|
| Status |
Public on May 17, 2017 |
| Title |
DSM 16831 4.15a planktonic |
| Sample type |
RNA |
| |
|
| Source name |
S. gallolyticus DSM 16831; planktonic BHI medium 2 hrs
|
| Organism |
Streptococcus gallolyticus subsp. gallolyticus DSM 16831 |
| Characteristics |
growth type: BHI medium, planktonic
time point: 2 h incubation
|
| Treatment protocol |
An amount of 2 ml of bacterial culture (exponential phase) was added to 6-well plates with immobilized collagen type I (human) in comparison to 2 ml of bacterial culture in 6-well without collagen (planktonic). After incubation for 2 h, the supernatant with the non-adhered bacterial cells (planktonic) and the collagen-adhered bacterial cells were removed for RNA extraction.
|
| Growth protocol |
Bacterial cultures in the exponential growth phase were generated by inoculating 5 ml BHI medium with 100 µl overnight culture. The exponential growth phase was reached after 2.5 h at 37 °C and 220 rpm. The bacterial titer was determined by serial dilutions in Dulbecco’s phosphate-buffered saline (DPBS) and plating 100 µl of an adequate concentration in triplicate on tryptone soya agar (Thermo Scientific, Waltham, USA). Tryptone soya agar plates were incubated at 37 °C and the colonies grown were counted using an aCOLyte colony counter (Synbiosis, Cambridge, UK).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA was extracted with the peqGOLD Bacterial RNA Kit (VWR, Radnor, USA). Bacterial cells were suspended in TE buffer and lysis buffer T and transferred into Lysing Matrix B tubes (MP Biomedicals, Santa Ana, USA). The bacterial cells were disrupted by using Vortex-Genie 2 (scientific industries, New York, USA) for 3 min at full speed. Further RNA extraction was carried following the manufacturer’s instructions. The RNA was eluted with 30 µL RNase-free water and quantified using the NanoDrop 2000 (VWR).
|
| Label |
Cy3
|
| Label protocol |
The cDNA and cRNA synthesis with Cy3 labelling was carried out with the Quick Amp WT Labeling Kit, one-color (Agilent, Santa Clara, USA), following the manufacturer’s recommendations.
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| |
|
| Hybridization protocol |
The Hybridization was also carried out with the Quick Amp WT Labeling Kit, one-color (Agilent, Santa Clara, USA) according to the manufacturer’s recommendations. Hybridization was performed at 65 °C for 17 h. The slides were washed and hybridization was stabilized with Stabilization & Drying solution (Agilent, Santa Clara, USA).
|
| Scan protocol |
After drying, the hybridized microarrays were scanned with the high resolution Agilent microarray scanner G2565CA with a resolution of 3 µm and analyzed with the Feature extraction software (Agilent, Santa Clara, USA).
|
| Description |
SAMPLE 5
|
| Data processing |
Raw data were quantile-normalized and gene expression data were generated by the Direct Array software (OakLabs, Hennigsdorf, Germany).
All log2 values between -1 and 1 were ignored and only statistically significant values (p<0.05) have been taken.
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| |
|
| Submission date |
May 16, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Imke Grimm |
| E-mail(s) |
[email protected]
|
| Organization name |
Herz- und Diabeteszentrum NRW; Universitätsklinikum der Ruhr-Universität Bochum
|
| Department |
Institut für Laboratoriums- und Transfusionsmedizin
|
| Street address |
Georgstraße 11
|
| City |
Bad Oeynhausen |
| ZIP/Postal code |
32545 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23196 |
| Series (2) |
| GSE98953 |
Transcriptome analysis of collagen-adhered S. gallolyticus subsp. gallolyticus [DSM 16831] |
| GSE98955 |
Transcriptome analysis of S. gallolyticus subsp. gallolyticus |
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