|
| Status |
Public on Jan 31, 2018 |
| Title |
CF1 |
| Sample type |
SRA |
| |
|
| Source name |
Biofilm CF1
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: LYO-S2
cell type: sessile cells
condition: 24h-old-biofilm treated with 16 µg/mL of fosfomycin for 24h - Replica 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were produced by the ScriptSeq Complete Kit (Bacteria - Illumina)
RNA-seq : Libraries were sequenced with the Hiseq2500 system (Illumina) with a paired-end protocol and read lengths of 100bp
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Ribosomal RNA were removed with the RiboZero kit
|
| Data processing |
Reads were mapped against the genome of the reference strain S. aureus NCTC 8325 with the Bowtie2 v2.2.6 software. Only reads without mismatch were counted. Differentially expressed genes between biofilm treated with fosfomycin and its control (not treated) were determined by RSEM v1.2.23 software. Transcripts were considered at differentially expressed using the following criteria : adjusted p-value< 0.01 and |fold-change| > 2.
Transcrits were identified using a BLASTn searches against the reference strain S. aureus NCTC 8325.
genome build: NC_007795.1
|
| |
|
| Submission date |
Jun 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Christiane Forestier |
| E-mail(s) |
[email protected]
|
| Organization name |
Laboratoire Microorganismes Génome et Enironnement
|
| Department |
Université de Pharmacie
|
| Street address |
28 Place Henri Dunant
|
| City |
Clermont Ferrand |
| ZIP/Postal code |
63000 |
| Country |
France |
| |
|
| Platform ID |
GPL19006 |
| Series (1) |
| GSE83269 |
Effects of fosfomycin on biofilm of a clinical Staphylococcus aureus isolated from osteoarticular infection by transcriptomal approach |
|
| Relations |
| BioSample |
SAMN05232108 |
| SRA |
SRX1838291 |
