Hspg2C1532YNeo DBA Distal Humeral Cartilage Proteomic Comparison Dataset
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Mus Musculus (ncbitaxon:10090)
SUBMITTER: 
Sarah Calve
PROVIDER: MSV000084324 | MassIVE |
REPOSITORIES: MassIVE
Similar Datasets
Project description:Murine cartilage was dissected from the distal humerus, incubated ex vivo in culture media, and then media and residual cartilage were collected. Protein was precipitated from media and residual cartilage was physically disrupted. Protein was extracted in 4M GuHCl and digested into peptides. Mass spectra were obtained by LC-MS/MS and analyzed in silico using MaxQuant to compare relative protein abundance as a function of perlecan knockdown.
| MSV000084384 | MassIVE
Project description:The cartilage samples from patient with Internatinaol Cartilage Repair Society's Scoring 3-4 cartilage defects were analysed in order to understand the differences between healthy and damaged cartilage tissues from the knee.
2019-04-02 | GSE129147 | GEO
Project description:Objective: We used the destabilization of the medial meniscus (DMM) model to identify temporal changes in DNA methylation patterns associated with structural and transcriptomic changes in cartilage during osteoarthritis (OA) progression. Methods: RNA sequencing (RNAseq) and Reduced Representation Oxidative Bisulfite Sequencing (RRoxBS) analyses were done in total RNA and DNA obtained from micro-dissected cartilage at 4 and 12 weeks after DMM surgery. Murine and human primary chondrocytes were used to evaluate the cytokine- and methylation-dependent changes in the expression of Lrrc15, and its contribution to IL-1beta-induced changes in chondrocytes. Results: We identified time-dependent alterations in epigenomic patterns in cartilage after DMM, with significant changes in 5mC and 5hmC methylation comparing samples retrieved at 4 and 12 weeks after surgery. Integration of RNAseq and RRoxBS datasets identified Lrrc15 as a hypomethylated gene with increased expression at 4 weeks after surgery. We confirmed LRRC15 immunostaining in OA cartilage, and experiments in human and murine primary chondrocytes showed that the expression of Lrrc15 is DNA methylation-dependent and induced by IL1beta and TNFalfa in vitro. Knockdown experiments showed that Lrrc15 contributes to the IL1beta-driven expression of catabolic genes relevant to OA, including Mmp13. Significance: Our integrative analyses showed that the structural progression of OA is accompanied by transcriptomic and dynamic epigenomic changes in articular cartilage. We found that Lrrc15 is differentially methylated and expressed in OA cartilage, and that it may contribute to the cytokine-driven responses of OA chondrocytes. A better understanding of the role of Lrrc15 in cartilage homeostasis and osteoarthritis may help us uncover targets with therapeutic potential.
2021-09-01 | GSE175486 | GEO
Project description:Objective. Exercise is crucial for maintaining cartilage integrity and providing prophylaxis against the onset of osteoarthritis (OA). Here we systematically examined the exercise driven transcriptional activation/repression of genes from healthy articular cartilage to dissect the metabolic pathways responsible for its potential benefits. Methods. Healthy Sprague-Dawley rats were either not exercised (control) or subjected to daily exercise (low intensity treadmill walking) for 2, 5, or 15 days. Subsequently, articular cartilage from distal femoral heads was harvested, RNA extracted and the transcriptome-wide regulation of gene expression analyzed by Affymetrix microarray chips. Kyoto Encyclopedia of Genes and Genome (KEGG) database was used to identify the metabolic pathways regulated by exercise. Results. Microarray analysis of articular cartilage from exercised rats revealed two fold or greater up or down regulation of 926 transcripts for up to 15 days, as compared to control rat cartilage. The KEGG pathway analysis revealed that exercise transcriptionally activates/suppresses genes that encode proteins involved in regulating 123 metabolic pathways. These pathways control the biosynthesis of molecules associated with extracellular matrix, intermediate metabolites, cell signaling, cell growth and differentiation, cytoskeletal rearrangements, and inflammation including those associated with OA. Conclusions. Our findings highlight that exercise is a robust transcriptional regulator of a wide array of genes in the healthy cartilage. The actions of exercise collectively regulate metabolic pathways that are critical for strengthening cartilage while attenuating detrimental effects of proteolytic enzymes and inflammatory pathways to provide prophylaxis