|
| Status |
Public on Jan 19, 2007 |
| Title |
Terephthalate 3rdTPAcy5Pycy3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
experiment
|
| Organism |
Rhodococcus jostii RHA1 |
| Characteristics |
experiment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation involved vortexing with glass beads, hot phenol plus SDS, precipitation of debris with acetate, phenol plus chloroform, precipitation of nucleic acids with acetate plus isopropanol, DNase treatment and purification with an RNeasy mini column (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
Cy5 labeled cDNA were prepared by indirect labeling.
|
| |
|
| Channel 2 |
| Source name |
control
|
| Organism |
Rhodococcus jostii RHA1 |
| Characteristics |
control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation involved vortexing with glass beads, hot phenol plus SDS, precipitation of debris with acetate, phenol plus chloroform, precipitation of nucleic acids with acetate plus isopropanol, DNase treatment and purification with an RNeasy mini column (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Cy3 labeled cDNA were prepared by indirect labeling.
|
| |
|
| |
| Hybridization protocol |
The microarray slides were pre-hybridized using 5x SSC containing 0.1% SDS and 0.2% BSA for 45 minutes at 48oC and used immediately for hybridization in a GeneTac HybStation (Genomic Solution). The hybridization was carried out at 42oC for 18 hours with mixing using 120 μL per slide of SlideHyb#1 hybridization solution (Ambion). The post hybridization washing consisted of 3 cycles of 20 second incubations with each of the following solutions: 2x SSC plus 0.1% SDS (medium stringency) at 42oC; 0.1x SSC plus 0.05% SDS (high stringency) at 25oC; and 0.1x SSC (low stringency) at 25oC.
|
| Scan protocol |
The slides scanned with a GenePix 4000B scanner (Axon Instruments). The spot intensities were quantified using Imagene 5.6 (BioDiscovery, Inc.).
|
| Description |
To correct for non-specific (background) signal for each channel (each dye), the mean signal of 10% of the probes in each sub grid with the lowest intensity was subtracted from that of all probes in the corresponding sub grid.
|
| Data processing |
Expression ratios were normalized using the LOWESS method. Average normalized expression ratios (treatment/control) were calculated for each gene and tested for significant variation between treatments (ANOVA p < 0.05).
|
| |
|
| Submission date |
Jan 09, 2007 |
| Last update date |
Jan 18, 2007 |
| Contact name |
Hirofumi Hara |
| E-mail(s) |
hara2950@mac.com
|
| Organization name |
University of British Columbia
|
| Department |
Microbilogy and Immunology
|
| Lab |
Mohn
|
| Street address |
2350 Health Science Mall
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V6T1Z3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL3918 |
| Series (2) |
| GSE6684 |
Effects of terephthalate on Rhodococcus sp. RHA1 |
| GSE6685 |
Effect of phthalate and terephthalate on Rhodococcus sp. RHA1 |
|
