|
| Status |
Public on Feb 04, 2022 |
| Title |
A1552 (#1) replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
in vitro bacterial culture
|
| Organism |
Vibrio cholerae |
| Characteristics |
strain: A1552 (#1)
genotype: wild-type (A1552)
growth medium: LB medium
|
| Treatment protocol |
The harvested bacteria were washed in pre-chilled PBS buffer, lysed through resuspension in Tri Reagent, and stored at -80C until their processing.
|
| Growth protocol |
V. cholerae strains were back-diluted 1:100 from an overnight culture in LB medium and grown for 3 h at 30°C with agitation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using standard RNA isolation kits. The RNA was cleaned up after DNAse treatment using a RNA clean-up procedure (GenElute Mammalian Total RNA miniprep kit; Sigma). Next, Illumina RNA libraries incl. bacterial Ribo-depletion were prepared.
RNA libraries were prepared with a TruSeq Stranded mRNA sample prep kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Data processing was done by Microsynth (Balgach, Switzerland) using their pipeline "Standard differential prokaryotic gene expression analysis"
Single end reads (1x75bp), which passed Illumina’s chastity filter, were demultiplexed and trimmed off the Illumina adaptors using Illumina’s bcl2fastq software version v2.20.0.422 (no further refinement or selection).
Reads were mapped to the reference genomes (A1552 chromosome 1 [CP028894] and 2 [CP028895]; ATCC25872 chromosome 1 [CP047305] and 2 [CP047306]) via bowtie2 (version 2.3.5.1)
Uniquely mapped reads to annotated genes were counted using the software htseq-count (HTSeq version 0.11.2)
Normalization of the raw counts and differential gene expression analysis was carried out with help of the R software package DESeq2 (version 1.22.2)
Genome_build: Reference genomes were A1552 chromosome 1 [CP028894] and 2 [CP028895] or ATCC25872 chromosome 1 [CP047305] and 2 [CP047306]
Supplementary_files_format_and_content: .tsv files for normalized counts
|
| |
|
| Submission date |
Feb 04, 2022 |
| Last update date |
Feb 04, 2022 |
| Contact name |
Melanie Blokesch |
| Organization name |
Swiss Federal Institute of Technology Lausanne (EPFL)
|
| Department |
School of Life Sciences
|
| Lab |
Laboratory of Molecular Microbiology
|
| Street address |
Station 19 / EPFL-SV-UPBLO
|
| City |
Lausanne |
| ZIP/Postal code |
CH-1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL31913 |
| Series (1) |
| GSE196165 |
Single nucleotide polymorphism determines constitutive versus inducible type VI secretion in Vibrio cholerae |
|
| Relations |
| BioSample |
SAMN25654179 |
| SRA |
SRX14046219 |
