Originally posted by horigen
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In the same paper, an alternative DNA preparation was also reported. It turned out to be much more suitable for Solexa, and bypassed the extra ligation step. Basically, the libraries were prepared according to the Solexa kit protocol prior to hybridization and the fragment sizes were much shorter (150-300), a much more suitable size for short read platforms. This resulted in 90% base pair coverage and a pretty high sequencing depth for such a large target size (6 Mb of one exon chip).
Most importantly, it is imperative to have the DNA fragments ligated to common oligo adaptors before hybridization. The reason for this is that thermal elution of the slides at 95 degrees, may result in oligo detachment. Therefore, having the DNA ligated with common oligos allows enrichment of the genomic DNA and avoids sequencing of oligos and non-specific material.
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