Abstract: Disclosed are methods and kits for detecting and visualizing biomolecules of interest, RNA molecules, and/or genomic loci, as well as the proteins, RNAs, or chromatin loci associated with the biomolecules of interest, RNA molecules, or genomic loci. The methods and kits can be used for elucidating molecular interactions in situ.

Abstract: Embodiments of the present disclosure provide a single stranded nucleic acid construct with a predetermined number of binding sites, wherein the construct comprises a targeting domain, at least one signaling domain, and at least one splint oligonucleotide that hybridizes to complementary regions on the targeting domain and the signaling domain to form a ligation junction to link each domain to form a functional unit. The present disclosure also provides for methods of using the construct to quantify a target nucleic acid through signal intensity. In other embodiments, the disclosure provides use of the construct in multiplexed target detection methods.

Abstract: The present disclosure provides methods, systems and compositions for detecting nucleic acid sequences in a biological sample having a three-dimensional matrix.

Abstract: A method of altering cells with a pooled library of bar-coded nucleic acids is provided including combining a group of cells with the pooled library of bar coded nucleic acids under conditions which promote uptake of one or more barcoded nucleic acids from the pooled library into the cells, analyzing an individual cell for phenotype, sequencing the individual cell to identify the one or more barcoded nucleic acids from the pooled library, and correlating the phenotype for the individual cell with the one or more barcoded nucleic acids from the pooled library.