|
| Status |
Public on Nov 18, 2013 |
| Title |
PD1222 in Cu-L replicate 3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
PD1222 in Cu-L media replicate 3
|
| Organism |
Paracoccus denitrificans PD1222 |
| Characteristics |
genotype: Wild type
|
| Treatment protocol |
The cells were treated with cold ethanol 20%, phenol 1% and left 30min on ice prior centrifugation.
|
| Growth protocol |
The media was inoculated with 1/1000 of over night culture and grown to OD600=0.4 at 30 C without agitation.
|
| 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: Wild type
|
| Treatment protocol |
The cells were treated with cold ethanol 20%, phenol 1% and left 30min on ice prior centrifugation.
|
| Growth protocol |
The media was inoculated with 1/1000 of over night culture and grown to OD600=0.4 at 30 C without agitation.
|
| Extracted molecule |
total RNA |
| 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
|
| 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 |
Jul 08, 2013 |
| Last update date |
Nov 18, 2013 |
| Contact name |
Matthew John Sullivan |
| E-mail(s) |
matthew.sullivan@uea.ac.uk
|
| Organization name |
University of East Anglia
|
| Department |
School of Biological Sciences
|
| Lab |
2.30
|
| Street address |
Earlham Road
|
| City |
Norwich |
| State/province |
Norfolk |
| ZIP/Postal code |
NR4 7TJ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17412 |
| Series (1) |
| GSE48577 |
Transcriptome analysis of Paracoccus denitrificans during Cu-limitation |
|
