ECM by granulation tissue cells, tissue sections were stained with van Gieson and Gomori’s staining methods. The statistical analyses were performed using Independent samples T-test with SPSS 16.0 software. Immunohistochemistry Formalin-fixed paraffin-embedded sections were rehydrated and processed for immunohistochemical staining with biotin-streptavidin-peroxidase complex based visualization system and using diaminobenzidine as substrate, as previously described. The primary antibodies against mouse CD34 and a-smooth muscle actin were used. For negative control staining, the primary antibodies were omitted and replaced by blocking reagent. The orientation of a-SMA-positive myofibroblasts was assessed by scoring 
as follows: weak, moderate and strong . Statistical significance was determined using Pearson’s x2-test. Blood vessel formation was assessed by determining the density of CD34 positive vessel structures in a defined area of each sample. The diameter of vessels was morphometrically analyzed with image analysis using cellD 2.6 software, and the vessels were divided into subgroups based on their diameter. Statistical significance was determined using Mann-Whitney U test. Materials and Methods Ethics statement All mouse experiments were performed according to institutional guidelines of the University of Turku and with the permission of the animal test review board of the Regional Government of Southern Finland. Experimental mouse granulation tissue model The establishment of experimental granulation tissue was performed as previously described. Wild type and MMP-13 knockout mice , were anesthetized with Hypnorm-Dormicum solution. A single vertical incision was made to dorsal skin under aseptic conditions, a sterile rectangular viscose cellulose sponge of size PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/22201214 565610 mm3 was implanted horizontally under the skin at cranial location, and the wound was closed with Gene expression profiling of mouse granulation tissue Genome wide gene expression profiling in mouse experimental granulation tissue with Affymetrix GeneChipH 39 IVT Expression Analysis was performed at The Finnish DNA Microarray and Sequencing Centre, Turku, Finland. Aliquots of total RNA were processed according to Affymetrix’s instructions and hybridized to Mouse Genome 430 2.0 oligonucleotide array. The data order GSK1363089 quality was checked with AGCC and MMP-13 in Wound Granulation Tissue Time point Genotype 7d WT Mmp132/2 14 d WT Mmp13 21 d WT Mmp132/2 2/2 + 0 3 0 0 3 0 ++ 2 3 2 2 2 2 +++ 3 0 4 3 0 3 p-value,0.05 n.s. ,0.05 Sections of experimental granulation tissue of wild-type and MMP-13 knockout mice were stained for myofibroblasts with a-SMA antibody and analyzed for myofibroblast orientation. Scoring: +, weak; ++, moderate; +++, strong. Scoring is based on the parallel orientation of myofibroblasts to the implant surface where weak implies negligible orientation, moderate implies lining of occasional myofibroblasts in certain areas, and strong indicates intensive parallel lining of myofibroblast masses. Statistical significance was determined by Pearson’s x2-test. n.s., not significant. doi:10.1371/journal.pone.0042596.t001 Expression ConsoleTM 1.1. The data were normalized between the chips using rma and subjected for statistical testing with Chipster v1.4.7 software. Statistical significances for differentially expressed genes were determined using linear modeling. The gene expression pattern was evaluated as comparison of the genotypes in a given time point. Moreover, dif
