Project description:Dlx1 and Rgs5 in the Ductus Arteriosus: Vessel-specific Genes Identified by Transcriptional Profiling of Laser-capture Microdissected Endothelial and Smooth Muscle Cells
Project description:RNA-seq analysis of total RNA isolated from laser capture microdissected intestinal epithelium. The analysis aimed at characterizing the epithelial gene expression changes in IBD patients vs. healthy controls.
Project description:We isolated glomeruli with amyloid deposits by performing laser-capture microdissection from formalin-fixed paraffin-embedded samples and identified amyloidosis-related protein using liquid chromatography–tandem mass spectrometry (LC-MS/MS)–based proteomics
Project description:This study aims to identify and characterize miRNA expression inATLOs isolated by laser microdissection from human AAA biopsy samples. The aim of this study was to profile (with microarray technology) miRNAs in ATLOs (Adventitial tertiary lymphoid organs), isolated by laser capture microdissection (LCM). Smooth muscle cells (SMCs) isolated from control non-aneurysmal aortas were the control group according to which data were normalized. ATLOs were microdissected (mean 13.5mm2) from two different biopsy samples of human abdominal aortic aneurysm. An area enriched in smooth muscle cells was microdissected from two biopsy samples of non aneurysmal abdominal aortas. Each microdissected samples were analyzed independently on microarray.
Project description:In this study we used microarray analysis to reveal the gene expression profile of the hippocampal CA1 subregion, which was laser-capture microdissected one week after kainic acid (KA)-induced status epilepticus (SE) in postnatal day 21 (P21) rats. These rats are developmentally roughly comparable to juvenile children, and KA-induced SE leads to selective damage of hippocampal CA1 pyramidal neurons in this age group while saving neurons of the other sub-regions. We searched for alterations in the gene expression pattern during the early epileptogenetic phase, i.e. one week after SE, and compared the results with those of age-matched control rats. To detect specifically changes in the CA1 pyramidal neurons, we used the laser-capture microdissection technique that allows the precise isolation of the region of interest. The RNA of this region was isolated, amplified, and labeled, and then hybridized to Illumina RatRef-12 Expression BeadChip Arrays. The gene expression data generated from the microarray was first normalized by the guantile normalization method, and then filtered by using the empirical Bayes method, and the contrasts were created by using the Limma R/Bioconductor. Finally, the data was clustered by using the non-hierarchical K-means clustering for genes, and the pathway analysis was performed by âGene set testâ, which analyzes the statistical significance of a set of genes simultaneously ranked by p-value and generates the KEGG categories (Chipster manual). The Illumina microarray analysis with the Chipster software v1.1.0 (http://chipster.csc.fi; CSC, Espoo, Finland) generated a total of 1592 differently expressed genes in the CA1 subregion of KA-treated rats compared to control rats. Using the K-means method the genes were classified in 10 different clusters. The subsequent KEGG-test for the probe set over-representation analysis revealed the 15 significantly (p<0.05) changed KEGG-pathways in response to KA-treatment, e.g. oxidative phosphorylation (26 genes changed), and long-term potentiation (LTP; 18 genes changed). Some of the differentially expressed genes were also identified to be involved in Ca2+ homeostasis, gliosis, inflammation, and GABAergic transmission.
Project description:The purpose of the experiment was to compare the transcriptional profile of lupus nephritis kidney tissue at a first flare and expression at a repeated lupus nephritis episode. All samples were laser microdissected into glomerular and tubular compartments and samples were ran in different cartridges. Fourteen lupus nephritis patients and ten normal controls (7 for glomeruli) FFPE samples were laser microdissected and then ran into 5 cartridges for glomeruli and 5 cartridges for tubulointerstitium. This dataset is part of the TransQST collection.
Project description:Glomeruli were isolated from formalin-fixed paraffin embedded (FFPE) preserved human kidney biopsies using laser capture micro-dissection. Isolated tissue was de-cellularized by extraction using an ammonium hydroxide/NP-40 protocol. The residual extra-cellular fraction was analyzed by 1-dimensional C18 RP LCMS.
