Gene expression responses of mouse neural cells to heparin-binding growth factors
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Steven Head
PROVIDER: E-GEOD-26010 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The general area of research interests of my lab is the glycobiology of HSPGs in cell-cell/cell-matrix interactions and growth factor signalling. Heparan sulfate binding proteins in neural development and differentiation. We used the Glyco-gene Chips to study the gene expression responses of mouse neural cells to heparin-binding growth factors. The experimental systems studied is in vivo (developing mouse brain). The goal is to examine the global responses of neural cells to particular growth factors during differentiation in terms of effects on HS biosynthetic enzymes and proteoglycan core proteins, as well as growth factors and their receptors.
2010-12-11 | GSE26010 | GEO
Project description:Dr. Panjwani's laboratory is focusing on the mechanism by which galectins-3 and 7 mediate corneal epithelial cell migration. We are currently performing studies to: (i) identify and characterize the corneal epithelial cell surface and extracellular matrix (ECM) molecules which serve as counterreceptors of galectin-3 and -7, to establish whether the lectins modulate corneal epithelial cell migration by binding to well known integrins, growth factor receptors, and/or ECM molecules and (ii) determine whether galectin-3 mediates corneal epithelial cell migration indirectly by modulating the expression of key adhesion and/or signal transduction molecules by using small interfering RNA, cDNA microarrays and glycogene arrays. We have prepared three independent preparations of total RNA of corneal epithelial cells from WT mice (total six samples) for analysis of glycogene expression. Samples are Normal Cornea (Left eye) and Laser ablation + 16-18 hours healing (right eye)
2010-12-11 | E-GEOD-26009 | biostudies-arrayexpress
Project description:In order to examine the role of macrophage heparan sulfate proteoglycans in atherogenesis, we inactivated the biosynthetic gene N-acetylglucosamine N-deacetylase-N-sulfotransferase 1 (Ndst1) in macrophages. In order to determine the impact of altering Ndst1 expression, we crossbred mice bearing a conditional loxP-flanked (“floxed”) allele of Ndst1 (Ndst1f/f) to transgenic mice expressing the bacterial Cre recombinase under control of the lysozyme 2 promoter (LysMCre) to drive inactivation of the gene in myeloid cells. We compared the transcriptome of bone marrow derived macrophages from Ndst1f/fLysMCre- and Ndst1f/fLysMCre+ macrophages in basal growth medium and after foam cell conversion using 50µg/ml of aggregated LDL (agLDL) to asses the impact of altered macrophage heparan sulfate sulfation on gene expression.
2014-11-04 | GSE51009 | GEO
Project description:In order to examine the role of macrophage heparan sulfate proteoglycans in atherogenesis, we inactivated the biosynthetic gene N-acetylglucosamine N-deacetylase-N-sulfotransferase 1 (Ndst1) in macrophages. In order to determine the impact of altering Ndst1 expression, we crossbred mice bearing a conditional loxP-flanked (M-bM-^@M-^\floxedM-bM-^@M-^]) allele of Ndst1 (Ndst1f/f) to transgenic mice expressing the bacterial Cre recombinase under control of the lysozyme 2 promoter (LysMCre) to drive inactivation of the gene in myeloid cells. We compared the transcriptome of bone marrow derived macrophages from Ndst1f/fLysMCre- and Ndst1f/fLysMCre+ macrophages in basal growth medium and after foam cell conversion using 50M-BM-5g/ml of aggregated LDL (agLDL) to asses the impact of altered macrophage heparan sulfate sulfation on gene expression. Total RNA obtained from bone marrow derived macrophages (BMDM) derived form two wild-type and two Ndfst1-deficient mice before and after foam cell conversion and analyzed in diplicate (n=4 for each conditions; total of 4 conditions)
2014-11-04 | E-GEOD-51009 | biostudies-arrayexpress
Project description:This laboratory studies 1) enzymes which are involved in selectin ligand formation in leukocytes, 2) how expression of those enzymes is controlled, and 3) basic cell biology of FucT-VII. B cells vs. plasma cells. Study of primary IgG plasma cells. Plasma cells constitute the final stage of B-cell differentiation, and their migration from the lymph nodes and spleen to bone marrow is thought to be an important step in the maintenance of a long-term antibody response to a pathogen. Dr. Kansas has purified primary IgG plasma cells from E-selectin/P-selectin double knockout mice by a negative selection technique and compared their gene expression profile to that of murine B cells using Affymetrix murine oligonucleotide microarray analysis. Highly distinct gene expression profiles were revealed (see Underhill GH et al, Blood. 2003;101:4013-4021). As a follow-up to that experiment, the same probes (in triplicate) derived from primary murine IgG plasma cells and normal B cells were used to probe Glyco-gene Chips. As a follow-up to that experiment, the same probes (in triplicate) derived from primary murine IgG plasma cells and normal B cells were used to probe Glyco-gene Chips.
