|
| Status |
Public on Oct 23, 2018 |
| Title |
VRE treated [18] |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria
|
| Organism |
Enterococcus faecium |
| Characteristics |
strain: RBWH1
agent: PBT2 and zinc
|
| Treatment protocol |
Bacteria were grown in the presence or absense of PBT2 and zinc
|
| Growth protocol |
Bacteria were grown in cation-adjusted Mueller-Hinton broth
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the FastRNA® Pro Blue Kit (MP Biomedicals) and the SV Total RNA Isolation System (Promega)
RNASeq analysis was performed at the Australian Genome Research Facility. The library was prepared using a Ribo-zero stranded protocol. Libraries were sequenced with a HiSeq 2500 ultra-high-throughput sequencing system (Illumina) to produce 100-base-paired end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
18
|
| Data processing |
An average of 45 million reads per sample were generated and mapped to the reference genome using the 2-passmethod of the STAR aligner with default parameters.
Duplicate reads were denoted with the MarkDuplicates tool of Picard (http://broadinstitute.github.io/picard)
Differential gene expression was analysed using Degust (http://victorian-bioinformatics-438 consortium.github.io/degust/)
genome build: Streptococcus pyogenes: NZ_AFRY01000001.1, Staphylococcus aureus: NC_007793.1, Enterococcus faecium: Bioproject PRJNA497960
Supplementary_files_format_and_content: xlsx files for each bacterial strain, CPM
|
| |
|
| Submission date |
Oct 22, 2018 |
| Last update date |
Oct 23, 2018 |
| Contact name |
Lisa Bohlmann |
| E-mail(s) |
lisa_bo1@yahoo.de
|
| Organization name |
University of Queensland
|
| Street address |
University of Queensland
|
| City |
St. Lucia |
| ZIP/Postal code |
4072 |
| Country |
Australia |
| |
|
| Platform ID |
GPL23589 |
| Series (1) |
| GSE121555 |
RNASeq analysis of untreated versus treated |
|
| Relations |
| BioSample |
SAMN10266251 |
| SRA |
SRX4910586 |
