Abstract: Described herein are methods, systems, compositions, and macromolecule complexes, for detecting, analyzing, evaluating, screening for, prognosing, diagnosing, and/or monitoring, of donor DNA in a transplant recipient for possible transplant rejection in the transplant recipient.

Abstract: Methods, systems, compositions and kits for detection of multiple analytes are disclosed. The methods, systems, compositions and kits may comprise an oligonucleotide that may bind to more than one analyte. The oligonucleotide may allow for the generation of different signal depending on the analyte that the oligonucleotide is hybridized to. The signals generated from may be used to identify the presence of an analyte. The signals generated from may be used may be used to simultaneously identify the presence of multiple analytes in a sample.

Abstract: Provided herein are methods for identification of an expression profile, a transcriptional profile, and/or an epigenetic profile from a cell-containing sample. Also provided are compositions for use in the disclosed methods.

Abstract: Surface chemistries for the visualization of labeled single molecules (analytes) with improved signal-to-noise properties are provided. To be observed, analyte molecules are bound to surface attachment features that are spaced apart on the surface such that when the analytes are labeled adjacent analytes are optically resolvable from each other. One way to express this concept is that binding elements should be spaced apart such that the Guassian point spread functions of adjacent labels do not overlap. Another way of expressing this concept is that the surface binding elements should be spaced apart by a distance equal to at least the diffraction limit for an optical label attached to the bound analytes.

Abstract: Methods and systems for detecting the locations of individual instances of an analyte (e.g., individual cells, individual molecules) in an environment are provided. The environment includes functionalized fluorophores that are configured to selective interact with (e.g., bind with) the analyte and that have a fluorescent property that can be modulated (e.g., a fluorescence intensity that can be affected by the presence of a magnetic field). Detecting the location of individual instances of the analyte includes illuminating the environment and detecting signals emitted from the fluorophores in response to the illumination during first and second periods of time. Detecting the location of individual instances of the analyte further includes modulating the modulatable fluorescent property of the fluorophores during the second period of time and determining which individual fluorophores in the environment are bound to the analyte based on the signals detected during the first and second periods of time.

Abstract: In some embodiments, methods of recovering a sequence-verified target nucleic acid are provided. In some embodiments, such methods may include tagging each member of a nucleic acid library with a set of adaptor sequences; sequencing the tagged members of the nucleic acid library; and recovering the sequence-verified target nucleic acid from the tagged and sequenced members of the nucleic acid library using a dial-out selection method. In certain embodiments, the members of the nucleic acid library may be tagged with a second set of adaptor sequences.

Abstract: Methods and systems for detecting the locations of individual instances of an analyte (e.g., individual cells, individual molecules) in an environment are provided. The environment includes functionalized fluorophores that are configured to selective interact with (e.g., bind with) the analyte and that have a fluorescent property that can be modulated (e.g., a fluorescence intensity that can be affected by the presence of a magnetic field). Detecting the location of individual instances of the analyte includes illuminating the environment and detecting signals emitted from the fluorophores in response to the illumination during first and second periods of time. Detecting the location of individual instances of the analyte further includes modulating the modulatable fluorescent property of the fluorophores during the second period of time and determining which individual fluorophores in the environment are bound to the analyte based on the signals detected during the first and second periods of time.

Abstract: Surface chemistries for the visualization of labeled single molecules (analytes) with improved signal-to-noise properties are provided. To be observed, analyte molecules are bound to surface attachment features that are spaced apart on the surface such that when the analytes are labeled adjacent analytes are optically resolvable from each other. One way to express this concept is that binding elements should be spaced apart such that the Guassian point spread functions of adjacent labels do not overlap. Another way of expressing this concept is that the surface binding elements should be spaced apart by a distance equal to at least the diffraction limit for an optical label attached to the bound analytes.

Abstract: In some embodiments, methods of recovering a sequence-verified target nucleic acid are provided. In some embodiments, such methods may include tagging each member of a nucleic acid library with a set of adaptor sequences; sequencing the tagged members of the nucleic acid library; and recovering the sequence-verified target nucleic acid from the tagged and sequenced members of the nucleic acid library using a dial-out selection method. In certain embodiments, the members of the nucleic acid library may be tagged with a second set of adaptor sequences.

Abstract: Surface chemistries for the visualization of labeled single molecules (analytes) with improved signal-to-noise properties are provided. To be observed, analyte molecules are bound to surface attachment features that are spaced apart on the surface such that when the analytes are labeled adjacent analytes are optically resolvable from each other. One way to express this concept is that binding elements should be spaced apart such that the Guassian point spread functions of adjacent labels do not overlap. Another way of expressing this concept is that the surface binding elements should be spaced apart by a distance equal to at least the diffraction limit for an optical label attached to the bound analytes.