|
| Status |
Public on Jan 01, 2018 |
| Title |
DMSO control_minusTEX, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Staphylococcus aureus whole cells_DMSO
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: NCTC 8325
|
| Treatment protocol |
100 µM compound 3 dissolved in DMSO or just DMSO as a control were added before the 20 h growth period in a 1:100 volume ratio.
|
| Growth protocol |
5 mL of B medium were inoculated with 50 µL ON culture (1:100). After 1-3 h the culture reached an OD600 between 0.38 and 0.59. Bacteria were then diluted in B medium in 4 steps to get a concentration of 3.4x10^4 bacteria per mL. Bacterial cultures were grown at 200 rpm for 20 h at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Isolation of the RNA from 1x109 bacteria/sample was done with Precellys Bacterial/Fungal RNA Kit (12-7611-01) including a DNAse I digest. RNA was eluted with 43 µL RNAse free ddH2O.
Library construction was done according to Dugar et al. (Dugar, G., et al., High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates. PLoS Genet, 2013. 9(5): p. e1003495.)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Demultiplexing
Fastq quality trimming using a cut-off value of 20 (via FastX toolkit)
Fastq to fasta conversion (via READemption)
Read mapping using segemehl (via READemption)
Coverage calculation and normalisation (via READemption)
Gene-wise quantification (via READemption)
Differential gene expression analysis (via READemption)
Genome_build: NC_007795.1
Supplementary_files_format_and_content: The pairwise expression comparision based on these gene quantifications was done with READemption's subcommand "deseq" with relies on DESeq version 1.12.1.
|
| |
|
| Submission date |
Mar 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jan Vomacka |
| Organization name |
Technische Universität München
|
| Department |
Department of Chemistry
|
| Lab |
Chair of Organic Chemistry II
|
| Street address |
Lichtenbergstraße 4
|
| City |
Garching |
| ZIP/Postal code |
85748 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19006 |
| Series (1) |
| GSE79407 |
Mode of action analysis: Distinct Staphylococcus aureus transcriptome changes upon antivirulence lactone treatment |
|
| Relations |
| BioSample |
SAMN04569905 |
| SRA |
SRX1648211 |
