholerae O1 biovar El Tor str. N16961 (GCA_003063785.1)
Supplementary_files_format_and_content: TPM normalized value and fold change
|
| |
|
| Submission date |
Jan 02, 2022 |
| Last update date |
Jan 05, 2022 |
| Contact name |
Yong-Joon Cho |
| Organization name |
Seoul National University
|
| Street address |
1 Gwanak-ro, Gwanak-gu
|
| City |
Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL31160 |
| Series (1) |
| GSE192900 |
A mannose-sensing AraC-type transcriptional activator regulates intestinal colonization of Vibrio cholerae |
|
| Relations |
| BioSample |
SAMN24579303 |
| SRA |
SRX13578278 |
