|
| Status |
Public on Dec 14, 2025 |
| Title |
V. cholerae C6706 cells grown in Brain Heart Infusion, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Vibrio cholerae C6706 |
| Characteristics |
cell type: bacterial cells
genotype: WT
treatment: No addition
|
| Growth protocol |
V. cholerae C6706 was grown overnight in LB medium at 37°C with shaking (200 rpm). The culture was diluted 1:200 in BHI broth containing either a control extract or an extract from E. citroniae WAL17108 and incubated at 37°C with shaking (200 rpm). After approximately 3 hours of growth (mid-log phase), cells were processed as described below.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacterial RNA was stabilized using RNAprotect Bacteria Reagent (Qiagen) according to the manufacturer’s instructions. Bacterial cells were pelleted by centrifugation, and total RNA was isolated using the SV Total RNA Isolation System (Promega), following the manufacturer’s recommendations. RNA samples were treated with Turbo DNase (2 U/μL; Life Technologies) to eliminate residual DNA, followed by an additional purification step using the SV Total RNA Isolation System (Promega), according to the manufacturer’s recommendations. RNA concentration and purity were assessed using an ND-1000 NanoDrop spectrophotometer (Thermo Fisher Scientific). Absence of DNA contamination in the RNA was checked by quantitative Real-Time PCR.
RNA sequencing (RNA-seq) was performed on an Illumina NextSeq 2000 platform using a P1 flow cell, as single reads (100 bp), at The University of Kansas Genome Sequencing Core.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
Library name: Control_2
|
| Data processing |
Read quality was assessed using FastQC v0.12.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC v1.14. Reads were then mapped against the V. cholerae C6706 reference genome (GCF_015482825.1) using STAR software v2.7.10b (parameter: --quantMode GeneCounts). Raw counts were normalized and the differentially expressed genes were determined with DESeq2 R package (Log2 fold-change ≥1, p-adjusted <0.05).
Assembly: GCF_015482825.1
Supplementary files format and content: xlsx file with normalized counts for each sample
|
| |
|
| Submission date |
Dec 10, 2025 |
| Last update date |
Dec 14, 2025 |
| Contact name |
Luis Caetano Antunes |
| E-mail(s) |
caetano@ku.edu
|
| Phone |
7859792527
|
| Organization name |
University of Kansas
|
| Street address |
1200 Sunnyside Avenue
|
| City |
Lawrence |
| State/province |
KS |
| ZIP/Postal code |
66045 |
| Country |
USA |
| |
|
| Platform ID |
GPL35328 |
| Series (1) |
| GSE313194 |
Enterocloster citroniae and related gut microbiome species modulate Vibrio cholerae biofilm formation through the production of bioactive small molecules |
|
| Relations |
| BioSample |
SAMN53855799 |
| SRA |
SRX31422038 |
