Transcriptomes From the Deep Cones During FIbroproliferative Cutaneous Healing in the Duroc/Yorkshire Porcine Model
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PROVIDER: PRJNA135171 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The goal was to obtain the differential transcriptome in the deep cones between shallow and deep wounds and between the Yorkshire and Duroc breeds over time.
2011-12-31 | GSE26095 | GEO
Project description:The goal was to obtain the differential transcriptome in the deep cones between shallow and deep wounds and between the Yorkshire and Duroc breeds over time. We made shallow and deep wounds on the backs of 3 Yorkshire and 3 Duroc pigs, biopsied the wounds at 1 2 3 12 and 20 weeks, extracted and amplified the RNA from the deep cones, and hybridized the Affymetrix GeneChip®. We compared wound depth by breed over time; the system included 3 factors (depth, breed and time). The system also included repeated measures since the same pigs were used at each time. It also included paired data since the shallow and deep wounds compared were located on the same pig.
2011-12-31 | E-GEOD-26095 | biostudies-arrayexpress
Project description:Sus scrofa strain:Duroc, Landrace, Yorkshire Metagenome
| PRJNA263439 | ENA
Project description:During the past decades there has been minimal improvement in prevention and treatment of hypertrophic scarring. Reasons include the lack of a validated animal model, imprecise techniques to dissect scar into the histologic components, and limited methodology for measurement of gene expression. These problems have been addressed with the Duroc/Yorkshire model of healing, laser capture microdissection, and the Affymetrix Porcine GeneChip. Here we compared collagen gene expression in fibroproliferative healing in the Duroc breed to nonfibroproliferative healing in the Yorkshires. We made shallow and deep dorsal wounds, biopsied at 1, 2, 3, 12, and 20 weeks. We sampled the dermal cones by laser capture microdissection, extracted and amplified the RNA, and hybridized Affymetrix Porcine GeneChips. We also obtained samples of human hypertrophic scar approximately 20 weeks postinjury. Data were normalized and statistical analysis performed with mixed linear regression using the Bioconductor R/maanova package. Genes for further analysis were also restricted with four biologic criteria, including that the 20-week deep Duroc expression match the human samples. Eleven collagen genes and seven collagen types were differentially over expressed in deep Duroc wounds including 1a1, 1a2, 3a1, 4a1, 4a2, 5a1, 5a2, 5a3, 6a3 (transcript variant 5), 14a1 and 15a1. COL7a1 gene was differentially under expressed in deep Duroc wounds. The results suggest that collagens I, III, IV, V, VI, VII, XIV, and XV [corrected] are involved in the process of fibroproliferative scarring. With these clues, we will attempt to construct the regulatory pathway(s) of fibroproliferative healing.
| S-EPMC2853751 | biostudies-literature
Project description:Duron and Yorkshire burn model study: mapping of transcriptome of Yorkshire and red Duroc pig breed during cutaneous burn-wound healing.
| PRJNA706694 | ENA
Project description:The goal was to obtain the differential transcriptome in the deep cones fibroblasts between shallow and deep wounds in Duroc breeds at 20 wks.
2011-09-30 | GSE29768 | GEO
Project description:The goal was to obtain the differential transcriptome in the deep cones fibroblasts between shallow and deep wounds in Duroc breeds at 20 wks. We made shallow and deep wounds on the backs 2 Duroc pigs, biopsied the wounds at 20 weeks, cultured fibroblasts, extracted and the RNA from the cultured fibroblasts, and hybridized the Affymetrix GeneChip. We compared wound depth, the system included 1 factors (depth). The system also included repeated measures since the same pigs were used at each time. It also included paired data since the shallow and deep wounds compared were located on the same pig.
2011-09-29 | E-GEOD-29768 | biostudies-arrayexpress
Project description:The experiment aimed at studying gene expression differences in longissimus dorsi muscle from pigs from two groups: High versus low intramuscular fat (IMF). The animals were selected from a crossbred population of Landrace x Yorkshire/Landrace x Duroc animals, where we have previously found a highly significant QTL for IMF (Grindflek et al. 2001: "Detection of quantitative trait loci for meat quality in a commercial slaughter pig cross", Mammalian Genome 12(4): 299-304), and by microarray analysis we hoped to identify candidate genes for the QTL and/or pathways that are affected by the genes responsible for the QTL. Keywords: phenotype comparison
2013-01-01 | GSE12927 | GEO
Project description:Hypertrophic scar was first described over 100 years ago; PubMed has more than 1,000 references on the topic. Nevertheless prevention and treatment remains poor, because 1) there has been no validated animal model; 2) human scar tissue, which is impossible to obtain in a controlled manner, has been the only source for study; 3) tissues typically have been homogenized, mixing cell populations; and 4) gene-by-gene studies are incomplete.We have assembled a system that overcomes these barriers and permits the study of genome-wide gene expression in microanatomical locations, in shallow and deep partial-thickness wounds, and pigmented and non-pigmented skin, using the Duroc(pigmented fibroproliferative)/Yorkshire(non-pigmented non-fibroproliferative) porcine model. We used this system to obtain the differential transcriptome at 1, 2, 3, 12 and 20 weeks post wounding. It is not clear when fibroproliferation begins, but it is fully developed in humans and the Duroc breed at 20 weeks. Therefore we obtained the derivative functional genomics unique to 20 weeks post wounding. We also obtained long-term, forty-six week follow-up with the model.1) The scars are still thick at forty-six weeks post wounding further validating the model. 2) The differential transcriptome provides new insights into the fibroproliferative process as several genes thought fundamental to fibroproliferation are absent and others differentially expressed are newly implicated. 3) The findings in the derivative functional genomics support old concepts, which further validates the model, and suggests new avenues for reductionist exploration. In the future, these findings will be searched for directed networks likely involved in cutaneous fibroproliferation. These clues may lead to a better understanding of the systems biology of cutaneous fibroproliferation, and ultimately prevention and treatment of hypertrophic scarring.
| S-EPMC3080398 | biostudies-literature
Project description:The experiment aimed at studying gene expression differences in longissimus dorsi muscle from pigs from two groups: High versus low intramuscular fat (IMF). The animals were selected from a crossbred population of Landrace x Yorkshire/Landrace x Duroc animals, where we have previously found a highly significant QTL for IMF (Grindflek et al. 2001: "Detection of quantitative trait loci for meat quality in a commercial slaughter pig cross", Mammalian Genome 12(4): 299-304), and by microarray analysis we hoped to identify candidate genes for the QTL and/or pathways that are affected by the genes responsible for the QTL. Keywords: phenotype comparison Direct dye-swap design, with 14 animals in each group (high IMF and low IMF) on 14 separate arrays
2013-01-01 | E-GEOD-12927 | biostudies-arrayexpress