|
| Status |
Public on Jun 16, 2017 |
| Title |
Growth with caspofungin (8 mg/L) - sample 1 |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria_with caspofungin
|
| Organism |
Enterococcus faecium |
| Characteristics |
strain: Aus0004
|
| Growth protocol |
Bacterial cells of E. faecium Aus0004 bacteria were cultured at 37°C to the late-exponential-growth phase in BHI broth
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from using the ZR Fungal/Bacterial RNA Miniprep kit (Zymo Research, Irvine, CA). Residual chromosomal DNA was removed by treating samples with the TURBO DNA-free kit (Life Technologies). The Ribo-Zero Magnetic Kit Gram-Positive Bacteria (Epicentre, Madison, WI) was used according to the manufacturer’s recommendations to remove the 23S, 16S, and 5S rRNAs from the total RNA samples.
The strand-specific library preparation was performed using the NEXTflex Directional RNA-Seq Kit (dUTP-Based) (Bio Scientific, Austin, TX) and the samples were sequenced using the Illumina HiSeq 2500 platform (multiplex protocol, single-end 50-bp reads).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The reads were mapped against the genomic sequence of E. faecium Aus0004 (Genbank accession no. CP003351) and counted using the CLC Genomics Workbench software v10.0.1 (Qiagen).
The expression of genes in different RNA-seq samples was compared using the R package DESeq2 R package.
genome build: E. faecium Aus0004 (Genbank accession no. CP003351)
processed data files format and content: Tab-delimited text files generated using the CLC Genomics Workbench software v10.0.1 (Qiagen).
|
| |
|
| Submission date |
Jun 15, 2017 |
| Last update date |
Jul 30, 2020 |
| Contact name |
Vincent Cattoir |
| E-mail(s) |
vincent.cattoir@chu-rennes.fr
|
| Organization name |
CHU de Rennes
|
| Street address |
2 rue Henri Le Guilloux
|
| City |
Rennes |
| ZIP/Postal code |
35033 |
| Country |
France |
| |
|
| Platform ID |
GPL23589 |
| Series (1) |
| GSE100091 |
Unexpected bactericidal activity of caspofungin against Enterococcus faecium |
|
| Relations |
| BioSample |
SAMN07248069 |
| SRA |
SRX2923099 |
