The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

The present disclosure relates to determining the location of analytes in fixed biological samples.

The present disclosure relates to determining the location of analytes in fixed biological samples.

Provided herein are methods, compositions, and kits for multiplex spatial detection of analytes in a biological sample.

Provided herein are methods, compositions, and kits for multiplex spatial detection of analytes in a biological sample.

The present disclosure provides methods for high throughput barcoding nucleic acids and/or protein inside the cells. The in-cell single cell capture method uses an individual cell itself as a compartment and delivers a plurality of unique identifiers, e.g., barcodes into the cell and captures the nucleic acid and/or protein targets within the cell directly. It significantly simplifies single cell analysis experimental setup and eliminates the need of external compartment generation. It provides a high throughput single cell expression profiling and cellular protein quantitation method, and targeted sequencing with in-cell capture will be able to significantly increase sensitivity and specificity for low frequent mutation detection, such as, somatic mutation in very early stage of cancer and truly enables early cancer detection. A spatial expression and/or variation detection method for a tissue sample is developed with the combination of the in-cell barcoding method and positional barcode on a planar array.

The present disclosure provides methods for high throughput barcoding nucleic acids and/or protein inside the cells. The in-cell single cell capture method uses an individual cell itself as a compartment and delivers a plurality of unique identifiers, e.g., barcodes into the cell and captures the nucleic acid and/or protein targets within the cell directly. It significantly simplifies single cell analysis experimental setup and eliminates the need of external compartment generation. It provides a high throughput single cell expression profiling and cellular protein quantitation method, and targeted sequencing with in-cell capture will be able to significantly increase sensitivity and specificity for low frequent mutation detection, such as, somatic mutation in very early stage of cancer and truly enables early cancer detection. A spatial expression and/or variation detection method for a tissue sample is developed with the combination of the in-cell barcoding method and positional barcode on a planar array.

Provided herein are methods and kits for determining nucleic acid integrity of a biological sample. Disclosed are methods comprising: (a) contacting a biological sample with a substrate comprising a plurality of capture probes; (b) hybridizing a nucleic acid analyte from the biological sample to the capture probe; (c) extending a 3′ end of the capture probe using the nucleic acid analyte as a template to generate an extended capture probe; (d) hybridizing a plurality of labeled oligonucleotide probes comprising a first label and a second label to the extended capture probe; and (e) detecting a first intensity of the first label and a second intensity of the second label of the plurality of labeled oligonucleotides hybridized to the extended capture probe, thereby detecting a length of the nucleic acid analyte and determining the nucleic acid integrity of the biological sample.

Provided herein are methods and kits for determining nucleic acid integrity of a biological sample. Disclosed are methods comprising: (a) contacting a biological sample with a substrate comprising a plurality of capture probes; (b) hybridizing a nucleic acid analyte from the biological sample to the capture probe; (c) extending a 3′ end of the capture probe using the nucleic acid analyte as a template to generate an extended capture probe; (d) hybridizing a plurality of labeled oligonucleotide probes comprising a first label and a second label to the extended capture probe; and (e) detecting a first intensity of the first label and a second intensity of the second label of the plurality of labeled oligonucleotides hybridized to the extended capture probe, thereby detecting a length of the nucleic acid analyte and determining the nucleic acid integrity of the biological sample.