Gene expression screening during early granulation tissue formation (II)
Ontology highlight
ABSTRACT:
ORGANISM(S): Rattus norvegicus
PROVIDER: GSE19749 | GEO | 2010/12/07
SECONDARY ACCESSION(S): PRJNA122217
REPOSITORIES: GEO
Similar Datasets
Project description:Subcutaneous implantation of cellulose sponges has been used for decades to induce vital granulation tissue formation. Illumina microarray was done in order to study the early gene expression in the granulation tissue formation. A total of six samples from six different rats was analyzed. Three samples were collected after 24 hours of implantation and three after 72 hours of implantation.
2010-12-07 | E-GEOD-19749 | biostudies-arrayexpress
Project description:Hydroxyapatite-coated cellulose induces a quicker and stronger inflammatory response compared to uncoated cellulose. Furthermore, the coated cellulose increases the homing at circulating bone-marrow derived progenitor cells. For this reason, Illumina microarray was used to study the early gene expression of the forming granulation tissue in the hydroxyapatite-coated sponges.
2010-12-07 | GSE19748 | GEO
Project description:Hydroxyapatite-coated cellulose induces a quicker and stronger inflammatory response compared to uncoated cellulose. Furthermore, the coated cellulose increases the homing at circulating bone-marrow derived progenitor cells. For this reason, Illumina microarray was used to study the early gene expression of the forming granulation tissue in the hydroxyapatite-coated sponges. A total of six samples from six different rats was analyzed. Three samples were collected after 24 hours of implantation and three after 72 hours of implantation.
2010-12-07 | E-GEOD-19748 | biostudies-arrayexpress
Project description:Proteinases play a pivotal role in wound healing by degrading molecular barriers, regulating cell-matrix interactions and availability of bioactive molecules. Matrix metalloproteinase-13 (MMP-13, collagenase-3) is a wide spectrum proteinase. Its expression and function is linked to the growth and invasion of many epithelial cancers such as squamous cell carcinoma. Moreover, the physiologic expression of MMP-13 is associated e.g. to scarless healing of human fetal skin and adult gingival wounds. While MMP-13 is not found in the normally healing skin wounds in human adults, it is expressed in mouse skin during wound healing. Thus, mouse wound healing models can be utilized for studying the role of MMP-13 in the events of wound healing. As the processes such as the migration and proliferation of keratinocytes, angiogenesis, inflammation and activation of fibroblasts are components of wound repair as well as of cancer, many results received from wound healing studies are also adaptable to cancer research. Classically, the process of wound healing can be devided into three phases which are histologically and functionally separate but temporally overlapping: 1) hemostasis and inflammation, 2) re-epithelialization and granulation tissue formation, and 3) matrix remodeling. Granulation tissue is formed into the wound via fibroplasia, angiogenesis and extracellular matrix (ECM) deposition by fibroblasts. Granulation tissue is rich in inflammatory cells, fibroblasts, myofibroblasts and blood vessels. After epidermal recovery, the granulation tissue is resolved via matrix remodeling and cell apoptosis. A sterile viscose cellulose sponge (VCS) characterized by defined size and structure can be used to experimentally induce formation of subcutaneous granulation tissue. Compared to normal granulation tissue, this model allows easy examination of the granulation tissue in its entirety but leaving out epidermal keratinocytes in the sample preparation. In this study, we studied the role of MMP-13 in the formation of mouse VCS-induced granulation tissue. We performed gene expression profiling of the granulation tissue samples of Mmp13-/- (KO) and wild type (WT) mice harvested at day 7, day 14 and day 21 after VCS implantation.