2011-01-07 | E-GEOD-26480 | biostudies-arrayexpress
Project description:This lab investigates how protein-carbohydrate interactions affect cell fate in the immune system. The specific focus is on the mechanism of galectin-1 mediated death of T lymphocytes, and the role of galectin-1 in immune development, lymphocyte homeostasis, response to pathogens, autoimmunity and tumor cell evasion of the immune response. T cell memory, the ability of T cells to respond to recall antigens rapidly and effectively, is a critical component of the adaptive immune response and the essential target of vaccine development. After naive T cells are exposed to a new antigen (or pathogen), expansion of antigen-specific T cells creates an effector population; the majority of effector T cells die once the antigen or pathogen is cleared. A small subset of T cells remains after antigen is cleared, the memory T cells. These memory cells can respond more rapidly than naive cells to recall antigen, and are also capable of homeostatic self-renewal. During the development of T cell memory, there are dramatic changes in gene transcription, protein expression and post-translational modification of proteins, compared to naive and effector T cells. Our labs have described some of these changes at the phenotypic level, and have found important distinctions in the glycotypes of naive, effector and memory T cells. However, there has not been a systematic examination of differential glycosyltransferase expression among these T cell populations. Gene expression during the development of T-cell memory: After naive T cells are exposed to a new antigen (or pathogen), expansion of antigen-specific T cells creates an effector T cell population, the majority of which dies once antigen is cleared. A small subset, the memory T cells, remains after antigen is cleared. Using the LCMV system in P14 TCR transgenic mice specific for the DbGP33-41 epitope of LCMV, RNA (triplicate samples) was isolated from FACS-sorted virus-specific CD8+ T-cell populations during a time course following viral infection. The time points are day 0, day 8 (the peak of T-cell expansion following viral infection), day 15 (during the contraction or apoptotic phase), day 22 (during the transitional phase), and day 40 or later (the stable memory phase). The RNA samples were analyzed by Glyco-gene Chip analysis.
2011-01-07 | E-GEOD-26479 | biostudies-arrayexpress
Project description:Assessment of sources of non-biological (technical) variability in the processing of RNA samples and gene chips during microarray analysis. The purpose of this experiment was to measure technical variability in microarray data introduced by various steps in preparation of the RNA, amplification/labeling of the RNA and hybridization of the sample to the arrays on separate days. The experimental design utilized a single tissue source - homogenized brain tissue pooled from 3 eight week old male C57/Bl mice. Variables examined include: I) Technician extracting RNA (technician #1 prepared Pools 1 and 2; technician #2 prepared pools 3 and 4). II) RNA extraction (Pools 1-4 represent four independent RNA extractions from 3 homogenized pooled whole mouse brains from 8 week old male C57/B6 mice) III) Independent RNA labeling/amplification reactions - three performed from each RNA pool labeled A, B and C) and IV) Day of hybridization to GLYCOv1 arrays (labeled samples were hybridized to arrays over 3 days - 11/14/02, 11/15/02 and 11/18/02). 32 samples made it through to completion generating a high quality .CEL file for analysis. Four samples failed at various steps in the preparation/hybridiztion. All samples were male 8 week old C57/Bl mouse brain total RNA.
