|
| Status |
Public on Feb 04, 2017 |
| Title |
Growth with no ciprofloxacin - sample 2 |
| Sample type |
SRA |
| |
|
| Source name |
Growth with no ciprofloxacin
|
| Organism |
Enterococcus faecium Aus0004 |
| 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 |
total 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) using the CLC Genomics Workbench software v8.1 (Qiagen).
The number of reads uniquely aligned to each genomic position was determined using the BEDTools program v2.16.2.
The expression of genes in different RNA-seq samples was compared using normalized RPKM values calculated as follows: (# reads for the gene*109)/(# total of reads*size of the gene).
Genome_build: E. faecium Aus0004 (Genbank accession no. CP003351)
Supplementary_files_format_and_content: Tab-delimited text files generated by BEDTools program v2.16.2 with RPKM values
|
| |
|
| Submission date |
Feb 03, 2017 |
| Last update date |
May 15, 2019 |
| 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 |
GPL23028 |
| Series (1) |
| GSE94507 |
Subinhibitory concentrations of ciprofloxacin enhance antimicrobial resistance and pathogenicity of Enterococcus faecium |
|
| Relations |
| BioSample |
SAMN06295749 |
| SRA |
SRX2537848 |
