|
| Status |
Public on Oct 09, 2024 |
| Title |
Wild type host infected with phage K- 0 min time point (replicate D) |
| Sample type |
SRA |
| |
|
| Source name |
NRS384
|
| Organism |
Staphylococcus aureus |
| Characteristics |
time point: 0 min
cell line: NRS384
cell type: bacterial cells
genotype: WT
treatment: infected with phage K
|
| Treatment protocol |
Phage K was added at an MOI of ~5 once the O.D. of the cultures reached 0.3
|
| Growth protocol |
25 ml TSB cultures were innoculated with 100 ul of overnight cultures and grown at 30 °C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1 mL samples were collected at 2, 5, 10, 20, 30, 40 min after addition of phage, and total RNA was extracted from these samples using the QIAGEN RNEasy Mini Kit.
The samples were further treated with Turbo DNAse to degrade phage/bacterial DNA, and the RNA quality was measured using an Agilent 2100 Bioanalyzer. Ribosomal RNA was depleted using the Illumina Ribozero plus kit, and Illumina RNA-seq libraries were prepared without any enrichment.
A strand-specific RNA seq Novaseq S2 100-bp paired end run was performed on the samples using an Illumina Novaseq 6000 instrument
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Novaseq S2 100 bp paired end run
WT_0_D
|
| Data processing |
Initial quality check was done using FastQC and read mapping distribution was analyzed using MultiQC
Reads were mapped using Bowtie2 and visualized using IGV. For quantitative analysis, read counts were obtained using Kallisto and differntial expression analysis was done using EdgeR package on the Rstudio platform
Assembly: Reads were mapped to the full length genome of phage K (NC_005880.2) and NRS384 (CP027476.1) using Bowtie2 to check for transcriptional activity. No genome building/assembly was performed for our analysis purposes.
Supplementary files format and content: Transcripts per million (TPM) data for all the gene and tRNA features annotated in phage K (as calculated by Kallisto) from all the samples are provided as a separate file
|
| |
|
| Submission date |
Jan 17, 2024 |
| Last update date |
Oct 09, 2024 |
| Contact name |
Ramchander Rohit Kongari |
| E-mail(s) |
[email protected]
|
| Phone |
9794225701
|
| Organization name |
United States Food and Drug Administration
|
| Department |
Department of Bacterial, Parasitic and Allergenic products
|
| Lab |
Laboratory of Mucosal Pathogens and Cellular Immunity
|
| Street address |
10903 New Hampshire Ave
|
| City |
Silver Spring |
| State/province |
Maryland |
| ZIP/Postal code |
20903 |
| Country |
USA |
| |
|
| Platform ID |
GPL27158 |
| Series (1) |
| GSE253516 |
The transcriptional program of Staphylococcus aureus phage K is affected by a host rpoC mutation that confers phage K resistance |
|
| Relations |
| BioSample |
SAMN39476172 |
| SRA |
SRX23266259 |
