System and method for single cell genetic analysis

A method for parallel analysis of a single cells' nucleic acid, the method comprising:

• (a) receiving into a cell reservoir a liquid medium containing a suspension of cells to be analyzed;
• (b) inducing said liquid medium to flow from said cell reservoir through a cell cage array with a plurality of cell cages, to thereby cause cells to enter each into a cell cage of said cell cage array;
• (c) associating said cell cage array with a microarray comprising a plurality of DNA spots, wherein each DNA spot comprises a probe and a nucleic acid identifier sequence unique for said DNA spot, such that each of the DNA spots is exposed to one of the cell cages;
• (d) introducing a buffer and inducing conditions for cell lysis and nucleic acid synthesis and amplification, to produce amplified nucleic acid molecules in the cells;
• and
• (e) sequencing the amplified nucleic acid molecules, and determining the nature of the amplified and sequenced nucleic acid molecules according to the nucleic acid identifier sequence.

A system comprising:

• i. a microarray comprising a plurality of DNA spots, wherein each DNA spot comprises a probe and a nucleic acid identifier sequence unique for said DNA spot;
• and
• ii. an apparatus configured to isolate cells from a liquid medium, comprising:
• (a) a cell reservoir configured for receiving a liquid medium containing a suspension of cells;
• (b) a cell cage array, wherein each cell cage has a large opening for receiving cells from the reservoir, a small opening;
• (c) a liquid medium pump configured to move said suspended cells into cell cages by flowing said liquid medium from said cell reservoir through said cell cage array;
• and
• (d) a mechanical element which when actuated, pushes said cell cage array against said microarray, thereby isolating each cell in each of said cell cages.