Oligonucleotide encoded chemical libraries

The method of claim 1, wherein the RNA is contacted with the second functionalized oligonucleotide, and the method further comprises:

• causing a poly-A tail located 3′ with respect to the capture sequence to hybridize to a poly-T region of a different second functionalized oligonucleotide, wherein the second functionalized oligonucleotide encodes a structure of the captured RNA.

The method of claim 2, wherein second functionalized oligonucleotides each comprise a unique molecular identifier (UMI) distinct from UMIs of other second functionalized oligonucleotides, and the method further comprises:

• quantifying RNA that has been captured based on a number of UMIs bound to RNA.

The method of claim 2, wherein the second functionalized oligonucleotide is hybridized to the RNA from the at least one cell, and the method further comprises:

• causing the different second functionalized oligonucleotide to hybridize to the poly-A tail.

The method of claim 1, wherein the compound is selected as a drug candidate from a combinatorial library.

The method of claim 1, wherein the capturing of the RNA comprises contacting a membrane of the at least one cell to the capture sequence.

The method of claim 1, further comprising:

• causing a first end of a first functionalized oligonucleotide to hybridize to a second end of the second functionalized oligonucleotide, wherein the first end is located 3′ with respect to the capture sequence and the second end comprises a 5′ end of the second functionalized oligonucleotide.

The method of claim 1, wherein the first functionalized oligonucleotides encode a date that the compound was synthesized, a disease that the compound is intended to treat, or a cellular event that the compound is intended to stimulate or inhibit.

The method of claim 1, further comprising maintaining said contact for a period sufficient to generate a transcriptome change in the RNA expressed by the at least one cell in response to said contacting.

The method of claim 1, further comprising applying the second functionalized oligonucleotide to the at least one cell while lysing the at least one cell.

The assay device of claim 12, further comprising second functionalized oligonucleotides, wherein the second functionalized oligonucleotides each comprise a unique molecular identifier (UMI) distinct from UMIs of other second functionalized oligonucleotides, wherein RNA that has been captured is quantified based on a number of UMIs bound to RNA.

The assay device of claim 12, wherein the second functionalized oligonucleotide is hybridized to the RNA from the at least one cell, and the second functionalized oligonucleotide and the different second functionalized oligonucleotide are within a same confined volume and comprise a common promoter region to indicate that the compound was contacted with the at least one cell.

The assay device of claim 12, wherein the second functionalized oligonucleotide and the different second functionalized oligonucleotide each comprise a sequence that is identical, wherein the sequence is different from other sequences belonging to other second functionalized oligonucleotides in different confined volumes.

The assay device of claim 11, wherein the compound is selected as a drug candidate from a combinatorial library.

The assay device of claim 11, wherein the capture sequence contacts a membrane of the at least one cell.

The assay device of claim 11, wherein a first functionalized oligonucleotide of the first functionalized oligonucleotides hybridizes to a second end of the second functionalized oligonucleotide, wherein the first end is located 3′ with respect to the capture sequence and the second end comprises a 5′ end of the second functionalized oligonucleotide.

The assay device of claim 11, wherein the first functionalized oligonucleotides encode a date that the compound was synthesized, a disease that the compound is intended to treat, or a cellular event that the compound is intended to stimulate or inhibit.

The assay device of claim 11, further comprising the second functionalized oligonucleotide which contacts the at least one cell, and wherein the at least one cell is lysed.