|
| Status |
Public on Feb 27, 2024 |
| Title |
20 s Irradiation vs Unirradiated Replicate 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Unirradiated cells (reference)
|
| Organism |
Escherichia coli |
| Characteristics |
strain: K12 MG1655 DSM498
treatment: Unirradiated
|
| Treatment protocol |
2.5 mL of cells (OD578 nm) were transfered to a 10x20 mm quartz cuvette, the cells were the irradiated (448 nm, blue laser) for 5 s (310 J/cm2) or 20 s (1240 J/cm2) both with an intensity of 62 W/cm2, the cells were then transfered to a 15 mL tube and incubated at room temperature under slight agitation for 60 min, the cells were then pelleted (5 min, 4000 xg) and stored at -80 °C
|
| Growth protocol |
E. coli cells were grown in LB-medium in baffled flasks until the exponential phase (180 rpm, 37 °C), sedimented (4000 xg, 10 min), washed three times and suspended in isotonic NaCl (9 g(L)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasyminiKit (Qiagen) and Dnase treated using TurboDNase (Thermo fisher) according to the manufacturers instructions
|
| Label |
cy3
|
| Label protocol |
“ULS Fluorescent Labeling Kit for Agilent Arrays with Cy3 and Cy5” (Kreatech Biotechnology, Amsterdam, Netherlands) was used following the manufacturer´s instruction for two-colour microarray-based gene expression analysis
|
| |
|
| Channel 2 |
| Source name |
irradiated cells 20 s
|
| Organism |
Escherichia coli |
| Characteristics |
strain: K12 MG1655 DSM498
treatment: Irradiated 20 s
|
| Treatment protocol |
2.5 mL of cells (OD578 nm) were transfered to a 10x20 mm quartz cuvette, the cells were the irradiated (448 nm, blue laser) for 5 s (310 J/cm2) or 20 s (1240 J/cm2) both with an intensity of 62 W/cm2, the cells were then transfered to a 15 mL tube and incubated at room temperature under slight agitation for 60 min, the cells were then pelleted (5 min, 4000 xg) and stored at -80 °C
|
| Growth protocol |
E. coli cells were grown in LB-medium in baffled flasks until the exponential phase (180 rpm, 37 °C), sedimented (4000 xg, 10 min), washed three times and suspended in isotonic NaCl (9 g(L)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasyminiKit (Qiagen) and Dnase treated using TurboDNase (Thermo fisher) according to the manufacturers instructions
|
| Label |
cy5
|
| Label protocol |
“ULS Fluorescent Labeling Kit for Agilent Arrays with Cy3 and Cy5” (Kreatech Biotechnology, Amsterdam, Netherlands) was used following the manufacturer´s instruction for two-colour microarray-based gene expression analysis
|
| |
|
| |
| Hybridization protocol |
using the Gene Assay Hybridization Kit (Agilent) according to the manufacturers instructions and samples were applied to microarrays. After hybridization, slides were washed sequential
|
| Scan protocol |
the Agilent C Scanner (Agilent; Scan Control 8.4.1; Feature Extraction 10.7.3.1)
|
| Description |
Biological replicate 1 of 3
|
| Data processing |
Agilent Scan Control 8.4.1 and Feature Extraction 10.7.3.1
normalized log10 ratio (Cy5/Cy3) representing test/reference
|
| |
|
| Submission date |
Feb 12, 2024 |
| Last update date |
Feb 28, 2024 |
| Contact name |
Mattes Hintmann |
| E-mail(s) |
mathintm@tu-braunschweig.de
|
| Organization name |
TU Braunschweig
|
| Department |
Institut für Mikrobiologie
|
| Lab |
AG Biedendieck
|
| Street address |
Rebenring 56
|
| City |
Braunschweig |
| ZIP/Postal code |
38106 |
| Country |
Germany |
| |
|
| Platform ID |
GPL34184 |
| Series (1) |
| GSE255630 |
Transcriptome analyses of blue laser radiation treated E. coli K12 MG1655 |
|
