Abstract: Provided herein are compositions and methods to identify a binding element (e.g., peptide, peptoid, or protein) that can be bound by an immunoreceptor (e.g., antibody). The binding element can be provided in a target binding unit comprising two binding elements separated by a spacer such that the two binding elements simultaneously bind to a single molecule comprising an antigen binding domain of an antibody. The present disclosure provides various methods to construct the spacer. The identified binding elements can be further used to manufacture an array which can be used to profile antibodies obtained from a blood sample.

Abstract: Provided herein are compositions and methods for assembling nucleic acid sequences encoding T-cell receptors.

Abstract: The present disclosure provides compositions and methods for antigen identification. The methods provided herein comprise capturing polypeptides such as cytokines secreted by TCR-expressing cells (e.g., T cells) by antigen-presenting cells (APCs) presenting the antigens recognized by the TCRs of the TCR-expressing cells. The APCs can be detected or selected for antigen identification.

Abstract: Provided herein are compositions and methods to identify a binding element (e.g., peptide, peptoid, or protein) that can be bound by an immunoreceptor (e.g., antibody). The binding element can be provided in a target binding unit comprising two binding elements separated by a spacer such that the two binding elements simultaneously bind to a single molecule comprising an antigen binding domain of an antibody. The present disclosure provides various methods to construct the spacer. The identified binding elements can be further used to manufacture an array which can be used to profile antibodies obtained from a blood sample.

Abstract: The present disclosure provides compositions and methods for identifying target-reactive T-cell receptors (TCRs). The identification may be based on comparing the frequency of a TCR before and after a marker-based selection. The identification may also be based on comparing the frequency of a TCR in a pool of cells stimulated by mutant and wildtype antigens.

Abstract: The present disclosure provides compositions and methods to make and use ribonucleic acid sequences encoding viral proteins (e.g., Rep and Cap proteins) derived from adeno-associated viruses. The RNA sequences can be delivered into a host cell for viral packaging.

Abstract: Provided herein are compositions and methods for high throughout cloning of fused bipartite immunoreceptor polynucleotides encoding cognate pairs of bipartite immunoreceptors. Also provided herein are various applications of the fused bipartite immunoreceptor polynucleotides, expression vectors containing the fused bipartite immunoreceptor polynucleotides, or cells containing the fused bipartite immunoreceptor polynucleotides or expression vectors.

Abstract: Compositions and methods are described for inducing an immune response against an immunogen in humans. The induced immune response is obtained by administering a heterologous prime-boost combination of an in vitro transcribed (IVT) self-replicating RNA (repRNA) and an adenovirus vector. The compositions and methods can be used to provide a protective immunity against a disease, such as a viral infection or a cancer, in humans.

Abstract: Provided herein are compositions and methods for assembling nucleic acid sequences encoding T-cell receptors.

Abstract: Provided herein are compositions and methods for assembling nucleic acid sequences encoding T-cell receptors.

Abstract: Provided herein are compositions and methods for high throughout cloning of fused bipartite immunoreceptor polynucleotides encoding cognate pairs of bipartite immunoreceptors. Also provided herein are various applications of the fused bipartite immunoreceptor polynucleotides, expression vectors containing the fused bipartite immunoreceptor polynucleotides, or cells containing the fused bipartite immunoreceptor polynucleotides or expression vectors.

Abstract: Provided herein are compositions and methods for high throughout cloning of fused bipartite immunoreceptor polynucleotides encoding cognate pairs of bipartite immunoreceptors. Also provided herein are various applications of the fused bipartite immunoreceptor polynucleotides, expression vectors containing the fused bipartite immunoreceptor polynucleotides, or cells containing the fused bipartite immunoreceptor polynucleotides or expression vectors.

Abstract: Provided herein are compositions and methods to identify a binding element (e.g., peptide, peptoid, or protein) that can be bound by an immunoreceptor (e.g., antibody). The binding element can be provided in a target binding unit comprising two binding elements separated by a spacer such that the two binding elements simultaneously bind to a single molecule comprising an antigen binding domain of an antibody. The present disclosure provides various methods to construct the spacer. The identified binding elements can be further used to manufacture an array which can be used to profile antibodies obtained from a blood sample.

Abstract: The application provides improved methods of analyzing biological particles and their constituents, including methods of generating truncated and barcoded nucleic acid molecules from at least two target polynucleotide sequences, each from distinct biological particles.

Abstract: The application provides improved methods of analyzing biological particles and their constituents, including methods of labeling at least one target nucleic acid molecule from a biological particle with a barcoded primer.

Abstract: Provided herein are compositions and methods to entrap a target in a hardened particle (e.g., a hydrogel particle) and barcode the target for downstream applications. The target provided herein can be a polynucleotide, a polypeptide, or an organelle from a single cell, a single complex of cell or a single exosome. The present disclosure provides various strategies to immobilize or restrict diffusion of the target within a hardened particle so that the target can be stably entrapped or embedded. A split-and-pool combinatorial strategy described herein can be used to barcode each hardened particle so that one or more targets from the same hardened particle can be barcoded with a common barcode sequence. The barcoded sequences can further be analyzed in a downstream application, for example, sequencing.