Oligonucleotide encoded chemical libraries

A method for identifying a transcriptome change in a cell induced by compound, wherein said compound is included in an assay of a combinatorial chemical library, the method comprising:

• a) generating an assay array wherein said array comprises:
• i) a plurality of confined volumes wherein each confined volume is separated from the other confined volumes and wherein each confined volume comprises a cell of interest;
• ii) a plurality of beads where each bead comprises a plurality of substantially the same compound such that each bead comprises a unique compound from said combinatorial library and each compound in said library is selected as a potential drug candidate;
• and a plurality of functionalized oligonucleotides, wherein said functionalized oligonucleotide comprises an oligonucleotide portion that encodes the structure of the unique compound or the synthetic steps used to make said unique compound and a RNA capturing element, wherein a single bead is disposed in each confined volume;
• b) contacting the cell in each confined volume with the compound released into the confined volume from the bead and maintaining said contact for a period sufficient to generate a transcriptome change in the RNA expressed by the cell in response to said contacting;
• c) capturing RNA from the cell in each confined volume by lysing the cell and contacting the RNA with the RNA capturing element on said bead;
• d) identifying the captured RNA from at least a portion of the plurality of beads and assessing any transcriptome change in said captured RNA;
• and
• e) identifying the structure of each of the compound that generated the transcriptome change.