2012-08-08 | GSE38822 | GEO
Project description:Proteinases play a pivotal role in wound healing by degrading molecular barriers, regulating cell-matrix interactions and availability of bioactive molecules. Matrix metalloproteinase-13 (MMP-13, collagenase-3) is a wide spectrum proteinase. Its expression and function is linked to the growth and invasion of many epithelial cancers such as squamous cell carcinoma. Moreover, the physiologic expression of MMP-13 is associated e.g. to scarless healing of human fetal skin and adult gingival wounds. While MMP-13 is not found in the normally healing skin wounds in human adults, it is expressed in mouse skin during wound healing. Thus, mouse wound healing models can be utilized for studying the role of MMP-13 in the events of wound healing. As the processes such as the migration and proliferation of keratinocytes, angiogenesis, inflammation and activation of fibroblasts are components of wound repair as well as of cancer, many results received from wound healing studies are also adaptable to cancer research. Classically, the process of wound healing can be devided into three phases which are histologically and functionally separate but temporally overlapping: 1) hemostasis and inflammation, 2) re-epithelialization and granulation tissue formation, and 3) matrix remodeling. Granulation tissue is formed into the wound via fibroplasia, angiogenesis and extracellular matrix (ECM) deposition by fibroblasts. Granulation tissue is rich in inflammatory cells, fibroblasts, myofibroblasts and blood vessels. After epidermal recovery, the granulation tissue is resolved via matrix remodeling and cell apoptosis. A sterile viscose cellulose sponge (VCS) characterized by defined size and structure can be used to experimentally induce formation of subcutaneous granulation tissue. Compared to normal granulation tissue, this model allows easy examination of the granulation tissue in its entirety but leaving out epidermal keratinocytes in the sample preparation. In this study, we studied the role of MMP-13 in the formation of mouse VCS-induced granulation tissue. We performed gene expression profiling of the granulation tissue samples of Mmp13-/- (KO) and wild type (WT) mice harvested at day 7, day 14 and day 21 after VCS implantation. Mmp13-/- (KO) mice were generated as described (Inada et al. 2004, PNAS, 101: 17192-17197) and used in these experiments after backcrossing at least seven generations into C57BL6 mice. The WT mice were generated from the backcrossed heterozygote Mmp13-/- (KO) mice. Granulation tissues were harvested at three time points (7d, 14d, 21d) from Mmp13-/- (KO) and WT mice. One sample of each mouse was analyzed (n=3, 7d; n=4, 14d; n=4, 21d; for each genotype). The samples were processed for RNA extraction and Affymetrix 3'IVT DNA microarray gene expression analysis.
2012-08-07 | E-GEOD-38822 | biostudies-arrayexpress
Project description:There is an urgent need to identify effective medications to inhibit the abnormal airway granulation fibroblast activity, which plays a critical role in granulation tissue hyperplasia and scar formation during wound-healing after endobronchial intervention in the human airway, so as to prevent benign airway restenosis. Our previous study shown that β-elemene, a widely used effective ingredient of traditional Chinese medicine, effectively inhibited proliferation and survival of primary human airway granulation fibroblasts (PHAGF) in vitro, and promotes granulation tissue degeneration in vivo. To further investigate the mechanistic basis of these effects, we have employed LncRNA Microarray expression profiling as a discovery platform to identify differentially expressed lncRNAs and mRNAs in β-Elemene-treated PHAGF, thus enriching β-Elemene-altered pathway associated with cell proliferation and apoptosis, and thereby constructing a β-elemene-altered competitive endogenous RNAs (ceRNA) network that modulates this pathway. The results revealed ILK/Akt pathway, containing the upstream factor, ILK, the downstream cell cycle gene, Cyclin D1, and the anti-apoptosis gene, Bcl-2, were suppressed in β-Elemene-treated PHAGF. LncRNA-MIR143HG, which acts as a miR-1275 ceRNA to modulate ILK expression was also suppressed. Furhter validation via wet-lab experiments revealed that β-Elemene down-regulated LncRNA MIR143HG in PHAGF to reduce the competing sponging effect of MIR143HG on microRNA miR-1275, which targets upstream gene ILK in ILK/Akt pathway, thereby inducing the fibroblasts cell cycle arrest and apoptosis by suppressing ILK/Akt pathway.