against inflammatory joint diseases. Sprague Dawley rats (n=5 per group, 12-14 weeks old females, Harlan Labs, IN) were housed at 5 animals/cage in individually ventilated cages with sterile Aspen bedding, and standard environmental enrichment. The cages were maintained at 12-h light/12-h dark cycle at 21°C in a pathogen free unit. All rats had ad libitum access to water and food and allowed normal cage activity. Animals randomly assigned to each group were either not exercised (Controls/Group I) or exercised (treadmill walking, 12 m/min for 45 min daily) for 2 (Group II), 5 (Group III), or 15 (Group IV) days13. Articular cartilage on the condyles of distal femurs were carefully dissected on ice under a stereomicroscope (10â15 mg/femur), immediately placed on dry ice and pulverized (3x30 seconds at 2500 RPM) in a Mikrodismembrator S (Sartorius, Germany). RNA was extracted using Trizol reagent (Invitrogen, CA), and RNA quality verified by a Bioanalyzer 2100 (Agilent, CA)13. The Whole Transcript (WT) cDNA Synthesis and Amplification Kit and WT Terminal Labeling Kit (Affymetrix, CA) were used for cDNA synthesis and labeling from 300 ng RNA template as recommended by the manufacturers. Labeled samples from 3 different rats from each group were hybridized to Affymetrix GeneChip Rat Gene 1.0 ST Array and scanned with GeneChip Scanner 3000 7G System (Microarray Shared Resource Facility, OSU Comprehensive Cancer Center)13.
2015-11-10 | E-GEOD-74898 | biostudies-arrayexpress
Project description:RATIONALE: Shark cartilage extract may help shrink or slow the growth of colorectal cancer or breast cancer cells.
PURPOSE: Randomized phase III trial to determine the effectiveness of shark cartilage in treating patients who have advanced colorectal cancer or advanced breast cancer.
| 2006841 | ecrin-mdr-crc
Project description:Objective. Identify novel genes and pathways specific to superficial (SZ), middle (MZ) and deep zones (DZ) of normal articular cartilage. Methods. Articular cartilage was obtained from knees of 4 normal human donors. The cartilage zones were dissected on a microtome. RNA was analyzed on human genome arrays. Data obtained with human tissue were compared to bovine cartilage zone specific DNA arrays. Genes differentially expressed between zones were evaluated using direct annotation for structural or functional features, and by enrichment analysis for integrated pathways or functions. Results. The greatest differences were observed between SZ and DZ in both human and bovine cartilage. The MZ was transitional between the SZ and DZ and thereby shared some of the same pathways as well as structural/functional features of the adjacent zones. Cellular functions and biological processes enriched in the SZ relative to the DZ, include most prominently ECM receptor interactions, cell adhesion molecules, regulation of actin cytoskeleton, ribosome-related functions and signaling aspects such as Interferon gamma, IL4, CDC42Rac and Jak-Stat. Two pathways were enriched in the DZ relative to the SZ, including PPARG and EGFR_SMRTE. Conclusion. These differences in cartilage zonal gene expression identify new markers and pathways that govern the unique differentiation status of chondrocyte subpopulations.
2012-08-01 | GSE39795 | GEO
Project description:Objective. Identify novel genes and pathways specific to superficial (SZ), middle (MZ) and deep zones (DZ) of normal articular cartilage. Methods. Articular cartilage was obtained from knees of 4 normal human donors. The cartilage zones were dissected on a microtome. RNA was analyzed on human genome arrays. Data obtained with human tissue were compared to bovine cartilage zone specific DNA arrays. Genes differentially expressed between zones were evaluated using direct annotation for structural or functional features, and by enrichment analysis for integrated pathways or functions. Results. The greatest differences were observed between SZ and DZ in both human and bovine cartilage. The MZ was transitional between the SZ and DZ and thereby shared some of the same pathways as well as structural/functional features of the adjacent zones. Cellular functions and biological processes enriched in the SZ relative to the DZ, include most prominently ECM receptor interactions, cell adhesion molecules, regulation of actin cytoskeleton, ribosome-related functions and signaling aspects such as Interferon gamma, IL4, CDC42Rac and Jak-Stat. Two pathways were enriched in the DZ relative to the SZ, including PPARG and EGFR_SMRTE. Conclusion. These differences in cartilage zonal gene expression identify new markers and pathways that govern the unique differentiation status of chondrocyte subpopulations.
