Figure 1.
The generation of DNA templates from microarrays and parallel analysis.
A ssDNA microarray was incubated with a primer (16 h) followed by elongation using Taq polymerase (16 h) producing as dsDNA microarray. The newly synthesized DNA strands were used as templates for solution phase PCR carried out over the microarray leading to amplification of the ssDNA displayed on the microarray. The dsDNA was amplified by PCR to produce fluorescently labeled ssDNA analogous to the ssDNA printed on the microarray. The fluorescently labeled ssDNA was hybridized to a complementary microarray or submitted to Solexa sequencing to allow decoding of the amplified ssDNA. FAM = 5(6)-carboxyfluorescein.
Table 1.
General sequences of microarray supported oligonucleotides and primer sequences.
Table 2.
Number of replicates of oligonucleotides on the scaled content 3,875-oligonucleotide microarray.
Figure 2.
(a) PCR products from the 1, 10, 3,875, 10,000 oligonucleotide microarrays. (b) Products from 5 repeats of PCR from the 10,000 oligonucleotide array. (c) dsDNA-10,000 and dsDNA-3875 (left) and their EcoICRI digestion (right). (d) PCR amplification with two primers producing dsDNA-10,000-FAM and dsDNA-3,875-FAM and dsDNA-10-FAM (left) and asymmetric PCR with a single primer producing ssDNA-10,000-FAM and ssDNA-3,875-FAM (right).
Figure 3.
The background corrected average intensities plotted versus the number of replicates.
(a) The dsDNA-10-FAM library. (b) The ssDNA-3,875-FAM library. (c) The ssDNA-10,000-FAM library. Error bars indicate ± s.d.
Table 3.
Oligonucleotide sequences not seen by Solexa sequencing and their background-corrected average microarray intensities.
Figure 4.
The number of times each oligonucleotide was seen by Solexa sequencing plotted versus the oligonucleotide sequences.
36-bp reads of the Solexa primer of the dsDNA-10,000 oligo-pool generated by “read-off” the 10,000 oligonucleotide microarray.