Technical comparison of qRT-PCR experiments with the GLYCOv2 custom array
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Steven Head
PROVIDER: E-GEOD-27595 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Gene expression patterns were surveyed using RNA from 4 different murine sources.
2011-03-02 | GSE27595 | GEO
Project description:The project is aimed at understanding the role of the Lex-containing L5 carbohydrate epitope in the developmental process of neural induction. We plan to identify 1) the protein to which the L5 glycan is attached, 2) glycosyltransferases upregulated during neural induction, 3) the corresponding L5 carbohydrate binding protein (CBP), 4) the mechanism of interaction between L5 and its CBP, and 5) the spatiotemporal regulation of L5 and L5-CBP expression during neural induction. There is evidence, by Westernblot and immunofluorescence, that the expression of the Lewis-x-like L5 carbohydrate epitope shows dramatic differences in expression between undifferentiated cells and cells differentiated with retinoic acid. We wish to know which enzyme(s) involved in the biosynthetic pathway may be up/downregulated under these experimental conditions. Two classes of p19 mouse embryonal carcinoma cell RNA were analyzed: undifferentiated and differentiated with retinotic acid. Classes were prepared in triplicate for a total of 6 samples. All samples were hybridized to the custom designed CFG GLYCOv2 glycogene array.
2011-03-02 | E-GEOD-27596 | biostudies-arrayexpress
Project description:This laboratory's focus is on the immune response to carbohydrate antigens, with an emphasis on modalities to analyze and to increase the immune response. We are also interested in carbohydrate drug targeting. The hypothesis is that these 2 variants have different cell surface carbohydrate expression, which results in different adhesion patterns, which ultimately results in different metastasis patterns. Evidence for expression differences and loss of the variants ability to metastasize to the lung could have clinical implications in the prevention of metastasis to different organs. The 4T1 mouse metastatic breast cancer cell line is known to change with passages in culture. Our data has shown changes cause the cells to metastasize to the intestine rather than to the lung. Four classes of RNA were analyzed: one each from 4T1 metastatic cell line variant #1, 4T1 variant #2, non-metastatic cell lines 4T07, and non-metastatic cell line 67NR. Classes were prepared in triplicate for a total of 12 samples. All samples were hybridized to the custom designed CFG GLYCOv2 glycogene array.
2011-02-17 | E-GEOD-27354 | biostudies-arrayexpress
Project description:Dr. Liu's research group is interested in studying the expression and functions of galectin-3, -7 and -12, in particular the roles of these proteins in inflammation and neoplasm. Members of the galectin family are known to participate in cellular homeostasis by modulating cell growth, controlling cell cycle progression, and inducing or inhibiting apoptosis. It is known that some galectins have similar functions. However, it is not fully understood whether they work cooperatively or not. Recent reports suggest that gal-3 deficiency may induce changes in cellular homeostatic mechanisms, leading to changes in expression of other galectins and galectin-related proteins. To analyze the coordinate regulation of galectins in the face of gal-3 deficiency, gene expression patterns of gal-3 / and gal-3 -/- keratinocytes exposed to UVB were compared. Murine epidermal keratinocytes from gal-3 / and gal-3 -/- mice will be irradiated with 200 J/m2 of UVB. Total RNA will be extracted at 0, 6, 12 and 24 h after irradiation. Classes were prepared in triplicate for a total of 24 samples. All samples were hybridized to the custom designed CFG GLYCOv2 glycogene array.
2011-03-02 | E-GEOD-27599 | biostudies-arrayexpress
Project description:This laboratory focuses on the molecular mechanisms of neuropsychiatric and neurodegenerative disorders Gene expression patterns from the pefrontal cortical region (Brodmann Area 46) of subjects with schizophrenia and age- and sex-match control subjects was analyzed. The prefrontal cortex was chosen since it is a primary brain region implicated in the pathophysiological of schizophrenia. Furthermore, this region was used in our previous proteomics studies, allowing for the direct comparison of changes in protein levels to gene expression results. 16 schizophrenic subjects were studied, consisting of 8 subjects with duration of illness (DOI) < 5 years and 8 subjects with DOI > 22 years. 16 age- and sex-matched controls were also studied. Gene expression profiles were analyzed from individual subjects; a total of 32 samples were hybridized to the custom designed CFG GLYCOv2 glycogene array.
