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.