Abstract: Provided herein are compositions and methods to assess the genomic landscape of fixed cells using light activated oligonucleotides that can be directed to the nucleus, mitochondria, or cytoplasm of fixed cells and that, upon activation, can be extended for in situ copying of nuclear single-stranded DNA (i.e., open chromatin), open mitochondrial DNA, and/or cytoplasmic RNA into barcoded complementary DNA. These methods also provide for gene specific 3D chromatin structural niche analysis.

Abstract: Provided herein are compositions and methods to assess the genomic landscape of fixed cells using light activated oligonucleotides that can be directed to the nucleus, mitochondria, or cytoplasm of fixed cells and that, upon activation, can be extended for in situ copying of nuclear single-stranded DNA (i.e., open chromatin), open mitochondrial DNA, and/or cytoplasmic RNA into barcoded complementary DNA. These methods also provide for gene specific 3D chromatin structural niche analysis.

Abstract: Provided herein are methods of using photocleavable labels for multiplex and serial antigen detection. The methods comprise detecting the presence of photocleavable labels, which are conjugated through functional linkers to antigen-binding complexes, which in turn non-covalently bind to antigens. The presence of a photocleavable label is indicative of the presence of an antigen specifically or selectively bound by an antigen-binding complex. Also provided are apparatuses for using photocleavable labels for multiplex and serial antigen detection.

Abstract: Provided herein are methods of using photocleavable labels for multiplex and serial antigen detection. The methods comprise detecting the presence of photocleavable labels, which are conjugated through functional linkers to antigen-binding complexes, which in turn non-covalently bind to antigens. The presence of a photocleavable label is indicative of the presence of an antigen specifically or selectively bound by an antigen-binding complex. Also provided are apparatuses for using photocleavable labels for multiplex and serial antigen detection.

Abstract: Provided herein are compositions and methods to assess the genomic landscape of fixed cells using light activated oligonucleotides that can be directed to the nucleus, mitochondria, or cytoplasm of fixed cells and that, upon activation, can be extended for in situ copying of nuclear single-stranded DNA (i.e., open chromatin), open mitochondrial DNA, and/or cytoplasmic RNA into barcoded complementary DNA. These methods also provide for gene specific 3D chromatin structural niche analysis.

Abstract: Provided herein are methods of using photocleavable labels for multiplex and serial antigen detection. The methods comprise detecting the presence of photocleavable labels, which are conjugated through functional linkers to antigen-binding complexes, which in turn non-covalently bind to antigens. The presence of a photocleavable label is indicative of the presence of an antigen specifically or selectively bound by an antigen-binding complex. Also provided are apparatuses for using photocleavable labels for multiplex and serial antigen detection.

Abstract: The present invention concerns identifying organisms based on detecting distinguishing patterns produced following RNA amplification that originates via a DNA template. In particular, the methods and compositions of the invention concern obtaining ds DNA from the organism in question, amplifying at least part of the DNA via RNA molecules from transcription using primers that target repetitive DNA, and detecting a hallmark pattern of the amplified RNA.