Project description:This study was designed to assess the global transcriptional differences between villin-Grem villi compared to normal villi of age-matched mice. We found changes in key gene signatures asscoiated with tumorigenesis. Total RNA obtained from isolated villi from Villin-Gremlin mouse (n=6) and wildtype controls (n=6)
Project description:This study was designed to assess the global transcriptional differences between villin-Grem villi compared to normal villi of age-matched mice. We found changes in key gene signatures asscoiated with tumorigenesis.
Project description:Total RNA was extracted from mouse Villin-creERT2:Cbx3-/- mice epithelial cells from the small intestine crypt, villi and colon epithelia
Project description:We hypothesize that gene expression in the cigarette smoke (CS) exposed neonatal lung and age-matched controls will be divergent. CS exposed lung will have divergence of immune response genes and structural genes. The lungs of (6) 2 week old neonatal mice exposed to 2 weeks of CS were compared to the lung of (4) 2 week old age-matched control mice. We utilized microarray analysis to examine transcriptional differences between smoke exposed neonatal lung and age-matched controls. Keywords: comparative expression profiling
Project description:Transcriptional profiling of murine lung tissue comparing wild type to gremlin-1 transgenic untreated or silicon dioxide (silica)-treated for two months. Gremlin-1 transgene expression in lung type II epithelial cells under SPC promoter. Aim was to compare expression of fibrosis and inflammation associated genes.
Project description:To assess the role of LSD1 in mouse small intestinal epithelium, we isolated small intestinal crypts and villus from wild type (WT) (Villin-Cre -; Lsd1f/f) and intestinal-epithelial-specific knock-out (cKO) (Villin-Cre+; Lsd1f/f) mice. This experiment uses a new Cre strain with 100% deletion efficiency. RNA was directly isolated from intestinal crypt and villus, and this was used for RNAseq. Gene expression analysis of cKO derived crypt and villus provides a spatially restricted outlook on the maturation status of the intestinal epithelium in the villi and the absence of Paneth cells in the crypt.
Project description:To attain deeper insight into metabolic alterations in Trpm7 gene deficient mice we used microarrays for profiling of transcripts in villi of Trpm7 ko and control mice. We identified a set of gene networks up- or down-regulated in villi of Trpm7 gene deficient mice.
Project description:To assess the role of LSD1 in mouse small intestinal epithelium, we isolated small intestinal crypts and villus from wild type (WT) (Villin-Cre -; Lsd1f/f) and intestinal-epithelial-specific knock-out (cKO) (Villin-Cre+; Lsd1f/f) mice. This experiment uses a new Cre strain with 100% recombination efficiency. RNA was directly isolated from the crypt and villus, and this was used for RNAseq. Gene expression analysis of cKO derived crypt and villus provides a spatially restricted outlook on the maturation status of the intestinal epithelium in the villi and the absence of Paneth cells in the crypt. Additionally, these mice were treated with antibiotics to study epithelium intrinsic changes related to LSD1 deletion but independent of the bacterial microbiome.
Project description:aCGH analysis of murine transgenic liver tissues affected with HCC, hybridized with age (18 months) and sex matched C57BL/6 mice. Moreover, 18months old C57BL/6 livers were hybridized with independent 18 months old C57BL/6 livers for control. Keywords: Array comparative genomic hybridization analysis (aCGH).
Project description:Purpose: NGS has revolutionized systems-based analysis of cell signaling pathways. The goal of this study is to determine the effects of PPARD in gastric corpus epithenial cell transcriptomes in relation to gastric progenitor cell transfromation and gastric tumorigenesis. Methods: NGS-derived mRNA transcriptome profiles of gastric corpus epithelial cells from villin-PPARD and their age and sex matched WT mice at 10, 25 and 55 weeks were generated by deep sequencing (4-5 mice per group) using Illumina HiSeq4000 .The transcriptomes of villin-PPARD and WT mice were compared to determine the differentially expressed genes. Differentially expressed genes in the top canonical pathways will be examined and validated by qRT-PCR. Results: The raw data was aligned to the MM10 genome with Tophat2/2.0.14, and the number of reads per gene was counted with HTSeq/0.6.1.The read counts were normalized with "DESeq2". We used cutoff: FDR< 0.01 and fold change larger than 2 to identify 407 differentially expressed genes (DEGs) for 10 weeks, 717 DEGs for 25 weeks and 2694 DEGs for 55 weeks. Among those DEGs, 255 are shared by the 3 ages, in which 219 were upregulated and 36 were downregulated in villin-PPARD mice compared with the WT mice. Ingenuity Pathway Analysis for the 255 DGEs among the 3 age groups showed that IFN-g signaling was the top canonical pathway that PPAR-d activated, with an overlap ratio of 36.1% of the known genes involved in this pathway. The next two top canonical pathways, with overlap ratios of 23.7% and 15.9%, were the antigen presentation pathway and the pathway for activation of IRF by cytosolic pattern recognition receptors, respectively, both of which are related to IFN-g signaling pathway activation and immune inflammation. Conclusions: Our study represents the detailed analysis of PPARD transcriptomes in gastric corpus epithelial cells regulated by villin-promoter, generated by mRNA-seq technology. Our results show that NGS offers a comprehensive and accurate quantitative and qualitative evaluations of mRNA contents in cells. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
