Project description:Gene Expression Profiling of Severed Rat Medial Collateral Ligament at 1, 2, 4, 7,1 0, and 14 days Following Injury with Control and Cultured Ligament Fibroblasts and Rat Universal Reference RNA; The aim of this study was to assess the genes involved in the repair of the the dense connective tissue of the a rat ligament in order to provide targets for improvement in healing. Rat whole genome microarrays (Agilent) were used in this study and Cy3 and Cy5 labeled total RNA was extracted and labeled with Cy3 or Cy5 prior to fragmentation and hybridization. Experiment Overall Design: To conserve microarrays to allow maximum replicates, two samples either Cy3 or Cy5 labeled were hybridized to each microarry. Total RNA from each rat medial collateral ligament was labeled and hybrided to a microarray. The fluorescence intensity for each column minus the background was extracted from each microarray for submission to BRB Array tools for statistical analysis.

2008-04-05 | E-GEOD-10720 | biostudies-arrayexpress

Gene profiling of the early healing rat medial collateral ligament

2013-06-06 | GSE47676 | GEO

Gene profiling of the early healing rat medial collateral ligament

Project description:The objective of the study was to better understand the mechanism behind scar formation by identifying ECM factors and other unique genes differentially expressed during rat ligament healing via microarray. Rat medial collateral ligaments (MCL) were surgically transected or left intact. MCLs were collected at day 3 or 7 post-injury and used for microarray analysis. Results were compared to the normal intact ligaments. A total of 27 rats were used in the study. Animals were randomly placed in 1 of 3 groups (day 3, day 7, intact CX) with nine animals included with each time (9 rats/group). At the time of collection, MCLs from each time were placed into 3 pools (3 MCLs/pool), resulting in 3 reps per time, and usd for microarray analysis. A total of 9 gene chips were used for the experiment (3 chips/day).

2013-06-06 | E-GEOD-47676 | biostudies-arrayexpress

Sequencing of Rattus norvegicus synovial fibroblasts

Project description:Knee osteoarthritis (KOA), as a degenerative multifactorial disease, affects the quality of life and mental health of patients, and also brings a huge socioeconomic burden. Treating synovitis have shown promise as anti-inflammatory therapeutics in mitigating OA symptoms and disease progression. Here, by analysing synovial single-cell sequencing (scRNA-seq) data from KOA, we found that synovial fibroblasts (FLS) in OA synovium showed a distinct pro-inflammatory phenotype. We collected synovial tissue from patients with clinical OA as well as from healthy donors, and histological examination was consistent with findings in scRNA-seq. Inspired by recent cross-tissue fibroblast lineage studies, we identified by sequencing that healthy FLS in synovial tissues share transcriptome-level similarities with dermal fibroblasts (DFb). Subsequently, we revealed the local as well as systemic distribution of intra-articular injected DFbs by constructing/extracting two types of rat fibroblasts (luciferase DFbs as well as GFP DFbs). The results demonstrate that DFbs can be locally retained in the synovium for up to three weeks following targeted engrafting on it. And intra-articular injection does not result in DFbs migration to vital organs or the occurrence of histological changes in these organs. A rat model of KOA was constructed by anterior cruciate ligament transection (ACLT) in order to study the therapeutic effect of DFbs on KOA. After injection, the rats showed improvement in painful gait. In addition, histological as well as imaging results showed reduced synovitis and improvement in articular cartilage. Finally we verified the protective effect of DFbs on cytokine-stimulated chondrocytes in a co-culture system.

2026-06-24 | GSE304724 | GEO

Transcription profiling of rat to study the effect of hindlimb unloading on healing of medial collateral ligaments 3 weeks after injury

Project description:A recent physiological study established that hindlimb unloading of rats at 3 and 7 weeks inhibits healing of injured ligaments, resulting in a badly aligned, discontinuous collagen matrix. Using tissue from these rats, we focused on the 3-week time point employing microarray analysis to identify what cellular processes or lack of processes could account for these observed deficiencies. We used the Affymetrix RG_U34A GeneChip and performed image analysis with Microarray Suite 5.0. For normalization we used the MAS global normalization protocol with a default target mean signal of 500. Gene expression in medial collateral ligament tissue under 4 different treatment conditions was measured: loaded control, loaded wound healing, unloaded control, and unloaded wound healing. From our results, it appears that unloaded tissue lags behind loaded tissue in its progression through the healing process and at 3 weeks is still engaged in the proliferative phase, whereas loaded tissue is actively remodeling its collagen matrix.

2007-10-26 | E-GEOD-1105 | biostudies-arrayexpress

Sequencing of Rattus norvegicus chondrocytes under dermal fibroblast co-culture

2026-06-24 | GSE304832 | GEO

Rattus norvegicus

Project description:Rat medial prefrontal cortex gene expression following heroin self-administration, abstinence, and extinction

| PRJNA109633 | ENA

Rattus norvegicus

Project description:miRNA expression in rat medial entorhinal cortex layers during postnatal development

| PRJNA339268 | ENA