A method of analyzing the nucleic acid of a plurality of cells comprising: forming a plurality of partitions, wherein each partition comprises: (i) a particle comprising a population of oligonucleotides having 5' to 3': a cleavage region, a barcode unique for that particle and a hairpin region, wherein the oligonucleotides comprise a 5' end that is linked to the particle and a 3' end that is available for extension by a polymerase, wherein the cleavage region comprises a uracil, an endonuclease recognition site, an acid or base labile bond, a disulfide linker, or a 5' thiol modified uracil, wherein the hairpin region includes a uracil, and wherein the particle is a hydrogel; (ii) a sample comprising a single cell comprising a target nucleic acid; and (iii) a reagent that cleaves the oligonucleotides conjugated to the plurality of particles from the particles at the cleavage region; lysing the cell in the partitions; extending the 3' end of the oligonucleotides with a polymerase using a portion of the oligonucleotide as a template; performing uracil excision to cleave the oligonucleotides at the hairpin; ligating the extended 3' end of the oligonucleotides and the 5' end of the oligonucleotides released from particles to at least a portion of the target nucleic acids in each partition, thereby covalently attaching oligonucleotides to at least a portion of the target nucleic acids in each partition; and then combining the partitions; and performing high throughput sequencing of target nucleic acids comprising the attached oligonucleotides. forming a plurality of partitions, wherein each partition comprises: (i) a particle comprising a population of oligonucleotides having 5' to 3': a cleavage region, a barcode unique for that particle and a hairpin region, wherein the oligonucleotides comprise a 5' end that is linked to the particle and a 3' end that is available for extension by a polymerase, wherein the cleavage region comprises a uracil, an endonuclease recognition site, an acid or base labile bond, a disulfide linker, or a 5' thiol modified uracil, wherein the hairpin region includes a uracil, and wherein the particle is a hydrogel; (ii) a sample comprising a single cell comprising a target nucleic acid; and (iii) a reagent that cleaves the oligonucleotides conjugated to the plurality of particles from the particles at the cleavage region; (i) a particle comprising a population of oligonucleotides having 5' to 3': a cleavage region, a barcode unique for that particle and a hairpin region, wherein the oligonucleotides comprise a 5' end that is linked to the particle and a 3' end that is available for extension by a polymerase, wherein the cleavage region comprises a uracil, an endonuclease recognition site, an acid or base labile bond, a disulfide linker, or a 5' thiol modified uracil, wherein the hairpin region includes a uracil, and wherein the particle is a hydrogel; a cleavage region, a barcode unique for that particle and a hairpin region, wherein the oligonucleotides comprise a 5' end that is linked to the particle and a 3' end that is available for extension by a polymerase, wherein the cleavage region comprises a uracil, an endonuclease recognition site, an acid or base labile bond, a disulfide linker, or a 5' thiol modified uracil, wherein the hairpin region includes a uracil, and wherein the particle is a hydrogel; (ii) a sample comprising a single cell comprising a target nucleic acid; and (iii) a reagent that cleaves the oligonucleotides conjugated to the plurality of particles from the particles at the cleavage region; lysing the cell in the partitions; extending the 3' end of the oligonucleotides with a polymerase using a portion of the oligonucleotide as a template; performing uracil excision to cleave the oligonucleotides at the hairpin; ligating the extended 3' end of the oligonucleotides and the 5' end of the oligonucleotides released from particles to at least a portion of the target nucleic acids in each partition, thereby covalently attaching oligonucleotides to at least a portion of the target nucleic acids in each partition; and then combining the partitions; and performing high throughput sequencing of target nucleic acids comprising the attached oligonucleotides.