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Sample GSM3439183 Query DataSets for GSM3439183
Status Public on Oct 23, 2018
Title VRE untreated [13]
Sample type SRA
 
Source name Bacteria
Organism Enterococcus faecium
Characteristics strain: RBWH1
agent: none
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 13
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 SAMN10266256
SRA SRX4910581

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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