|
| Status |
Public on Nov 16, 2020 |
| Title |
srn2050-deleted Aus0004 mutant with empty pAT29 plasmid - sample 2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria
|
| Organism |
Enterococcus faecium |
| Characteristics |
strain: Aus0004
genotype: srn2050-deleted
plasmid: empty pAT29 plasmid
|
| Growth protocol |
Bacterial cells of E. faecium Aus0004 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 phenol/chloroform method. Residual chromosomal DNA was removed by treating samples with the TURBO DNA-free kit (Life Technologies).
The strand-specific library preparation was performed using the Ovation Universal Prokaryotic RNA-Seq kit (Nugen) with custom depletion (Anydeplete rRNA design Enterococcus faecium) and the samples were sequenced using the Illumina NextSeq500 instrument (multiplex protocol, single-end 75-bp reads).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| 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)
Supplementary_files_format_and_content: Tab-delimited text files generated using the CLC Genomics Workbench software v10.0.1 (Qiagen).
|
| |
|
| Submission date |
Nov 15, 2020 |
| Last update date |
Nov 16, 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 |
GPL29418 |
| Series (1) |
| GSE161499 |
A dual T-box riboswitch in Enterococcus faecium binds two tRNAs |
|
| Relations |
| BioSample |
SAMN16803217 |
| SRA |
SRX9510408 |
