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Sample GSM317610 Query DataSets for GSM317610
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
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

Supplementary file Size Download File type/resource
GSM317610.CEL.gz 3.0 Mb (ftp)(http) CEL
GSM317610.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data not applicable for this record

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