A method of generating a nucleic acid signature for identifying particles associated in a partition, the method comprising: (a) partitioning a sample into a plurality of partitions having 0, 1, or more than 1 particle(s) per partition, wherein the particle(s) comprises/comprise a solid support surface, the solid support surface having a plurality of oligonucleotide primers conjugated thereon, wherein the oligonucleotide primers comprise a particle barcode sequence, wherein at least a majority of the plurality of oligonucleotide primers conjugated to a solid support surface comprise the same barcode sequence, and wherein at least some partitions have two or more particles comprising at least a first particle conjugated to oligonucleotide primers comprising a first barcode sequence and a second particle conjugated to oligonucleotide primers comprising a second barcode sequence; (b) providing, to the at least some partitions of step (a) having two or more particles, a plurality of substrates comprising a barcode sequence or repeating clonal barcode sequences, wherein the plurality of substrates comprise distinguishable barcode sequences, and wherein the barcode sequence or repeating clonal barcode sequences of the substrates comprises/comprise a region of nucleotide sequence that is a unique identifier sequence for the barcode sequence(s) from each substrate and distinct from the barcodes of the oligonucleotide primers conjugated to the particles; and (c) generating, in the at least some partitions of step (b) having two or more of the particles, a nucleic acid signature unique to the particles in that partition by associating the barcode sequences from each substrate to the oligonucleotide primers conjugated to the two or more particles; thereby generating a nucleic acid signature for the particles that are in the at least some partitions. (a) partitioning a sample into a plurality of partitions having 0, 1, or more than 1 particle(s) per partition, wherein the particle(s) comprises/comprise a solid support surface, the solid support surface having a plurality of oligonucleotide primers conjugated thereon, wherein the oligonucleotide primers comprise a particle barcode sequence, wherein at least a majority of the plurality of oligonucleotide primers conjugated to a solid support surface comprise the same barcode sequence, and wherein at least some partitions have two or more particles comprising at least a first particle conjugated to oligonucleotide primers comprising a first barcode sequence and a second particle conjugated to oligonucleotide primers comprising a second barcode sequence; (b) providing, to the at least some partitions of step (a) having two or more particles, a plurality of substrates comprising a barcode sequence or repeating clonal barcode sequences, wherein the plurality of substrates comprise distinguishable barcode sequences, and wherein the barcode sequence or repeating clonal barcode sequences of the substrates comprises/comprise a region of nucleotide sequence that is a unique identifier sequence for the barcode sequence(s) from each substrate and distinct from the barcodes of the oligonucleotide primers conjugated to the particles; and (c) generating, in the at least some partitions of step (b) having two or more of the particles, a nucleic acid signature unique to the particles in that partition by associating the barcode sequences from each substrate to the oligonucleotide primers conjugated to the two or more particles;