E-MTAB-3186
Ontology highlight
ABSTRACT:
DISEASE(S): Normal,Post-traumatic Osteoarthritis
PROVIDER: E-MTAB-3186 | ExpressionAtlas | 2019-05-02
REPOSITORIES: ExpressionAtlas
Similar Datasets
Project description:Synovium mRNA expression data derived from a pig model of post-traumatic osteoarthritis. Samples were collected from both knees of control pigs (n=6x2=12) and injured knees of pigs that went under unilateral anterior cruciate ligament transection 1, 5, 9 and 14 days after surgery (n=6 per time-point).
2015-03-01 | E-MTAB-3186 | biostudies-arrayexpress
Project description:Injury to anterior cruciate ligament (ACL) is common in young individuals and a frequent cause of functional instability and early onset of osteoarthritis. The healing potential of an injured ACL is known to decay over time. The molecular origin of this healing deficiency largely remains elusive but plausibly involves gene transcripts associated with tissue healing. To explore this possibility, we set out to identify transcript expression differences in injured ACL remnants recovered at the time of surgical reconstruction, via microarray (n=24) and RNA-seq (n=8) technologies in transcriptome profiling. We found that time-from-injury was an important determinant of changes in gene expression signatures predominately resulting in repression of several biological processes as identified by gene ontology. The most interesting observation was a time-dependent decline in the gene transcripts as well as the biological processes common to both microarray and RNA-seq analyses. Compared to acute tears, in chronic several important biological processes were namely extracellular matrix organization, angiogenesis, cell adhesion, wound healing, mesenchyme transition, and response to hypoxia. Furthermore, the cross-platform concordance in terms of differentially expressed transcripts or enriched pathways was linearly correlated (r=0.64). Microfluidic digital PCR confirmed the expression of selected differentially expressed transcripts. These intriguing findings suggest an initial attempt of the injured ACL to repair, which drops with time. These findings have implications for efforts to repair the ACL and may be relevant for its reconstruction. These findings also emphasize the utility of differentially expressed transcripts as prognostic biomarkers in patients with ACL injury. Examination of transcript expression differences by time-from-injury in anterior cruciate ligament
2015-01-30 | E-GEOD-65469 | biostudies-arrayexpress
Project description:This dataset includes 2*76bp RNA-seq reads from 9 pigs sequenced using Illumina NextSeq500.
| EGAD00001009783 | EGA
Project description:We describe the effects of Treg ST2 expression on muscle regeneration. We compare regneration from cryo-injured tibialis anterior muscle from Foxp3-Cre/ST2-flox vs Foxp3-Cre mice 8 days post-injury. These analyses from whole muscle provide insight into the role of muscle Tregs in the context of regeneration. The tibialis anterior muscle from male Foxp3-Cre/ST2 flox or Foxp3-Cre/ST2 WT C57BL/6 mice (2 months old) were cryo-injured using a liquid nitrogen chilled metal probe for 8 seconds. 8 days post-injury whole muscle was harvested and snap frozen in liquid nitrogen. Whole muscle was then homogenized directly in TriZol and gene expression profiling was performed on Affymetrix Mouse Gene 1.0 ST Arrays.
2016-01-10 | E-GEOD-76697 | biostudies-arrayexpress
Project description:RNA-Seq has been an effective method for exploring pathology-associated transcriptional changes in peripheral blood. The main goal of this study is to explore the expression changes of transcripts in the peripheral blood of sick pigs which may be infected with multiple pathogens on farms. We aim to find a subset of marker genes which may be useful candidate genes in the evaluation and prediction of health status in pigs under commercial production conditions.
2020-03-15 | GSE96640 | GEO
Project description:Raw data from E-MTAB-1585 was normalized by using reads per million. https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585/ Strand specific RNA-Seq data E-MTAB-1585 was normalized and subtracted control from knockdown to generate tracks that more clearly displayed the unusual pattern of RNA expression caused by knockdown of 7SK. The following wig files were generated from multiple samples (i.e.raw data files), as indicated in the 'readme.txt' file. 7sk_3p_KD_norm.wig: 7SK 3P Knockdown normalized 7sk_3p_KDF_norm.wig: 7SK 3P Knockdown normalized (Forward) 7sk_3p_KDR_norm.wig: 7SK 3P Knockdown normalized (Reverse) 7sk_5p_KD_norm.wig: 7SK 5P Knockdown normalized 7sk_5p_KDF_norm.wig: 7SK 5P Knockdown normalized (Forward) 7sk_5p_KDR_norm.wig: 7SK 5P Knockdown normalized (Reverse) 7sk_Control_norm.wig: 7SK Control normalized 7sk_ControlF_norm.wig: 7SK Control normalized (Forward) 7sk_ControlR_norm.wig: 7SK Control normalized (Reverse) 7sk_3p_KDF-ControlF.wig: 7SK 3P Knockdown-Control (Forward) 7sk_3p_KDR-ControlR.wig: 7SK 3P Knockdown-Control (Reverse) 7sk_5p_KDF-ControlF.wig: 7SK 5P Knockdown-Control (Forward) 7sk_5p_KDR-ControlR.wig: 7SK 5P Knockdown-Control (Reverse)
2013-09-19 | E-GEOD-50860 | biostudies-arrayexpress
Project description:Utilizing glycerol and cardiotoxin (CTX) injections in the tibialis anterior muscles of M. musculus provides models of skeletal muscle damages followed by skeletal muscle regeneration. In particular, glycerol-induced muscle regeneration is known to be associated with ectopic adipogenesis. We characterized genome-wide expression profiles of tibialis anterior muscles from wild-type mice injured by either glycerol or CTX injection. Our goal was to detect gene expression changes during the time course of glycerol-induced and CTX-induced muscle regeneration models, that can lead to ectopic adipocyte accumulation. Tibialis anterior muscle of 12 week old wildtype C57BL/6J male mice injected i.m with either glycerol or CTX were collected 3, 7, 14 or 21 days after injection. 6 biological replicates were used for each time points. Please note that a few replicate samples did not pass QC test, thus, were removed from the submission. Unchallenged tibialis anterior muscles from a group of 5 wildtype C57BL/6J mice were also as a control. Total RNA was extracted, QCed and hybridized to Affymetrix microarrays.
2013-08-16 | E-GEOD-45577 | biostudies-arrayexpress
Project description:To gain insight into the role of testosterone in modulating hepatic fat accumulation, we collected liver tissues from high fat diet-fed intact male pigs, castrated male pigs, and castrated male pigs with testosterone replacement. RNA-Seq was employed to profile hepatic gene expression in pigs with different testosterone levels.
2015-01-08 | GSE62696 | GEO