|
| Status |
Public on Mar 30, 2022 |
| Title |
SAM1 infection of Staphylococcus aureus at 15 mins (replicate 2) |
| Sample type |
SRA |
| |
|
| Source name |
Staphylococcus phage SAM1
|
| Organism |
Staphylococcus phage SAM1 |
| Characteristics |
time: 15 mins
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Supernatants were subject to total RNA extraction using the Direct-zol RNA miniprep kit (Zymo research, USA, as per manufacturer instructions). RNA samples were subject to rRNA depletion and before library creation
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads where mapped to genomes of Staphylococcus phage SAM1 and that of host Staphylococcus aureus strain E1185(IV)ST12 using bowtie2 (v.2.3.4.1) by end-to-end alignment
Read alignments were then sorted by Samtools (v.1.7)
Read counts and coverage tables were then imported into R environment and then compared using DESeq2, using Wald test and parametric fit
Genome_build: MT338525.1
Supplementary_files_format_and_content: tab-delimited text file containg DESEQ calculated differential expression of genes of Staphylococcus phage SAM1 during host infection
|
| |
|
| Submission date |
Dec 29, 2021 |
| Last update date |
Mar 30, 2022 |
| Contact name |
Colin T.H. Buttimer |
| E-mail(s) |
colin.buttimer@mycit.ie
|
| Organization name |
University College Cork
|
| Department |
APC Microbiome Ireland
|
| Lab |
3.36
|
| Street address |
College Road
|
| City |
Cork |
| State/province |
Cork |
| ZIP/Postal code |
T12 YT20 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL31154 |
| Series (1) |
| GSE192733 |
RNA-seq of total RNA from Staphylococcus aureus culture infected with Staphlococcus phage SAM1 |
|
| Relations |
| BioSample |
SAMN24493656 |
| SRA |
SRX13548512 |
