Systems and methods for barcoding nucleic acids

An article for barcoding nucleic acids, comprising:

• a plurality of at least 10,000 monodisperse microfluidic droplets, at least 90% of the droplets encapsulating a fluid containing hydrogel particles, an oligonucleotide tag in solution, and cell lysate comprising nucleic acids,
• wherein a plurality of the nucleic acids within a droplet are bound to the oligonucleotide tag,
• wherein the oligonucleotide tag within the droplet is distinguishable from oligonucleotide tags within the other droplets of the plurality of 10,000 microfluidic droplets,
• wherein the plurality of droplets contains an average of no more than about 1 particle/droplet,
• wherein each droplet containing a hydrogel particle contains one unique oligonucleotide tag,
• wherein each droplet comprises primers specific to the same unique oligonucleotide tag, which is different from oligonucleotide tags in other droplets,
• wherein the oligonucleotide tag further comprises a random hexanucleotide,
• wherein the random hexanucleotide is located outside a target binding region,
• wherein each droplet ranges from 1 nL to 5 nL in volume,
• wherein each random hexanucleotide is associated with one read;
• wherein the oligonucleotide tag is a single-stranded oligonucleotide.