Decoding process. (A) The sequential hybridization process is illustrated for a single bead, of bead type 2. In stage 1, a complementary decoder hybridizes to the oligonucleotide probe that is attached to the bead (for details of the procedure, see Methods). The decoder is labeled with a fluorophore (green in stage 1, red in stage 2, and green in stage 3). The fluorescent signal is read by imaging the entire array. The array is then dehybridized, and the process is repeated for two more stages. (B) A scanning electron micrograph of an array of beads, artificially colored to represent three sequential hybridization stages. The images, taken collectively, reveal a combinatorial code for each bead. Note that the bead circled in yellow has the color signature GRG or code 010. (C) Colors, or states, are assigned to individual decoder sequences in each stage to produce a unique combination across stages. This signature, or code, identifies each bead type. As indicated in the parity code column, an extra decoding stage (data not shown) can be performed to provide an error checking parity bit. After three stages of decoding, all the beads are uniquely identified by their color.
