Microarray expression analysis of patients Dupuytren´s contracture (DC)
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Ivana Ratkaj
PROVIDER: E-GEOD-31356 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The objective of this study was to analyze gene expression associated to extracellular matrix components of normal palmar fascia and tissues affected by Dupuytren's disease. We used microarrays to detail the global programme of gene expression associated to Dupuytren's disease. Total RNA was isolated from three different samples corresponding to two different individuals with Dupuytren's disease: Dupuytren's diseased contracture cords (DDC), palmar fascia clinically unaffected by Dupuytren's disease contracture (NPF), and normal forehand fascia (NFF).
2014-07-25 | E-GEOD-59746 | biostudies-arrayexpress
Project description:We used a high-throughput technology, DNA microarray, to screen the entire genome for the changes in gene expression in diseased tissue to characterize Dupuytren's contracture at a molecular level and find genes that are involved in development of the disease.
2011-08-13 | GSE31356 | GEO
Project description:Dupuytren's contracture (DC) is the most common inherited connective tissue disease of humans and is hypothesized to be associated with aberrant wound healing of the palmar fascia. Fibroblasts and myofibroblasts are believed to play an important role in the genesis of DC and the fibroproliferation and contraction that are hallmarks of this disease. This study compares the gene expression profiles of fibroblasts isolated from DC patients and controls in an attempt to identify key genes whose regulation might be significantly altered in fibroblasts found within the palmar fascia of Dupuytren's patients. Total RNA isolated from diseased palmar fascia (DC) and normal palmar fascia (obtained during carpal tunnel release; 6 samples per group) was subjected to quantitative analyses using two different microarray platforms (GE Code Link™ and Illumina™) to identify and validate differentially expressed genes. The data obtained was analyzed using The Significance Analysis of Microarrays (SAM) software through which we identified 69 and 40 differentially regulated gene transcripts using the CodeLink™ and Illumina™ platforms, respectively. The CodeLink™ platform identified 18 upregulated and 51 downregulated genes. Using the Illumina™ platform, 40 genes were identified as downregulated, eleven of which were identified by both platforms. Quantitative RT-PCR confirmed the downregulation of three high-interest candidate genes which are all components of the extracellular matrix: proteoglycan 4 (PRG4), fibulin-1 (FBLN-1) transcript variant D, and type XV collagen alpha 1 chain. Overall, our study has identified a variety of candidate genes that may be involved in the pathophysiology of Dupuytren's contracture and may ultimately serve as attractive molecular targets for alternative therapies. Dupuytren's contracture and may ultimately serve as attractive molecular targets for alternative therapies. 6 Samples from carpal-tunnel derived fibroblasts and 6 Samples from Dupuytren's contracture-derived fibroblasts were hybridized to Illumina's Sentrix Human-6 Expression Beadchip and GE Code Link arrays.
2010-04-16 | E-GEOD-21221 | biostudies-arrayexpress
Project description:Dupuytren's contracture (DC) is the most common inherited connective tissue disease of humans and is hypothesized to be associated with aberrant wound healing of the palmar fascia. Fibroblasts and myofibroblasts are believed to play an important role in the genesis of DC and the fibroproliferation and contraction that are hallmarks of this disease. This study compares the gene expression profiles of fibroblasts isolated from DC patients and controls in an attempt to identify key genes whose regulation might be significantly altered in fibroblasts found within the palmar fascia of Dupuytren's patients. Total RNA isolated from diseased palmar fascia (DC) and normal palmar fascia (obtained during carpal tunnel release; 6 samples per group) was subjected to quantitative analyses using two different microarray platforms (GE Code Link™ and Illumina™) to identify and validate differentially expressed genes. The data obtained was analyzed using The Significance Analysis of Microarrays (SAM) software through which we identified 69 and 40 differentially regulated gene transcripts using the CodeLink™ and Illumina™ platforms, respectively. The CodeLink™ platform identified 18 upregulated and 51 downregulated genes. Using the Illumina™ platform, 40 genes were identified as downregulated, eleven of which were identified by both platforms. Quantitative RT-PCR confirmed the downregulation of three high-interest candidate genes which are all components of the extracellular matrix: proteoglycan 4 (PRG4), fibulin-1 (FBLN-1) transcript variant D, and type XV collagen alpha 1 chain. Overall, our study has identified a variety of candidate genes that may be involved in the pathophysiology of Dupuytren's contracture and may ultimately serve as attractive molecular targets for alternative therapies. Dupuytren's contracture and may ultimately serve as attractive molecular targets for alternative therapies.