2012-08-01 | GSE39796 | GEO
Project description:Objective. Identify novel genes and pathways specific to superficial (SZ), middle (MZ) and deep zones (DZ) of normal articular cartilage. Methods. Articular cartilage was obtained from knees of 4 normal human donors. The cartilage zones were dissected on a microtome. RNA was analyzed on human genome arrays. Data obtained with human tissue were compared to bovine cartilage zone specific DNA arrays. Genes differentially expressed between zones were evaluated using direct annotation for structural or functional features, and by enrichment analysis for integrated pathways or functions. Results. The greatest differences were observed between SZ and DZ in both human and bovine cartilage. The MZ was transitional between the SZ and DZ and thereby shared some of the same pathways as well as structural/functional features of the adjacent zones. Cellular functions and biological processes enriched in the SZ relative to the DZ, include most prominently ECM receptor interactions, cell adhesion molecules, regulation of actin cytoskeleton, ribosome-related functions and signaling aspects such as Interferon gamma, IL4, CDC42Rac and Jak-Stat. Two pathways were enriched in the DZ relative to the SZ, including PPARG and EGFR_SMRTE. Conclusion. These differences in cartilage zonal gene expression identify new markers and pathways that govern the unique differentiation status of chondrocyte subpopulations. 12 samples, 4 donors, 3 conditions each donor (SZ, MZ and DZ), 0 donor replicates, comparisons made between SZ, MZ and DZ to identify differentially expressed genes.
2012-07-31 | E-GEOD-39795 | biostudies-arrayexpress
Project description:Objective. Identify novel genes and pathways specific to superficial (SZ), middle (MZ) and deep zones (DZ) of normal articular cartilage. Methods. Articular cartilage was obtained from knees of 4 normal human donors. The cartilage zones were dissected on a microtome. RNA was analyzed on human genome arrays. Data obtained with human tissue were compared to bovine cartilage zone specific DNA arrays. Genes differentially expressed between zones were evaluated using direct annotation for structural or functional features, and by enrichment analysis for integrated pathways or functions. Results. The greatest differences were observed between SZ and DZ in both human and bovine cartilage. The MZ was transitional between the SZ and DZ and thereby shared some of the same pathways as well as structural/functional features of the adjacent zones. Cellular functions and biological processes enriched in the SZ relative to the DZ, include most prominently ECM receptor interactions, cell adhesion molecules, regulation of actin cytoskeleton, ribosome-related functions and signaling aspects such as Interferon gamma, IL4, CDC42Rac and Jak-Stat. Two pathways were enriched in the DZ relative to the SZ, including PPARG and EGFR_SMRTE. Conclusion. These differences in cartilage zonal gene expression identify new markers and pathways that govern the unique differentiation status of chondrocyte subpopulations. 6 samples, 2 bovine donors, 3 conditions each donor (SZ, MZ and DZ), 0 donor replicates, comparisons made between SZ, MZ and DZ to identify differentially expressed genes.
2012-07-31 | E-GEOD-39796 | biostudies-arrayexpress
Project description:Affymetrix Chicken Gene 1.0 ST Array (ChiGene-1_1-st) profiles were generated from growth plate cartilage derived from the distal femur and proximal tibia of embryonic chickens at three developmental stages (day 12, 13 and 15) corresponding to stages prior to and immediately after the acqusition of mechano-responsive cartilage growth in the femur but not tibia (which does not respond to mechanical stimuli until later stages). Additionally, array profiles were generated from growth plate cartilage from the distal femur and proximal tibia of E15 chicks which were pharmacologically immobilized by decamethonium bromide treatment, which reduces longitudinal growth of the femur only at this stage.
2016-12-31 | GSE77412 | GEO