2010-12-11 | E-GEOD-26008 | biostudies-arrayexpress
Project description:Our laboratory has held a long interest in the glycosylation changes seen on the surface of airway epithelia of patients with the disease cystic fibrosis (CF). Experiments from our laboratory have detailed a CF glycosylation phenotype of increased Fuca1,3/4 and decreased Fuca1,2 and sialic acid on the surfaces of immortalized and primary CF cells compared to non-CF cells. Further, we have shown that gene transfer and subsequent expression of a wild type CF plasmid in CF airway cells results in correction or reversal of this glycosylation phenotype. We hypothesize that the changes in glycosylation seen in CF cells are key in the pathophysiology of the cystic fibrosis airway disease. For example, it has been shown that Pseudomonas aeruginosa, a bacterium that has a predilection for colonizing CF airways, adheres to asialylated glycolipids and glycoconjugates with terminal Fuca1,3/4. One focus of our laboratory is to elucidate the etiology of the glycosylation changes seen in CF cells and the mechanism by which these changes are reversed by wild type CFTR gene transfer. We propose to study the gene expression of immortalized and primary CF and non-CF airway epithelial cells: 1. CF/T43 vs. BEAS-2B cells. These are two widely used immortalized airway cell lines that we have used extensively in the past. 2. C38 cells; C38 cells are IB3 cells expressing wtCFTR. The experimental focus is to elucidate the etiology of the glycosylation changes seen in Cystic Fibrosis (CF) cells and the mechanism by which these changes are reversed by wild type CFTR gene transfer. To do so, the gene expression of immortalized and primary CF and non-CF airway epithelial cells were compared and studied. Cell lines used were CF/T43 and BEAS-2B, both widely used immortalized airway cell lines. Other cell lines studied included C38 cell lines (clonal derivatives of IB3 cells expressing wtCFTR).
2011-01-07 | E-GEOD-26482 | biostudies-arrayexpress
Project description:Dr. Clausen's laboratory is interested in the structure, biosynthesis and genetic regulation of glycoconjugates, with a major focus on mucins. This laboratory is studying the glycosylation and secretion process of mucins and biological functions involving mucins. This lab is also interested in receptor modulation mediated by glycosylation or through glycosphingolipids. RNA samples from two human pancreatic cell lines. The relevance of the variable expression levels of isoforms belonging to the polypeptide GalNAc-transferase gene-family is still a puzzle to us. The polypeptide GalNAc-transferase gene family is estimated to contain 24 gene-members all participating in the initiation of mucin-type O-glycosylation. It has become apparent that each of these individual isoforms have different tissue distribution profiles and kinetic capabilities. Mucin-type O-glycosylation is thus controlled, and dependent upon the repetoir of expressed GalNAc-transferases in any given organ and cell type at any given time. We have been trying to contribute to the understanding of the ordered process controlling mucin-type O-glycosylation in both normal and malignant models, and are currently investigating a pancreatic cell line model in the lab. The pancreatic tumor cell line ASPC-1 has been found to possess low metastatic potential in mouse models, in contrast to the pancreatic tumor cell line Suit-T2 possessing high metastatic potential. Immunohistochemical analysis of both cell lines, ASPC-1 and Suit-T2, using our monoclonal antibodies to 7 isoforms has revealed great differences in the expression profile of these 7 isoforms in theses two cell lines, and for instance GalNAc-T3 has been found to be highly expressed in Suit-T2 but completely lacking in ASPC-1. Two cell lines: ASPC-1 and Suit-T2 are analyzed with 3 independent replicate prepared for each cell line.
2010-12-11 | E-GEOD-26011 | biostudies-arrayexpress
Project description:Dr. Jameson's research focus is on development and regulation of lymphocytes, especially T cells. Recent work has suggested that differential glycosylation effects the sensitivity of the T cell receptors and its coreceptors, suggesting that regulation of glycosylation may be a critical element in controlling T cell development, survival and functional activity. Determination of how glycosylation enzymes/substrates change in gene expression during development of mouse CD8 T cells. Highly purified pre-selection CD4+8+ thymocytes (using transgenic/knockout mice in our colony) are compared to mature CD8 T cells from the lymph node. The goal is to build on data suggesting that this developmental step involves regulated expression of sialyltransferases (and/or neuraminidases). Highly purified pre-selection CD4+8+ thymocytes (using transgenic/knockout mice in our colony) are compared to mature CD8 T cells from the lymph node. Pre-selection CD4+8+ (DP) thymocytes were sorted from TCRa-/- thymi. Post-selection (post-positive selection) DP thymocytes came from an OT-I TCR transgenic mouse. Naïve (CD44lo) CD8 T cells from lymph node of OT-I mice were used as naïve CD8 T cells. For activated cells, naïve OT-I T cells were activated for 48 hours in vitro with cognate antigen (SIINFEKL peptide/Kb) (displayed on cell sized latex beads) in the presence of IL-2 and IL-12.
2010-12-11 | E-GEOD-26012 | biostudies-arrayexpress