Project description:To examine whether Hormad1&2SFB/SFB (dsfb) male mice has defect in the meiotic sex chromosome inactivation (MSCI) process or not, three pairs of P19 testes were collected from each strain and mRNA-sequencing was performed. The data revealed that the transcription of X and Y chromosomes, but not autosomes, were specifically elevated. Therefore, MSCI was defective in dsfb spermatocytes.
Project description:H3K27Ac enrichment in intestinal epithelial cells from intestine of germ-free and segmented filamentous bacteria (SFB)-monoassociated mice. Intestinal epithelial cells were harvested from the terminal ileum of germ-free or SFB mice. Chromatin immunoprecipitation was performed with anti-H3K27Ac. Sequencing was performed using the Illumina HiSeq2500. Reads were mapped to the mm10 genome using Bowtie.
Project description:Expression in intestinal epithelial cells from intestine of germ-free and segmented filamentous bacteria (SFB)-monoassociated mice during infection. Intestinal epithelial cells were harvested from the terminal ileum of germ-free or SFB mice infected with Citrobacter rodentium for 6 days. RNA was isolated using RNeasy Kit (Qiagen). Sequencing was performed using the Illumina HiSeq2500. Reads were mapped to the mm10 genome using Bowtie.
Project description:To investigate SFB-host interactions and the host response to SFB, we compared gene expression profiles in terminal ileal mucosa collected from 5 SFB-positive and 5-negative age-matched patients identified from SFB PCR. We observed that 472 genes were different between the two groups (P < 0.05). Among them, 290 genes were up-regulated and 182 were down-regulated. GO biological pathway analysis of up-regulated genes revealed positive regulation of T-cell differentiation and activation pathways were enhanced (P < 0.001), suggesting that SFB colonization stimulated the human immune system, specifically T-cell maturation. Indeed, enhanced expression of Cd3e, Ifng, IL10, Foxp3 was observed in terminal ileal mucosa of 5 SFB-positive patients.
Project description:To investigate SFB-host interactions and the host response to SFB, we compared gene expression profiles in terminal ileal mucosa collected from 5 SFB-positive and 5-negative age-matched patients identified from SFB PCR. We observed that 472 genes were different between the two groups (P < 0.05). Among them, 290 genes were up-regulated and 182 were down-regulated. GO biological pathway analysis of up-regulated genes revealed positive regulation of T-cell differentiation and activation pathways were enhanced (P < 0.001), suggesting that SFB colonization stimulated the human immune system, specifically T-cell maturation. Indeed, enhanced expression of Cd3e, Ifng, IL10, Foxp3 was observed in terminal ileal mucosa of 5 SFB-positive patients. To find immune-related genes significantly expressed (p < 0.05) between SFB-positive and -negative
Project description:Purpose: The goal of this study is to identify gut dendritic cells that induces CD4 Th17 cells that play an critical role in mucosal immunity Methods: C57BL/6 mice were orally gavaged with fecal material derived from SFB-positive donor mice. Five days post oral gavage, mesenteric lymph nodes were harvested and dendritic cells were FACS-sorted. cDNA library from migratory dendritic cells (MHCII-highCD11c+) and resident dendritic cells (MHCII+CD11c-high) were generated using Chromium Single Cell 3' Library v2 Kit (10x Genomics). RNA sequencing was performed using NovaSeq S4 flow cell (Illumina). Data was processed using the Cell Ranger software (10x Genomics) followed by analysis using the R-based package Seurat. Results: Gut colonization with SFB increased the migration of type 2 but not type 1 dendritic cells to the mesenteric lymph nodes. Based on transcriptomic profiles, migratory type 2 dendritic cells consist of 2 major cell clusters (Cd40-Ccl22 and Cd1d1-Tnfrsf4-enriched cells). The Th17 response inducing cytokine IL-6 co-localized with the Cd40-Ccl22-expressing cells. Conclusion: Our study represents the first to carefully characterize the mucosal dendritic cells at steady state and during acute CD4 Th17 response. Transcriptomic profiling enabled the subsetting of dendritic cells based on functional markers (such as cytokines and chemokines) that are otherwise difficult to measure at the protein level. These results provide a focused look at mucosal dendritic cells and their roles in dictating different T cell responses.
Project description:There are two aims in this study – (1) To figure out the pathogenic sub-populations of CD4+ T cells in the spinal cord of EAE model; and (2) by comparing the gene expression profile of pathogenic Th17 cells in EAE model to that of the non-pathogenic Th17 cells induced by SFB in SILP, to identify genes candidates that are potentially selectively essential to pathogenic ones.
Project description:We performed RNA-sequencing of testes derived from Atr+/+ or Atr+/KD 7 weeks old mice. Since Atr+/KD male mice are sterile and present severe spermatogenesis defects, we aimed at analyzing the possible changes in gene expression given by the ATR kinase-dead (KD) mutation