Abstract: Provided herein are compositions and methods for therapeutic and/or prophylactic treatment of an intracellular bacterial infection in a subject in need thereof, comprising one or more modulating agents, wherein the one or more modulating agents increase expression of IFN?, IL-2, TNF, and/or IL-17 in systemic and/or lung T cells. In some embodiments, the increase of expression of IFN?, IL-2, TNF, and/or IL-17 occurs in lung T cells. The lung T cells can be lung resident T cells or systemic T cells that are recruited to the lung. In some embodiments, the T cells are CD4+ and/or CD8+ T cells. In some embodiments, the intracellular bacterial infection is a Mycobacterium tuberculosis (MTB) infection.

Abstract: The present invention relates to methods of detecting region(s) of interest in a gene comprising a polyA tail. The region(s) of interest can include gene(s), region(s), mutation(s), deletion(s), insertion(s), indel(s), and/or translocation(s). The region(s) can be greater than or less than 1 kilobases from the polyA tail. Methods can include forming a library of single cell transcripts comprising the region(s) in close proximity to a cell barcode and a unique molecular identifier (UMI). Methods for distinguishing cells by genotype can include amplifying the transcripts using PCR methods and detecting the cell barcode and UMI using single cell sequencing methods. Transcripts can be enriched using tagged region-specific PCR primers. Cell barcodes can be brought into close proximity to the region(s) by circularizing the transcripts. Sequencing of the transcripts can include using primer binding sites added during PCR amplification and library indexes for multiplexed sequencing.

Abstract: The present invention relates to methods of detecting region(s) of interest in a gene comprising a polyA tail. The region(s) of interest can include gene(s), region(s), mutation(s), deletion(s), insertion(s), indel(s), and/or translocation(s). The region(s) can be greater than or less than 1 kilobases from the polyA tail. Methods can include forming a library of single cell transcripts comprising the region(s) in close proximity to a cell barcode and a unique molecular identifier (UMI). Methods for distinguishing cells by genotype can include amplifying the transcripts using PCR methods and detecting the cell barcode and UMI using single cell sequencing methods. Transcripts can be enriched using tagged region-specific PCR primers. Cell barcodes can be brought into close proximity to the region(s) by circularizing the transcripts. Sequencing of the transcripts can include using primer binding sites added during PCR amplification and library indexes for multiplexed sequencing.

Abstract: Provided herein are compositions and methods for therapeutic and/or prophylactic treatment of an intracellular bacterial infection in a subject in need thereof, comprising one or more modulating agents, wherein the one or more modulating agents increase expression of IFN?, IL-2, TNF, and/or IL-17 in systemic and/or lung T cells. In some embodiments, the increase of expression of IFN?, IL-2, TNF, and/or IL-17 occurs in lung T cells. The lung T cells can be lung resident T cells or systemic T cells that are recruited to the lung. In some embodiments, the T cells are CD4+ and/or CD8+ T cells. In some embodiments, the intracellular bacterial infection is a Mycobacterium tuberculosis (MTB) infection.

Abstract: The present invention relates to methods of deriving genetic information from RNA-seq libraries, that can enable an overlay of genetic information (such as cancer driver mutations) onto single-cell transcriptomes and permitting efficient identification, localization, and quantification of certain cells of interest within a population as well as provide low-cost selection and sequencing of any portion of a transcript, including at the 5? end.

Abstract: Methods of delivering transgenes to target cells using plasmids comprising viral inverted terminal repeat (ITR) sequences are described. Such plasmids are capable of directing sustained transgene expression in target cells in rats provided that at least one adeno-associated virus (AAV) ITR sequence is present in the plasmid, regardless of whether that ITR is located upstream or downstream of the transgene. In a particular embodiment, plasmids comprising one or more AAV ITR sequence and an IL-10 transgene are shown to be effective in sustained reversal of pain in an animal model of neuropathic pain.

Abstract: Methods of delivering transgenes to target cells using plasmids comprising viral inverted terminal repeat (ITR) sequences are described. Such plasmids are capable of directing sustained transgene expression in target cells in rats provided that at least one adeno-associated virus (AAV) ITR sequence is present in the plasmid, regardless of whether that ITR is located upstream or downstream of the transgene. In a particular embodiment, plasmids comprising one or more AAV ITR sequence and an IL-10 transgene are shown to be effective in sustained reversal of pain in an animal model of neuropathic pain.

Abstract: Methods of delivering transgenes to target cells using plasmids comprising viral inverted terminal repeat (ITR) sequences are described. Such plasmids are capable of directing sustained transgene expression in target cells in rats provided that at least one adeno-associated virus (AAV) ITR sequence is present in the plasmid, regardless of whether that ITR is located upstream or downstream of the transgene. In a particular embodiment, plasmids comprising one or more AAV ITR sequence and an IL-10 transgene are shown to be effective in sustained reversal of pain in an animal model of neuropathic pain.