2021-06-16 | GSE155297 | GEO
Project description:Denitrification sludge granulation Raw sequence reads
| PRJNA1166089 | ENA
Project description:Intensive research in past two decades has uncovered the presence and importance of noncoding RNAs (ncRNAs), which includes microRNAs (miRs) and long ncRNAs (lncRNAs). These two classes of ncRNAs interact to a certain extent, as some lncRNAs bind to miRs to sequester them. Such lncRNAs are collectively called 'competing endogenous RNAs' or 'miRNA sponges'. In this study, we screened for lncRNAs that may act as miRNA sponges using the publicly available data sets and databases. To uncover the roles of miRNA sponges, loss-of-function experiments were conducted, which revealed the biological roles as miRNA sponges. LINC00324 is important for the cell survival by binding to miR-615-5p leading to the de-repression of its target BTG2 LOC400043 controls several biological functions via sequestering miR-28-3p and miR-96-5p, thereby changing the expressions of transcriptional regulators. Finally, we also screened for circular RNAs (circRNAs) that may function as miRNA sponges. The results were negative at least for the selected circRNAs in this study. In conclusion, miRNA sponges can be identified by applying a series of bioinformatics techniques and validated with biological experiments. The expressions of miRs were examined in HEK-293, HUVEC and Hs68 cells.
2016-07-06 | E-GEOD-73690 | biostudies-arrayexpress
Project description:Intensive research in past two decades has uncovered the presence and importance of noncoding RNAs (ncRNAs), which includes microRNAs (miRs) and long ncRNAs (lncRNAs). These two classes of ncRNAs interact to a certain extent, as some lncRNAs bind to miRs to sequester them. Such lncRNAs are collectively called 'competing endogenous RNAs' or 'miRNA sponges'. In this study, we screened for lncRNAs that may act as miRNA sponges using the publicly available data sets and databases. To uncover the roles of miRNA sponges, loss-of-function experiments were conducted, which revealed the biological roles as miRNA sponges. LINC00324 is important for the cell survival by binding to miR-615-5p leading to the de-repression of its target BTG2 LOC400043 controls several biological functions via sequestering miR-28-3p and miR-96-5p, thereby changing the expressions of transcriptional regulators. Finally, we also screened for circular RNAs (circRNAs) that may function as miRNA sponges. The results were negative at least for the selected circRNAs in this study. In conclusion, miRNA sponges can be identified by applying a series of bioinformatics techniques and validated with biological experiments. The expressions of miRs were examined in HEK-293 cells that were LINC00324- or LOC400043-silenced using siRNA.
2016-07-06 | E-GEOD-73689 | biostudies-arrayexpress
Project description:Intensive research in past two decades has uncovered the presence and importance of noncoding RNAs (ncRNAs), which includes microRNAs (miRs) and long ncRNAs (lncRNAs). These two classes of ncRNAs interact to a certain extent, as some lncRNAs bind to miRs to sequester them. Such lncRNAs are collectively called 'competing endogenous RNAs' or 'miRNA sponges'. In this study, we screened for lncRNAs that may act as miRNA sponges using the publicly available data sets and databases. To uncover the roles of miRNA sponges, loss-of-function experiments were conducted, which revealed the biological roles as miRNA sponges. LINC00324 is important for the cell survival by binding to miR-615-5p leading to the de-repression of its target BTG2 LOC400043 controls several biological functions via sequestering miR-28-3p and miR-96-5p, thereby changing the expressions of transcriptional regulators. Finally, we also screened for circular RNAs (circRNAs) that may function as miRNA sponges. The results were negative at least for the selected circRNAs in this study. In conclusion, miRNA sponges can be identified by applying a series of bioinformatics techniques and validated with biological experiments. Using HEK-293 cells, we performed microarray experiments (n=2) for siRNA-mediated silencing of LINC00324 and LOC40043.
2016-07-06 | E-GEOD-73683 | biostudies-arrayexpress