Flow cells with passivation components

A flow cell, comprising:

• a substrate including depressions separated by interstitial regions;
• a polymeric hydrogel positioned within each of the depressions;
• a primer set attached to the polymeric hydrogel;
• and
• one of:
• a passivation component attached to the interstitial regions, a passivation component the polymeric hydrogel, or respective passivation components attached to each of the interstitial regions and the polymeric hydrogel, wherein:
• the passivation component is exclusively attached to the interstitial regions and includes i) a silane, siloxane, or alkoxy silane small molecule with an alkoxy, hydroxyl, carboxylic acid, or perfluorinated end group, or ii) a first linker selected from the group consisting of alkylene, poly(ethylene glycol), poly(meth)acrylic acid, polyacrylamide, poly(2-hydroxyl ethyl (meth)acrylate), and poly(2-hydroxypropyl (meth)acrylamide) and a first end group selected from the group consisting of phosphate, phosphonate, a zwitterionic end group and an amphoteric polymer end group;
• or
• the passivation component is exclusively attached to the polymeric hydrogel and includes i) a second linker selected from the group consisting of alkylene, poly(ethylene glycol), poly(meth)acrylate, polyacrylamide, pentaerythritol, and combinations thereof, and a second end group selected from the group consisting of a poly(ethylene glycol) end group when the linker is poly(meth)acrylate, polyacrylamide, pentaerythritol, and combinations thereof, a zwitterionic end group, a hydroxyl end group, a carboxylic acid end group, a sulfonic acid end group, a positively chargeable end group, an alkoxy end group, an anionic polymer end group, and an amphoteric polymer end group, or ii) a dibenzocyclooctyne-functionalized passivation agent;
• or
• the respective passivation components are attached to each of the interstitial regions and to the polymeric hydrogel, the respective passivation component attached to the interstitial regions includes i) a silane, siloxane, or alkoxy silane small molecule with an alkoxy, hydroxyl, carboxylic acid, or perfluorinated end group, or ii) a third linker selected from the group consisting of alkylene, poly(ethylene glycol), poly(meth)acrylic acid, polyacrylamide, poly(2-hydroxyl ethyl (meth)acrylate), and poly(2-hydroxypropyl (meth)acrylamide) and a third end group selected from the group consisting of a zwitterionic end group and an amphoteric polymer end group, and the respective passivation component attached to the polymeric hydrogel includes i) a fourth linker selected from the group consisting of alkylene, poly(ethylene glycol), poly(meth)acrylate, polyacrylamide, and pentaerythritol, and combinations thereof, and a fourth end group selected from the group consisting of a poly(ethylene glycol) end group when the linker is poly(meth)acrylate, polyacrylamide, or pentaerythritol, a zwitterionic end group, a hydroxyl end group, a carboxylic acid end group, a sulfonic acid end group, a positively chargeable end group, an alkoxy end group, an anionic polymer end group, and an amphoteric polymer end group, or ii) a dibenzocyclooctyne-functionalized passivation agent.