|
| Status |
Public on Jun 21, 2024 |
| Title |
wild type-1 |
| Sample type |
SRA |
| |
|
| Source name |
14028S
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S |
| Characteristics |
strain: 14028S
genotype: wild type
|
| Growth protocol |
Bacteria were grown at 37°C in N-minimal media (30) supplemented with 0.1% casamino acids, 38 mM glycerol, and the 10 mM MgCl2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy Kit (Qiagen), according to the manufacturer’s instructions.
For ribosomal RNA depletion, 5 μg of the total RNA was processed by Ribo-Zero rRNA Removal Kit (Bacteria). Sequencing libraries for RNA-Seq were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760S), following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
wild type replcate 1
|
| Data processing |
The sequencing adapter removal and quality-based trimming for the raw data were performed using Trimmomatic v. 0.36.
Cleaned reads were mapped to the reference genome using bowtie2 with a default parameter.
For counting the reads mapped to each CDS (coding sequence), featureCounts was used.
Finally, the count from each CDS was normalized using DeSeq2 package.
Assembly: GCF_000022165.1
Supplementary files format and content: tab-limited file includes DeSeq2 normalized result between wild type and sehB mutant
|
| |
|
| Submission date |
Jun 16, 2024 |
| Last update date |
Jun 21, 2024 |
| 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 |
GPL23619 |
| Series (1) |
| GSE269990 |
A HigB-like toxin induces non-replicating Salmonella inside macrophages by inhibiting RNase III-dependent rRNA maturation [sehB_RNA-Seq] |
|
| Relations |
| BioSample |
SAMN41860161 |
| SRA |
SRX24942033 |
