Apparatus and system for nucleic acid detection

An apparatus comprising:

• a holder configured to accept a sample container, wherein the sample container comprises a plurality of cells;
• a temperature controller configured to maintain the sample container at a selected temperature;
• one or more fluid reservoirs that are fluidly connected to the sample container;
• a fluid handling element fluidly connected to the sample container and configured to add fluid to and/or remove fluid from the sample container;
• a mixing element configured to mix contents of the sample container;
• and
• a detector for detecting one or more signals from within individual cells of the plurality of cells in the sample container.

A system comprising:

• a sample container comprising a plurality of cells, wherein the cells comprise or are suspected of comprising two or more nucleic acid targets, and wherein the nucleic acid targets are immobilized in the sample container;
• reagents for detecting nucleic acid targets in the sample container, wherein the reagents comprise:
• (i) a label probe system for each nucleic acid target, wherein each label probe system comprises two or more identical label probe complexes, each of which comprises a nucleic acid component and one or more labels, wherein the labels of the label probe systems are distinct for each target nucleic acid;
• and
• (ii) a capture probe system for each nucleic acid target, wherein the capture probe system comprises two or more sets of capture probes, wherein each set of capture probes comprises two or more different capture probes, wherein all capture probes in the capture probe system comprise a T section and an L section, wherein the T section is a nucleic acid sequence complementary to a section on the nucleic acid target and the L section is a nucleic acid sequence complementary to a section on the nucleic acid component of the label probe complex, and wherein the T sections of the two or more different capture probes are complementary to non-overlapping regions of the nucleic acid target, and the L sections of the two or more different capture probes are complementary to nonoverlapping regions of the nucleic acid component of the label probe complex;
• a fluid handling system to add the reagents to the sample container, to hybridize the capture probe system to the two or more nucleic acid targets, and to capture the label probe system to the capture probe system hybridized to the two or more nucleic acid targets;
• and
• a temperature control module coupled to the sample container.