|
| Status |
Public on Oct 01, 2015 |
| Title |
S. aureus in LB medium rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Exponential growing S. aureus in LB medium
|
| Organism |
Staphylococcus aureus |
| Characteristics |
genome: SAU060112
od600: 0.5
|
| Treatment protocol |
The samples were centrifuged at 13 000 g for 2 minutes. The pellets were snap-frozen in liquid nitrogen and stored at -80 C until RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with RiboPure Bacteria Kit (Ambion). Genomic DNA was removed with Dnase I treatment. MicroExpress (Ambion) was used to remove ribosomal RNA.
Illumina Truseq RNA sample preparation Kit v2 according to manufacturers instruction. Paired end sequenced using Truseq SBS kit v.3-HS Sequencing kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
The isolated S. aureus from the infection was grown to OD600=0.5 at 37C with shaking (200 RPM)
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2, Hiseq control software: HCS 1.5.15.1/RTA 1.13/SAV 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Then using RNA-seq analysis function in CLC genomic workbench v. 6.5.1, the reads were mapped to SAU060112 genome allowing a minimum length fraction of 80% and minimum similarity fraction of 95%. The resulting output is a table summarizing the read mapping which includes Reads Per Kilobase of exon per Megabase of library size (RPKM), total mapped reads, uniquely mapped reads etc. for each gene.
The RNA-seq analysis output for each sample were used as input for differential gene expression using EdgeR.
Genome_build: SAU060112
Supplementary_files_format_and_content: tab-delimited text files include gene length, unique gene reads, total gene reads, RPKM values, chromosome region start and end for each Sample; The file "Supplementary_file_1.txt" is available on the series record and contains genes identified with differential expression and includes gene description, fold-change values and statistics.
|
| |
|
| Submission date |
Oct 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yijuan Xu |
| E-mail(s) |
xuyijuan@bio.aau.dk
|
| Organization name |
Aalborg University
|
| Department |
Department of biotechnology, chemistry and environmental engineering
|
| Street address |
Fredrik Bajers vej 7H
|
| City |
Aalborg East |
| ZIP/Postal code |
9220 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL17452 |
| Series (1) |
| GSE62091 |
In situ Staphylococcus aureus gene expression in a human prosthetic joint infection |
|
| Relations |
| BioSample |
SAMN03097427 |
| SRA |
SRX724856 |
