Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample.

Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample.

DNA is sequenced by: (a) combining dsDNA fragments with Y-adapters and hairpin adapters comprising an affinity-label under conditions wherein the adapters ligate to fragments forming a mixture of fragment inserts flanked by two Y-adapters, a Y-adapter and a hairpin adapter, and two hairpin adapters; and (b) sequencing the selected fragment inserts with sequencing primers selecting for the Y-adapters.

DNA is sequenced by: (a) combining dsDNA fragments with Y-adapters and hairpin adapters comprising an affinity-label under conditions wherein the adapters ligate to fragments forming a mixture of fragment inserts flanked by two Y-adapters, a Y-adapter and a hairpin adapter, and two hairpin adapters; and (b) sequencing the selected fragment inserts with sequencing primers selecting for the Y-adapters.

Systems and methods for associating single cell imaging data with RNA transcriptomics. Single cells are isolated into microwells with a microbead having oligonucleotides conjugated on its surface. Each oligonucleotide includes a cell identifying optical barcode that is unique to that bead and binding sequence for RNA capture after cell lysis. The system is configured for loading single cells into the microarray and for flowing cell lysis buffers and other reagents into the microarray for performing RNA library sample preparation. The system is also configured for lowing optical hybridization probes that are complementary to the cell identifying optical barcodes and optically labeled onto the microwell array and for obtaining images of the microwells in response to the probes. The system and unique cell identifying optical barcodes and complementary optical hybridization probes facilitate a link between phenotypic imaging of cells resident on the microwell array with single cell whole transcriptome sequencing.

Systems and methods for associating single cell imaging data with RNA transcriptomics. Single cells are isolated into microwells with a microbead having oligonucleotides conjugated on its surface. Each oligonucleotide includes a cell identifying optical barcode that is unique to that bead and binding sequence for RNA capture after cell lysis. The system is configured for loading single cells into the microarray and for flowing cell lysis buffers and other reagents into the microarray for performing RNA library sample preparation. The system is also configured for lowing optical hybridization probes that are complementary to the cell identifying optical barcodes and optically labeled onto the microwell array and for obtaining images of the microwells in response to the probes. The system and unique cell identifying optical barcodes and complementary optical hybridization probes facilitate a link between phenotypic imaging of cells resident on the microwell array with single cell whole transcriptome sequencing.

The present disclosure relates to the field of biotechnology, in particular, to a combination product for detecting DNA. The product includes ribonuclease H II and a probe; the probe is a single-stranded probe and has a sequence which can be partially or entirely complementary to a target DNA molecule to be detected, and one or more RNA bases are embedded in the complementary region of the probe and divide the complementary region of the probe into at least two segments, each of which independently has DNA bases and base substitutions of less than or equal to 13 in total.

The present disclosure relates to the field of biotechnology, in particular, to a combination product for detecting DNA. The product includes ribonuclease H II and a probe; the probe is a single-stranded probe and has a sequence which can be partially or entirely complementary to a target DNA molecule to be detected, and one or more RNA bases are embedded in the complementary region of the probe and divide the complementary region of the probe into at least two segments, each of which independently has DNA bases and base substitutions of less than or equal to 13 in total.

The present disclosure relates to the field of biotechnology, in particular, to a combination product for detecting DNA. The product includes ribonuclease H II and a probe; the probe is a single-stranded probe and has a sequence which can be partially or entirely complementary to a target DNA molecule to be detected, and one or more RNA bases are embedded in the complementary region of the probe and divide the complementary region of the probe into at least two segments, each of which independently has DNA bases and base substitutions of less than or equal to 13 in total.

The present disclosure provides genetic constructs comprising a recombinant internal ribosome entry site (IRES), which may be used as riboswitches to modulate translation of an operably-mRNA sequence encoding a protein of interest. In other aspects, the disclosure provides recombinant cells, methods, kits and systems that utilize the same, e.g., to provide a platform for modulating the expression of essentially any protein of interest in a eukaryotic cell.