|
| Status |
Public on Jun 30, 2017 |
| Title |
PD1222 in Aerobic continuous culture (CSTR) replicate 1 |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
PD1222 in Aerobic continuous culture (CSTR)
|
| Organism |
Paracoccus denitrificans PD1222 |
| Characteristics |
genotype/variation: Wild type
culture condition: Aerobic continuous culture (CSTR)
|
| Treatment protocol |
The cells were treated with cold ethanol 20%, phenol 1% and left 30min on ice prior centrifugation.
|
| Growth protocol |
P. denitrifican was grown in minimal medium, containing 20mM NO3-, in continuous culture reactiors (continuous culture (CSTR)) with (aerobic) and without (anaerobic) air supply for aprox 120 hours. At 120 hours, samples were take for transcriptional analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Promega SV total RNA extration kit following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
Total RNA (10 μg) was converted to cDNA and fluorescently labelled by random priming to incorporate Cy5-dCTP (Amersham) using reverse transcriptase (AffinityScript, Stratagene).
|
| |
|
| Channel 2 |
| Source name |
Wild Type in LB
|
| Organism |
Paracoccus denitrificans PD1222 |
| Characteristics |
genotype/variation: Wild type
sample type: chromosomal DNA reference
|
| Treatment protocol |
The cells were treated with cold ethanol 20%, phenol 1% and left 30min on ice prior centrifugation.
|
| Growth protocol |
P. denitrifican was grown in minimal medium, containing 20mM NO3-, in continuous culture reactiors (continuous culture (CSTR)) with (aerobic) and without (anaerobic) air supply for aprox 120 hours. At 120 hours, samples were take for transcriptional analysis.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total RNA extracted using Promega SV total RNA extration kit following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Total RNA (10 μg) was converted to cDNA and fluorescently labelled by random priming to incorporate Cy5-dCTP (Amersham) using reverse transcriptase (AffinityScript, Stratagene).
|
| |
|
| |
| Hybridization protocol |
CyDye-labelled DNA samples were mixed with hybridisation buffer (Morpholine-4-ethanesulfonic acid (MES) hydrate (pH 6.5) 50 mM, Sodium chloride 1 M, 99% Formamide 20% (w/v), EDTA 20 mM, Triton X-100 1% (w/v)) and applied to microarray slides in a tight chamber at 55°C for 60 hours at 8 rpm
|
| Scan protocol |
Scanned on an GenePix 4000B scanner (Axon Instruments, Inc.).Images were quantified using Axon GenePix Pro7
|
| Description |
Aerobic_30
|
| Data processing |
BABAR R-package was used in R v2.9.2 (Alston et al 2010, BMC Bioinformatics 11:73) was used for background subtraction and LOWESS normalization.
|
| |
|
| Submission date |
Apr 19, 2017 |
| Last update date |
Jun 30, 2017 |
| Contact name |
Georgios Giannopoulos |
| E-mail(s) |
george.z.giannopoulos@gmail.com
|
| Organization name |
Virginia Commonwealth University
|
| Department |
Biology
|
| Lab |
Microbial Ecology
|
| Street address |
1000 W Cary st
|
| City |
Richmond |
| State/province |
Virginia |
| ZIP/Postal code |
23284 |
| Country |
USA |
| |
|
| Platform ID |
GPL17412 |
| Series (1) |
| GSE97959 |
Transcriptome analysis of Paracoccus denitrificans during aerobic and anaerobic respiration (denitrification) |
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