2011-02-17 | E-GEOD-27356 | biostudies-arrayexpress
Project description:The major focus of Dr. Argueso's research is to characterize the carbohydrate portion of the different mucins expressed by the ocular surface epithelia as well as the enzymes involved with their synthesis, and to determine whether the alteration of mucin glycosylation is associated with ocular surface disease. Highly glycosylated mucins on the ocular surface (cornea and conjunctiva) are the first line of defense of the eye against injury and infection. Changes in O-glycosylation of mucins may cause ocular surface disorders, such as dry eye. Gene expression patterns in the conjunctival epithelium of three normal subjects were analyzed. The three subjects have the same ABO-blood-group. For each donor, conjunctival cells were obtained by impression cytology. Conjunctival impression cytology was performed on each eye two times with a one-week interval. Conjunctival cells obtained from each individual were pooled and the RNA isolated. All three samples were hybridized to the custom designed CFG GLYCOv2 glycogene array.
2011-03-02 | E-GEOD-27593 | biostudies-arrayexpress
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. This study seeks the role of carbohydrate-based recognition system in the pathogenesis of glaucoma. In this study, RNA preparations of four normal and five glaucoma TM samples harvested over the last year from cadavers were hybridized and analyzed using the GLYCOv2 array. We have an NIH RO3 grant award to study the role of carbohydrate-based recognition system in the pathogenesis of glaucoma. In particular, it is known that a carbohydrate-binding protein, ELAM, serves as a marker for glaucoma. Other preliminary studies in my lab have shown that galectin-8 plays a role in the adhesion and spreading of trabecular meshwork cells (TM; the cells which modulate ocular pressure) and galectin-3 influences phagocytic capacity of TM cells. These studies suggest that galectins as well as ELAM and their counterreceptors may contribute to the pathogenesis of glaucoma. We would therefore like to compare glycogene expression patterns of normal and glaucomatous TM tissue. To this end, last month we submitted RNA preparations of five each of normal and glaucoma TM tissue harvested over the last year from cadavers. The data of these samples are now being analyzed. Meanwhile, we have analyzed RNA preparations of TM cells grown in culture from five normal and six glaucoma eyes. It is our hope that data from the two projects will enable us conclusively identify glycogenes which are differentially expressed in normal and glaucoma TM cell. Overall, the goal is to shed light on the role of carbohydrate-based recognition system and the carbohydrate-binding proteins in the pathogenesis of glaucoma.
2011-02-04 | E-GEOD-27058 | biostudies-arrayexpress
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:The mitochondrial superoxide dismutase (SOD2) is a major antioxidant protein which detoxifies superoxide anion radicals generated by mitochondrial respiration (Weisiger and Fridovich, J. Biol. Chem. 1973). We designed a model of oxidative stress-induced anemia caused by SOD2-deficiency (Friedman et al. J. Exp. Med. 2001). Our previous work showed that mice reconstituted with SOD2-deficient hematopoietic stem cells develop an anemia with striking similarity to human sideroblastic anemia (SA) (Friedman et al. Blood 2004; Martin et al. Exp Hematol 2005). Our overall goal was to define early events in the pathogenesis of SOD2-deficiency SA and, in particular, to identify genes involved in the response of erythroid progenitors to oxidative stress. We compared gene expression of sorted TER-119+ CD71+ erythroblasts from SOD2-/- ('KO') versus Sod2+/+ ('WT') hematopoietic stem cell recipients using cDNA microarrays. Samples used in this study were re-hybridized with GLYCOv2 oligonucleotide arrays. GLYCOv2 oligonucleotide arrays are custom Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA) designed for the Functional Glycomics Gateway, collaboration between the Consortium for Functional Glycomics (CFG, http://www.functionalglycomics.org/) and Nature Publishing Group. A complete description of the array can be found at http://www.functionalglycomics.org/static/consortium/resources/resourcecoree.shtml . Hybridization results and quality control details can be found at https://www.functionalglycomics.org/glycomics/publicdata/microarray.jsp , by clicking on the ‘Raw Data’ icon link for microarray experiment ‘Jeff Friedman 1: Sod2 KO anemic mice’. Briefly but importantly, one Sod2-/- sample, which was prepared separately, and whose GAPDH 3'/5' ratio was off range, was legitimately removed from the analysis of the GLYCOv2 and 430 2.0 arrays. Keywords: Genotype comparison, genetic modification
2008-08-06 | GSE8726 | GEO
Project description:Hydrocortisone (HC) and triiodothyronine (T3) have both been shown to be capable of independently inhibiting hyaluronate (HA, hyaluronic acid) synthesis in a self-assembled human dermal equivalent (human dermal matrix). We sought to investigate the action of these two hormones in concert on extracellular matrix formation and HA inhibition in a tissue engineered human dermal matrix. RNA preparations were sent to CFG Microarray Core (E). Three replicate samples from each condition were used in the study. The RNA was amplified, labeled, and hybridized to the GLYCOv4 microarrays.
2015-04-08 | E-GEOD-56616 | biostudies-arrayexpress