Collagen fibrils were analyzed using transmission electron microscopy (TEM).

<p>Collagen fibril diameter distribution and average fibril diameter per tumor in 4T1 (n = 7 and n = 5) tumors (A, B), showed a shift towards thinner fibrils in SCID integrin α11-deficient (α11-KO) mice. RM11 tumors (n = 4 and n = 3) (C, D) and dermis (n = 4 and n = 3) (E, F) showed no significant differences in average collagen fibril diameter in SCID integrin α11 wild type (WT) and SCID integrin α11-deficient (α11-KO) mice (RM11 p = 0.20, dermis p = 0.47) using unpaired two-tailed t-test. Mean ± SD. * p < 0.006. Representative TEM images of collagen fibrils from both genotypes in 4T1 tumors (G, H), RM11 tumors (I, J) and dermis (K, L) are shown. Scale bars indicate 0.2 μm.</p

Image analysis of collagen in Picrosirius Red stained sections under polarised light.

<p>Collagen content is expressed as the percent of positive pixels to all pixels. * denotes P<0.05 compared to the contralateral kidney (CL). # denotes P<0.05 compared to OK in Mmp2+/+.</p

Representative images of Picrosirius Red stained sections under polarised light from the obstructed kidney (OK, 3 B, D, F) compared to the contralateral kidney (CL, 3 A, C, E).

<p>There is a higher level of collagen in Mmp2+/+ OK (3 B) compared to OK in both Mmp2+/- and Mmp2-/- (3 D, F). Only minimal levels of collagen are detected in CL kidneys across all groups (3 A, C, E).</p

Histomorphometric quantification of H & E -stained lungs from the 4T1 model from SCID integrin α11 wild type (WT) (n = 4) and SCID integrin α11-deficient (α11-KO) (n = 5) mice.

<p>Average number of metastasis per section (A) and average area per section (B) is shown. The horizontal lines indicate the mean values. No significant differences were observed (p = 0.73 and p = 0.79) using Mann U Whitney t-test and unpaired two-tailed t-test, respectively. A representative lung with metastasis from a WT mouse is shown (C, D). Scale bar indicates 100 μm.</p

Representative images of Period Acid-Schiff (PAS) stained transversal sections showing increased morphological damage in the Mmp2+/+ obstructed kidney (OK, 1B) compared to the other groups (1 D, F).

<p>The Mmp2+/+ OK (1B) shows severe hydronephrosis and inflammation of the renal pelvis, while the Mmp2-/- OK (1F) and Mmp2+/- OK (1D) only display slight dilatation and minimal inflammation. The contralateral kidneys (CL, 1 A, C, E) do not differ from each other and show normal morphology.</p

Morphological damage in the obstructed kidney (OK, 2B, D, F) compared to the contralateral kidney (CL, 2 A, C, E).

<p>All OK kidneys show tubular dilatation, flattened tubular epithelium with loss of brush border and reactive nuclear enlargement. Only Mmp2+/+ OK (2B) shows necrotic tubules (asterix) and many apoptotic cells (arrows). The morphology of the CL kidney is normal. (PAS stain).</p

Pathway signature of VEGF and NOTCH mediated EMT in ccRCC.

<p>Comparison of gene expression data from the FFPE and from the RNAlater^® dataset with published results [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0149743#pone.0149743.ref020" target="_blank">20</a>] and between themselves. <i>F = FFPE samples</i>, <i>R = RNAlater</i>^<i>®</i> <i>samples</i>, <i>Numbers = fold change of up-regulation (red) or down-regulation (blue)</i>.</p

Gene expression analyses.

<p>The 20 most up- or down-regulated genes in the FFPE data set with corresponding RNAlater^® values (upper panel), and the 20 most up- or down regulated genes in the RNAlater^® dataset with corresponding FFPE values (lower panel), filtered by adjusted p-value≤0.05. Rank indicates the rank of the gene within the list of differentially genes sorted by largest to smallest absolute fold change. 14 genes are shared between the two lists. <i>TU</i>: <i>tumour</i>, <i>NO</i>: <i>normal</i>, <i>FC</i>: <i>fold change</i>, <i>ND</i>: <i>not detected</i>, <i>did not pass the expression filter</i>.</p

Correlation of gene expression data.

<p>The correlation of commonly differentially expressed genes is given with respect to (A) average expression and (B) log2 fold changes.</p

Immunohistochemistry and mRNA plots.

<p>(A) Immunohistochemistry of UMOD, NTPX2 and CA9. <i>Magnification x20</i>, <i>scale bar 50 μm</i>. (B) Respective mRNA abundance plots in the FFPE and in the RNAlater^® datasets.</p