Methods for encapsulating and assaying cells

A microfluidic device comprising:

• an enclosure comprising a channel and a plurality of chambers,
• wherein each chamber of the plurality of chambers has a chamber opening fluidically connecting the chamber to the channel,
• wherein each chamber of the plurality of chambers is formed by a plurality of surfaces having a total surface area, with a first portion of the total surface area of each chamber comprising a hydrophobic coating and a second portion of the total surface area of each chamber comprising a hydrophilic coating, and
• wherein the first portion of the total surface area of each chamber is located proximal to a boundary between the chamber opening and the channel.

A microfluidic device comprising:

• an enclosure comprising a channel and a plurality of sequestration pens,
• wherein each sequestration pen of the plurality of sequestration pens has an opening fluidically connecting the sequestration pen to the channel,
• wherein each sequestration pen of the plurality of sequestration pens is formed by a plurality of surfaces having a total surface area, with a first portion of the total surface area of each chamber comprising a hydrophobic coating, and a second portion of the total surface area of each chamber comprising a hydrophilic coating,
• wherein the first portion of the total surface area of each sequestration pen of the plurality of sequestration pens is located proximal to a boundary between the sequestration pen opening and the channel, and
• wherein each sequestration pen of the plurality of sequestration pens includes an isolation region and a connection region fluidically connecting the isolation region to the channel, wherein the hydrophobic coating is formed into part of the connection region.