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It's depth that can be used for photographic effects," says Federighi when I ask about other uses for the array.
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These experiments included an additional cell line from a Golden Retriever hemangiosarcoma (Emma) that was recently developed and therefore not used for the array experiments, but allowed us to validate gene set enrichment in an independent sample.
From the same original total RNAs used for the array experiments, cDNA was generated from 1 µg RNA using SuperScript II reverse transcriptase (Invitrogen).
Twenty of them, 12 male and 8 female, were used for the array screening assays and the rest for the real time quantitative PCR validation.
Array-CGH has the potential to analyze alterations of DNA copy number on a genome-wide scale with relatively high resolution, depending on whether BACs, PCR products or oligonucleotides are used for the array elements.
The more robust and sustained decrease in N-myc levels in these cells versus those used for the array may explain the somewhat more pronounced reductions in expression of klf2, klf4, lif, and lin28b.
The same RNA samples used for the array analysis were also used for the qRT-PCR.
Arrays were hybridized with fluorescently labeled targets from all genotypes used for the array development.
JL carried out the animal experimentation and isolated the RNA used for the array work.
More details of the method used for the array CGH analysis are described in Data S1.
Affymetrix Yeast Genome 2.0 GeneChips were used for the array hybridizations with duplicate biological RNA samples.
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