Single Cell Mapping and Transcriptome Analysis

A method of measuring one or more parameters of interest in individual cells of a sample comprising a multicellular structure and of mapping the one or more measured parameters to the position of the individual cells in the sample, comprising the steps of

• obtaining a sample comprising a multicellular structure;
• labeling individual cells in the sample with one or more identifiers comprising structurally and/or chemically unique constructs in a spatially defined manner, wherein each identifier is associated with a discrete physical position within the sample;
• dissociating the cells of the sample into individual cells and performing a single cell analysis wherein, for each individual cell, the one or more identifiers applied to the individual cell is determined and the one or more selected cellular parameters is measured;
• and
• by the association between physical position within the sample and the structurally and/or chemically unique constructs present on the individual cells, generating a map of the one or more measured parameters across the sample.

A system for labeling cells in a multicellular structure with oligonucleotide constructs comprising unique identifiers, wherein each identifier is associated with a specific site in the sample, the system comprising

• a sample substrate upon which the sample is placed;
• a microscopy system for imaging the sample;
• a microfluidic chamber encasing the sample, wherein the microfluidic chamber is in connection with a plurality of reservoirs, wherein a first reservoir will contain a buffer solution for washing steps;
• a second reservoir will comprise a solution comprising a foundation construct;
• and a plurality of additional reservoirs wherein each contains a solution comprising a unique coding segment;
• and pumping means and suitable control systems for selectively introducing each of the solutions to the microfluidic chamber, and pumping solutions out of the chamber to a waste collection vessel;
• an illumination system for selectively delivering light energy to selected sites in the sample, the light being of sufficient energy to cleave photolabile protection groups;
• an X-Y staging system that enables movement of the sample within the field of view of the microscope, and which allows for selective illumination at precisely defined points by the illumination source;
• and
• computer control elements for coordinating the activity of the components.

A kit comprising

• a foundation construct for synthesis of oligonucleotide constructs on the surface of a cell, the foundation construct comprising
• an anchoring moiety that has affinity for the cell surface;
• and
• an oligonucleotide comprising an overhang, wherein the overhang is protected by photolabile protection groups that prevent its hybridization with complementary sequences;
• and
• a plurality of coding segments for incorporation into a oligonucleotide construct comprising a unique identifier.