Abstract: This invention relates to methods for capturing and encoding nucleic acid from a plurality of single cells. A plurality of solid supports is randomly placed into a plurality of compartments, such that the average number of solid supports per compartment, ?1, is less than 1, wherein each solid support carries (a) a unique identification sequence and (b) a capture moiety. A plurality of single cells is randomly placing into the plurality of compartments, such that the average number of cells per compartment, ?2, is less than 1. These random placement steps may be performed in any order. Nucleic acid is then released from each single cell and captured via the capture moiety, such that nucleic acid from each single cell is tagged with a unique identification sequence.

Abstract: Provided herein are systems and methods for pooling samples from separated sub-arrays in multi-well devices into collection wells of a multi-well sample collection device (e.g., allowing samples in a 100 well sub-array in a 9600-well chip to be pooled into a single collection well of a 96-well plate). In certain embodiments, the systems are composed of: i) a multi-well device, ii) an extraction device; and iii) an extraction device gasket. Also provided herein are dual barcoding (e.g., X-Y barcoding), pooling (e.g., dual pooling), RNA amplification methods (e.g., for single cell analysis), that may employ the extraction devices described herein.