|
| Status |
Public on Sep 01, 2020 |
| Title |
3xdelta-relQ-30min-mit-AHT-d_S8_R1_001 |
| Sample type |
SRA |
| |
|
| Source name |
3xdelta-relQ-30min-mit-AHT-d_S8_R1_001
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: HG001
genotype: [delta]rshsyn[delta]relP[delta]relQ
induction of rsh-syn or relq: yes
|
| Treatment protocol |
At OD600=0.3 strains were split into two groups. One remained the untreated control and the second RSH or RelQ were induced using 0.1µg/ml anhydrotetracycline (AHT or Atc)
|
| Growth protocol |
Strain were grown over night in CDM. OD600 was measured and diluted to an OD600 =0.05 for day cultures and grown until early exponential phase (OD600=0.3)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pellet was solved in Trizol. Strains were lysed using 0.5mm circonia silicia beads. Chloroform was used seperate RNA from DNA and proteins. RNA extraction was performed following the protocol by Amp Tech ExpressArt® RNA ready
RNA was examined by a capillary electrophoresis on a Shimadzu MultiNA microchip followed by rRNA depletion using Ribo-Zero rRNA removel Kit from Illumina. RNA was converted to cDNA by fragmenting RNA samples by ultrasound and ligating an oligonucleotide adapter to the 3’end of the RNA. Using M-MLV reverse transcriptase first strand cDNA was created using 3’ adapter as primer. The 5’Illumina TruSeq sequencing adapter was ligated to the 3’end of the purified (Agencourt AMPure XP kit) cDNA and PCR was performed. Samples were pooled in equimolar amounts and fractionated in a size range of 200-500 bp using a preparative agarose gel and Illumina sequencing was performed using 75bp reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
3xdelta-relQ-30min-mit-AHT-d_S8_R1_001
|
| Data processing |
Data were processed using CLC Genomic Workbench from Qiagen
Reads were trimmed for adaptor and reads shorter than 15bp were discarded . Trimmed reads were aligned to reference genome HG001. Calculation of RPKM was automatically performed by CLC Genomic Workbench. Statistical analysis was also performed by CLC Genomic workbench. Genes with p>0.001 and 3-fold difference were included
Genome_build: Refence genome: HG001 provided by Ulrike Mäder
Supplementary_files_format_and_content: RPKM
|
| |
|
| Submission date |
Feb 12, 2020 |
| Last update date |
Sep 02, 2020 |
| Contact name |
Christiane Wolz |
| E-mail(s) |
[email protected]
|
| Organization name |
University Tübingen
|
| Street address |
Elfriede-Aulhorn-Strasse 6
|
| City |
Tübingen |
| ZIP/Postal code |
72076 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24034 |
| Series (1) |
| GSE145144 |
Increasing the cellular (pp)pGpp level is associated with activation of stress response genes in Staphylococcus aureus |
|
| Relations |
| BioSample |
SAMN14087173 |
| SRA |
SRX7711435 |
