Methods and systems for analysis

A method for processing or analyzing a single cell or nucleus, the method comprising:

• (a) forming a partition, comprising:
• (i) providing (1) an aqueous first liquid comprising a single cell or nucleus, (2) an aqueous second liquid comprising one or more polymeric or gel precursors, and (3) a third liquid that is immiscible with the first liquid and the second liquid;
• (ii) forming a droplet comprising an aqueous two-phase system surrounded by the third liquid, wherein the aqueous first liquid and the aqueous second liquid form an inner phase and an outer phase, respectively, of the aqueous two-phase system;
• (iii) providing a stimulus to the outer phase to generate a gel or polymer shell encapsulating the inner phase comprising the single cell or nucleus to thereby form the partition, wherein the gel or polymer shell is diffusively permeable to one or more reagents;
• and
• (b) introducing the one or more reagents to the inner phase of the partition comprising the single cell or nucleus via diffusion through the gel or polymer shell encapsulating the inner phase comprising the single cell or nucleus.