|
| Status |
Public on Oct 16, 2020 |
| Title |
Gox621H_L-arabinose_vs_control_I |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
G. oxydans treated with L-arabinose
|
| Organism |
Gluconobacter oxydans 621H |
| Characteristics |
strain: 621H
treatment: 4% D-mannitol + 1% L-arabinose
growth phase: exponential
|
| Growth protocol |
For comparison of the transcriptomes, G. oxydans 621H were cultivated in complex medium with 4% (w/v) D-mannitol. In the mid-exponential growth phase, 1% (w/v) L-arabinose was supplemented to G. oxydans 621H cells cultured in 4% (w/v) mannitol medium and the same volume of water in another 621H culture as a control. After 30 min of cultivation, each cell suspension was harvested by centrifugation (4500 g, 5 min, 4°C). The resulting pellets were directly frozen in liquid nitrogen and stored at -80°C until RNA preparation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The preparation of total RNA samples were performed as described previously (Kranz et al., Global mRNA Decay and 23S rRNA Fragmentation in Gluconobacter oxydans 621H, BMC Genomics 2018 Oct 16;19(1):753; doi: 10.1186/s12864-018-5111-1).
|
| Label |
Cy5
|
| Label protocol |
Synthesis of fluorescently labelled cDNA were performed as described previously (Kranz et al., Global mRNA Decay and 23S rRNA Fragmentation in Gluconobacter oxydans 621H, BMC Genomics 2018 Oct 16;19(1):753; doi: 10.1186/s12864-018-5111-1).
|
| |
|
| Channel 2 |
| Source name |
non-treated G.oxydans
|
| Organism |
Gluconobacter oxydans 621H |
| Characteristics |
strain: 621H
treatment: 4% D-mannitol only
growth phase: exponential
|
| Growth protocol |
For comparison of the transcriptomes, G. oxydans 621H were cultivated in complex medium with 4% (w/v) D-mannitol. In the mid-exponential growth phase, 1% (w/v) L-arabinose was supplemented to G. oxydans 621H cells cultured in 4% (w/v) mannitol medium and the same volume of water in another 621H culture as a control. After 30 min of cultivation, each cell suspension was harvested by centrifugation (4500 g, 5 min, 4°C). The resulting pellets were directly frozen in liquid nitrogen and stored at -80°C until RNA preparation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The preparation of total RNA samples were performed as described previously (Kranz et al., Global mRNA Decay and 23S rRNA Fragmentation in Gluconobacter oxydans 621H, BMC Genomics 2018 Oct 16;19(1):753; doi: 10.1186/s12864-018-5111-1).
|
| Label |
Cy3
|
| Label protocol |
Synthesis of fluorescently labelled cDNA were performed as described previously (Kranz et al., Global mRNA Decay and 23S rRNA Fragmentation in Gluconobacter oxydans 621H, BMC Genomics 2018 Oct 16;19(1):753; doi: 10.1186/s12864-018-5111-1).
|
| |
|
| |
| Hybridization protocol |
Purified cDNA samples to be compared were pooled and the prepared two-color samples were hybridized at 65°C while rotating for 17 hours using Agilent’s Gene Expression Hybridization Kit, hybridization oven and hybridization chamber. After hybridization the arrays were washed using Agilent’s Wash Buffer Kit according to the manufacturer’s instructions.
|
| Scan protocol |
Fluorescence of hybridized DNA microarrays was determined at 532 nm (Cy3) and 635 nm (Cy5) at 5 μm resolution with a GenePix 4000B laser scanner and GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA, USA). Fluorescence images were saved to raw data files in TIFF format (GenePix Pro 6.0). Quantitative TIFF image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 6.0).
|
| Data processing |
For ratio calculation and ratio normalization, GPR-files were processed using the BioConductor R-packages limma and marray (http://www.bioconductor.org).
|
| |
|
| Submission date |
Jun 01, 2020 |
| Last update date |
Oct 16, 2020 |
| Contact name |
Tino Polen |
| E-mail(s) |
t.polen@fz-juelich.de
|
| Organization name |
Forschungszentrum Jülich GmbH
|
| Department |
IBG-1: Biotechnology
|
| Street address |
Leo Brandt Str.
|
| City |
Juelich |
| State/province |
NRW |
| ZIP/Postal code |
52425 |
| Country |
Germany |
| |
|
| Platform ID |
GPL28615 |
| Series (1) |
| GSE151596 |
Transcriptome analysis of G. oxydans 621H in response to L-arabinose |
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