This disclosure provides methods and devices for the label-free detection of target molecules of interest. The principles of the disclosure are particularly applicable to the detection of biological molecules (e.g., DNA, RNA, and protein) using tandard SiO.sub.2-based microarray technology.

This disclosure provides methods and devices for the label-free detection of target molecules of interest. The principles of the disclosure are particularly applicable to the detection of biological molecules (e.g., DNA, RNA, and protein) using standard SiO.sub.2-based microarray technology.

This disclosure provides methods and devices for the label-free detection of target molecules of interest. The principles of the disclosure are particularly applicable to the detection of biological molecules (e.g., DNA, RNA, and protein) using standard SiO.sub.2-based microarray technology.

An image sensor structure includes an image layer having an array of light detectors disposed therein. A device stack is disposed over the image layer. An array of light guides is disposed in the device stack. Each light guide is associated with a light detector. An array of nanowells is disposed over the device stack. Each nanowell is associated with a first light guide of the array of light guides. A first primer set is disposed throughout a first well region of each nanowell. A second primer set is disposed throughout a second well region of each nanowell. The second well region is adjacent the first well region. The first and second primer sets are operable to attach a forward strand cluster of forward polynucleotide strands in the first well region and a reverse strand cluster of reverse polynucleotide strands in the second well region.

An image sensor structure includes an image layer having an array of light detectors disposed therein. A device stack is disposed over the image layer. An array of light guides is disposed in the device stack. Each light guide is associated with a light detector. An array of nanowells is disposed over the device stack. Each nanowell is associated with a first light guide of the array of light guides. A first primer set is disposed throughout a first well region of each nanowell. A second primer set is disposed throughout a second well region of each nanowell. The second well region is adjacent the first well region. The first and second primer sets are operable to attach a forward strand cluster of forward polynucleotide strands in the first well region and a reverse strand cluster of reverse polynucleotide strands in the second well region.

Disclosed herein include systems, methods, compositions, and kits for methods of assigning sequencing data to partitions. There are provided, in some embodiments, methods of associating sequencing data and phenotypic data of single cells. There are provided, in some embodiments, methods of reducing noise in sequencing data. Disclosed herein include partition indexing oligonucleotides comprising a partition indexing sequence. The partition indexing oligonucleotides can be associated with partitions. Partition indexing oligonucleotides situated within the same partition can comprise the same partition indexing sequence. Partition indexing oligonucleotides situated within different partitions comprise different partition indexing sequences.

Disclosed herein include systems, methods, compositions, and kits for methods of assigning sequencing data to partitions. There are provided, in some embodiments, methods of associating sequencing data and phenotypic data of single cells. There are provided, in some embodiments, methods of reducing noise in sequencing data. Disclosed herein include partition indexing oligonucleotides comprising a partition indexing sequence. The partition indexing oligonucleotides can be associated with partitions. Partition indexing oligonucleotides situated within the same partition can comprise the same partition indexing sequence. Partition indexing oligonucleotides situated within different partitions comprise different partition indexing sequences.

A method for determining a presence or absence of one or more target analytes in a sample includes contacting the sample with an array of particles comprising at least first and second particle subsets disposed therein with a known particle number ratio with respect to each other. The first particle subset has at least one binding site configured to bind with a first target analyte and the second particle subset has at least one binding site configured to bind with a second, different target analyte. Changes are detected in a detectable signal emitted by the particles after contacting the sample with the array. A number of the particles that emit the change in the detectable signal are counted and this number is compared to the known particle number ratio of the subsets so as to determine the presence or absence of the one or more of the target analytes.

A method for determining a presence or absence of one or more target analytes in a sample includes contacting the sample with an array of particles comprising at least first and second particle subsets disposed therein with a known particle number ratio with respect to each other. The first particle subset has at least one binding site configured to bind with a first target analyte and the second particle subset has at least one binding site configured to bind with a second, different target analyte. Changes are detected in a detectable signal emitted by the particles after contacting the sample with the array. A number of the particles that emit the change in the detectable signal are counted and this number is compared to the known particle number ratio of the subsets so as to determine the presence or absence of the one or more of the target analytes.

An integrated end-to-end system for large-scale, high-quality nucleic acid sequencing having a nucleic acid extraction module, a library preparation module, a nucleic acid sequencing module, and a data analysis module reversibly integrated with one another and having components that are physically loosely-coupled within such system and reversibly integrated for sequence interrogation and analysis. This system is fully automated from sample to data output. A workflow management system is integrated across all system components and provides an intuitive user interface for managing system operations.