Project description:In this work we have employed a single cell sequencing approach of both ileum and colon organoids using 10x Genomics scRNAseq and TAP-seq targeted single-cell RNA-seq.
Project description:To describe the protein profile in hippocampus, colon and ileum tissue’ changing after the old faeces transplants, we adopted a quantitative label free proteomics approach.
Project description:The goal of this study was to characterize a single-cell clone derived from pig ileum epithelium. Analyses including RNA-seq demonstrated that this clone was derived from an enteric smooth muscle cell. This clone is named PIC7 in the manuscript.
Project description:To establish better understanding of specific epithelial cells found across different regions of the small intestine in pigs, we utilized single-cell RNA sequencing (scRNA-seq) to recover and analyze epithelial cells from duodenum, jejunum, and ileum. Cells identified included crypt cells, enterocytes, BEST4 enterocytes, goblet cells, and enteroendocrine (EE) cells. Overall, results provide new information on regional localization and transcriptional profiles of epithelial cells in the pig small intestine.
Project description:Determination of differentially expressed genes in the proximal colon and distal ileum tissue in MR1 and IL-17A deficiency at steady-state. Tissue from naïve mice was harvested, total RNA extracted and subjected to RNASeq analysis.
Project description:The first GSSM of V. vinifera was reconstructed (MODEL2408120001). Tissue-specific models for stem, leaf, and berry of the Cabernet Sauvignon cultivar were generated from the original model, through the integration of RNA-Seq data. These models have been merged into diel multi-tissue models to study the interactions between tissues at light and dark phases.
Project description:This study underlines the beneficial use of excess dietary zinc in preventing colitis and inflammatory events. Zn-induced gene expression profiles were analyzed at ileum and colon level. A total number of 101 profiles were found differentially expressed during Zn supplemented diet, with an unbalanced pattern between these two tissues. A largest number of genes were found up-regulated in colon (22 genes), unlike the ileum (6 genes). At the other side, the number of down-regulated genes was higher in ileum (63 genes) against the colon (15 genes). Very few common profiles were detected in these two tissues, 3 up- and 2 down-regulated genes respectively. Genes coding for metallothioneins (Mt1, Mt2) and for phosphatidylinositol-4-phosphate 5-kinase (Pip5k1a) were found commonly up-regulated in ileum and colon, with the highest FC values. Genes coding for the zinc transporter of solute carrier family 39 (Slc39a4) and for lymphotoxin B (Ltb) were found commonly down-regulated with among the lowest FC values. Despite the different patterns, functional clustering of expressed genes converged for substantially the same physiological activities in both ileum and colon: intestinal tissue protection and epithelium reestablishment, immune system regulation as well as digestive and metabolic targeted functions.
Project description:To establish better understanding of cells found in jejunal and ileal Peyer's patches of pigs, we utilized single-cell RNA sequencing scRNA-seq and spatial transcriptomics to recover and analyze cells and spatial regions from sections of jejunum and ileum containing Peyer's patches. Cells identified via single-cell RNA sequencing included B, T/innate lymphoid cell, myeloid, epithelial, and stromal lineage cells. Spatial dots recovered via spatial transcriptomics belonged to regions including villi, crypts, interfollicular/parafollicular zones, follicles, and muscularis. Overall, results provide new information on regional localization and transcriptional profiles of cells in the pig small intestine.