Project description:We set out to better understand the cellular heterogeneity and niche cues of the remodeling porcine intestine after weaning by performing single-cell mRNA sequencing (scRNA-seq) survey of 42,149 cells from ileum tissue in piglets. Substantial heterogeneity among diverse epithelial, stromal, and immune cell subsets was observed. We map the various cell committed state within ileum tissue, and connect them through cell-cell interactions. We delineated a new classification of different epithelium secretory cells. Apart from goblet cell and enteroendocrine cell, we found that few pH-sensing BEST4/OTOP2 cells also exist in the ileum13. The immune component of early-weaned piglet was shifted as reduction of Th17 and abundance of CTL. Th17 cells harbor features of classical phonotype in normal suckling piglet (NSP) and pathogenicity in early weaning piglet (EWP), which may be induced by special cytokine milieu suggested as previous stduy14,15. We conclusively showed enrichment of the pathogenic effector CD8+ GZMB+ CTL cells may be a critical factor exacerbating ileal inflammation via mitochondrial dysfunction inducing epithelia cell apoptosis in EWP. Keywords: Expression profiling by high throughput sequencing
Project description:As a mild, highly contagious, respiratory disease, swine influenza always damages the innate immune systems, and increases susceptibility to secondary infections which results in considerable morbidity and mortality in pigs. Nevertheless, the systematical host response of pigs to swine influenza virus infection remains largely unknown. To explore these, a time-course gene expression profiling was performed to detect comprehensive analysis of the global host response induced by H1N1 swine influenza virus in pigs. At the age of day 35, 15 pigs were randomly allocated to the non-infected group and 15 to the infected group. Each piglet of the infected group was intranasaly challenged with A/swine/Hubei/101/2009(H1N1) strain and Each piglet of the non-infected group was treated similarly with an identical volume of PBS as control.
Project description:We performed single-cell RNA sequencing (scRNA-seq) on cortical samples obtained fromGatad2bstop/+ and WT littermates at a single embryonic time point (E16.5) in order to explore underlying mechanisms of Gatad2b function. We also generated Gatad2bstop/stop scRNA-seq data to identify dosage sensitive targets of Gatad2b
Project description:In order to provide multi-omic resolution to human retinal organoid developmental dynamics, we performed scRNA-seq and scATAC-seq from the same cell suspension across a time course (6-46 weeks) of human retinal organoid development. This data set covers all the retinal organoid scRNA-seq data generated from IMR90 and409B2-iCas9 cell lines.
Project description:To further characterize the T cell response to the neoantigen vaccine, we performed single-cell RNA and T cell receptor (scRNA/TCR-seq) of peripheral blood T cells at the 12-week post-vaccination time point.
Project description:This experiment is aimed at studying the effect of two different chemotherapies (FOLFOX and FOLFIRI) on chromatin accessibility of HCT116 colorectal cancer cell line at different time points. Two early time points (8h and 16h) are used to evaluate the acute response, while a late time point (two weeks, LT) is used to evaluate the long-term effect. After two week exposure, cells are grown without treatments for additional two weeks, to evaluate the chromatin landscapes of cells which survived the chemotherapy. A pool of the same cells has been independently profiled by scRNA-seq.
