|
| Status |
Public on Jun 28, 2024 |
| Title |
Cronobacter_turicencer_BHI_2 |
| Sample type |
SRA |
| |
|
| Source name |
stationary phase cell culture
|
| Organism |
Cronobacter turicensis |
| Characteristics |
cell type: stationary phase cell culture
genotype: z3032
treatment: LB
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cronobacter turicensis z3032 cultures grown in LB to stationary phase (18 – 24 h).Cell were harvested and RNA extractions were performed using the miRNeasy Mini kit (Qiagen) according to the manufacturer’s protocols. An additional DNase treatment was performed with a TURBO DNA-free kit (Ambion) according to the manufacturer’s protocols. The concentration of the extracted RNA was measured using a NanoDrop Spectrophotometer.
125 bp paired-end RNA Sequencing on a HiSeq2500 (Illumina) were performed at the Functional Genomic Center at University Zurich (FGCZ), Zurich, Switzerland, accoring to the Illumina protocl
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequencing data were assessed for quality using fastqc 0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The RNAseq reads were mapped against the C. turicensis z3032 genome (accesion numbers NC_013282.2-NC_013285.1) using botwie2. Samtools was used to convert and sort the output and featureCounts summarized the aligned reads. Data normalization and determination of significance of differential expression was performed in R (R-project.org) using the GLM method in the EdgeR package as described previously [CIT].
Assembly: z3032 genome (NC_013282.2-NC_013285.1)
Supplementary files format and content: .csv file with edgeR normalised read counts
|
| |
|
| Submission date |
Jun 30, 2023 |
| Last update date |
Jun 28, 2024 |
| Contact name |
Marc Stevens |
| E-mail(s) |
marc.stevens@uzh.ch
|
| Organization name |
University of Zurich
|
| Department |
Vetsuisse
|
| Lab |
Institute for Food Safety and Hygiene
|
| Street address |
Winterthurerstrasse 272
|
| City |
Zürich |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL33542 |
| Series (1) |
| GSE236313 |
Transcriptomics of pathogen Cronobacter turicensis z3032 in lysogenic broth |
|
| Relations |
| BioSample |
SAMN36182145 |
| SRA |
SRX20853501 |
