|
| Status |
Public on Jan 23, 2024 |
| Title |
Y. pseudotuberculosis YP356, 25°C, time 0, replicate III |
| Sample type |
SRA |
| |
|
| Source name |
YP356
|
| Organism |
Yersinia pseudotuberculosis |
| Characteristics |
cell type: YP356
genotype: delta_rnc (RNase III-deficient mutant)
treatment: 25 degrees C growth in LB
|
| Treatment protocol |
The cultures were split and grown at 25°C (time 0), 37°C, or 37°C in the presence of 20 mM Na2C2O4 and 20 mM MgCl2 (Ca2+ depletion) in triplicates. After 1 h (time 1) and 4 h ( time 2).
|
| Growth protocol |
Y. pseudotuberculosis YPIII and the isogenic Δrnc mutant YP356 were grown in LB medium to exponential phase (OD600 0.5)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pellet from 2ml bacteria culture were snap frozen in liquid nitrogen and resuspended, lysed and later incubated with Roti® Aqua Phenol. Aqueous layer was washed with chloroform/isoamyl-alocohol (24:1) and RNA precipitated adding 1/10 volume of 3M NaOAc (pH 4.5) and 3 volumes of 95% EtOH. RNA pellet was washed with 70% EtOH and resupsended in RNase free water.
RNAseq libraries were prepared using a NEBNext Ultra II Directional RNA Library Prep Kit - Bacteria, according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
rnc_T0_25_III
III_T0_25_vs_rnc_T0_25.csv
rnc_T0_25_vs_III_T1_37_plusCa.csv
rnc_T0_25_vs_rnc_T1_37_plusCa.csv
rnc_T0_25_vs_III_T1_37_minusCa.csv
rnc_T0_25_vs_rnc_T1_37_minusCa.csv
rnc_T0_25_vs_III_T2_37_plusCa.csv
rnc_T0_25_vs_rnc_T2_37_plusCa.csv
rnc_T0_25_vs_III_T2_37_minusCa.csv
rnc_T0_25_vs_rnc_T2_37_minusCa.csv
|
| Data processing |
Downstream analysis, included assessment of the general quality of sequencing output FastQC (Babraham Bioinformatics)) and mapping to the reference genomes (YPIII chromosome and virulence plasmid pYV) (NC_010465.1 and NC_006153.2) (Bowtie2 with default parameters (Langmead and Salzberg, 2012)). Uniquely mapped reads were obtained using SAMtools (Li et al., 2009)
Assembly: YPIII chromosome (NC_010465.1 ) and virulence plasmid pYV (NC_006153.2)
Supplementary files format and content: csv files containing reports obtained by DESeq2 R-package.
|
| |
|
| Submission date |
Dec 05, 2023 |
| Last update date |
Jan 23, 2024 |
| Contact name |
Ileana Salto |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute für Infektiologie. ZMBE. Münster
|
| Street address |
Von-Esmarch-Str. 56
|
| City |
Münster |
| State/province |
Nordrhein-Westfalen |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL28682 |
| Series (1) |
| GSE249386 |
RNase-mediated reprogramming of Yersinia virulence |
|
| Relations |
| BioSample |
SAMN38689735 |
| SRA |
SRX22795122 |
