|
| Status |
Public on Sep 04, 2008 |
| Title |
Xenopus borealis genomic DNA |
| Sample type |
genomic |
| |
|
| Source name |
Xenopus borealis male and female adult blood
|
| Organism |
Xenopus borealis |
| Characteristics |
Adult
|
| Treatment protocol |
Animal was immersed in MS222 and blood was immediately extracted
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Five micrograms of gDNA from each species was fragmented with Dpn I at 37°C for 3 hours. Fragmented gDNA was purified with Qiagen PCR clean-up kit and the fragment distribution was checked on Agilent Bioanalyzer (Agilent) using the DNA 1000 assay.
|
| Label |
biotin
|
| Label protocol |
50-100 nanograms of fragmented gDNA were then amplified using the BioPrime Labeling System (Invitrogen) following the manufacturers instructions.
|
| |
|
| Hybridization protocol |
After completion of the Klenow Pol I catalyzed reaction, the distribution of PCR products was examined on Agilent Bioanalyzer with the DNA 1000 kit. The entire volume of the product (~50 μl) was used in the hybridization reaction on the Affymetrix Xenopus laevis Gene Chip following manufacturers instructions
|
| Scan protocol |
GeneChip was scanned using the Affymetrix GeneChip Scanner 3000 7G.
|
| Description |
gDNA hybridization intensities for a non-target organism
|
| Data processing |
Normalization was not performed due to the nature of our experiment (because we are using genomic DNA, essentially all probes should hybridize well in target species). The goal was to identify probes that do not hybridize well in non-target species.
|
| |
|
| Submission date |
Sep 03, 2008 |
| Last update date |
Sep 03, 2008 |
| Contact name |
Frederic Chain |
| E-mail(s) |
chainfj@mcmaster.ca
|
| Organization name |
McMaster University
|
| Department |
Biology
|
| Lab |
LSB 324
|
| Street address |
1280 Main Street West
|
| City |
Hamilton |
| State/province |
Ontario |
| ZIP/Postal code |
L8S4K1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL1318 |
| Series (1) |
| GSE12625 |
Expression data for a study on cross-species hybridization on single-species microarrays |
|