2010-04-16 | GSE21221 | GEO
Project description:Dupuytren's disease (DD) is characterized by nodular fibroblastic proliferation of the palmar fascia leading to contracture of the hand. We performed a cDNA microarray analysis of DD palmar cord tissue. Normal-appearing palmar fascia adjacent to the diseased cord from the same patient and palmar fascia from patients undergoing carpal tunnel release were used as controls. A type II microarray experiment was used on amplified sample RNA. Samples were hybridized to arrays containing 42,000 gene elements. Array data was analyzed with the on-line software from the Stanford Microarray Database. A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Type: disease_state_design Series_overall_design: Computed Keywords: other
2010-06-11 | E-GEOD-2688 | biostudies-arrayexpress
Project description:Dupuytren's disease (DD) is characterized by nodular fibroblastic proliferation of the palmar fascia leading to contracture of the hand. We performed a cDNA microarray analysis of DD palmar cord tissue. Normal-appearing palmar fascia adjacent to the diseased cord from the same patient and palmar fascia from patients undergoing carpal tunnel release were used as controls. A type II microarray experiment was used on amplified sample RNA. Samples were hybridized to arrays containing 42,000 gene elements. Array data was analyzed with the on-line software from the Stanford Microarray Database. A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Type: disease_state_design Series_overall_design: Computed Keywords: other
2006-05-19 | GSE2688 | GEO
Project description:Osteosarcoma (OS) is the primary bone tumor in children and young adults. Currently, there are no reliable, non-invasive biological markers to detect the presence or progression of disease, assess therapy response, or provide upfront prognostic insights. Using a qPCR-based platform that analyzes more than 750 miRNAs, we analyzed control and diseased-associated plasma from human cases of OS to identify a profile of differentially expressed miRNAs. Comprehensive miRNA expression profiling was completed using the Exiqon miRNome platform (human panels I+II, V3) on 20 disease samples (10 localized, 10 metastatic) and 15 healthy controls.
2015-01-17 | E-GEOD-65071 | biostudies-arrayexpress
Project description:Identification of differentially expressed genes in fibroblasts derived from patients with Dupuytren's Contracture
| PRJNA126535 | ENA
Project description:Florida’s coral reefs are currently experiencing a multi-year disease-related mortality event, that has resulted in massive die-offs in multiple coral species. Approximately 21 species of coral, including both Endangered Species Act-listed and the primary reef-building species, have displayed tissue loss lesions which often result in whole colony mortality [Stony Coral Tissue Loss Disease (SCTLD)]. Determining the causative agent(s) of coral disease relies on a multidisciplinary approach since the causation may be a combination of abiotic, microbial or viral agents. Metaproteomics was used to survey changes in the molecular landscape in the coral holobiont with the goal of providing useful information not only in diagnosis, but for prediction and prognosis. Specifically, in the case of SCTLD, defining molecular changes in the coral holobiont will help define disease progression and aid in identifying the causative agent by clearly defining traits of disease progression shared across affected species. Using samples from nine coral species (46 samples total; those appearing healthy, n = 23, and diseased, n = 23), analysis of the coral and its associated microbiome were performed using bottom-up proteomics. Ongoing analysis (including improving coral holobiont genome-based search space) will demonstrate the utility of this approach and help define improved future experiments.
2021-05-21 | PXD026192 | Pride
Project description:Understanding the mechanisms by which long-term memories are formed and stored in the brain represents a central aim of neuroscience. Prevailing theory suggests that long-term memory encoding involves early plasticity within hippocampal circuits, while reorganization of the neocortex is thought to occur weeks to months later to subserve remote memory storage. Here we report that long-term memory encoding can elicit early transcriptional, structural and functional remodeling of the neocortex. Parallel studies using genome-wide RNA-sequencing, ultrastructural imaging, and whole-cell recording in wild-type mice suggest that contextual fear conditioning initiates a transcriptional program in the medial prefrontal cortex (mPFC) that is accompanied by rapid expansion of the synaptic active zone and postsynaptic density, enhanced dendritic spine plasticity, and increased synaptic efficacy. To address the real-time contribution of the mPFC to long-term memory encoding, we performed temporally precise optogenetic inhibition of excitatory mPFC neurons during contextual fear conditioning. Using this approach, we found that real-time inhibition of the mPFC inhibited activation of the entorhinal-hippocampal circuit and impaired the formation of long-term associative memory. These findings suggest that encoding of long-term episodic memory is associated with early remodeling of neocortical circuits, identify the prefrontal cortex as a critical regulator of encoding-induced hippocampal activation and long-term memory formation, and have important implications for understanding memory processing in healthy and diseased brain states. 4 biological replicates per group were analyzed. The material analyzed was medial prefrontal cortex (mPFC; anterior cingulate cortex subregion) from both brain hemispheres, from which total RNA was extracted.
2014-06-16 | E-GEOD-58510 | biostudies-arrayexpress