Optimization of cDNA microarrays procedures using criteria that do not rely on external standards-5

<p><b>Copyright information:</b></p><p>Taken from "Optimization of cDNA microarrays procedures using criteria that do not rely on external standards"</p><p>http://www.biomedcentral.com/1471-2164/8/377</p><p>BMC Genomics 2007;8():377-377.</p><p>Published online 18 Oct 2007</p><p>PMCID:PMC2147032.</p><p></p

Optimization of cDNA microarrays procedures using criteria that do not rely on external standards-4

<p><b>Copyright information:</b></p><p>Taken from "Optimization of cDNA microarrays procedures using criteria that do not rely on external standards"</p><p>http://www.biomedcentral.com/1471-2164/8/377</p><p>BMC Genomics 2007;8():377-377.</p><p>Published online 18 Oct 2007</p><p>PMCID:PMC2147032.</p><p></p> lines NRK52E and AR42J) compared to self-self hybridization (rat cell line AR42J). The samples were hybridized to rat 15 k cDNA duplicates under six different blocking conditions including no blocker, 1000 ng poly(dA), and 25 to 1000 ng LNA dT blocker. Dye-swap and self self were performed for all blocking conditions (total of 24 hybridizations). Green-labelled samples are placed at the tail and red labelled samples at the head of the arrows

Optimization of cDNA microarrays procedures using criteria that do not rely on external standards-1

<p><b>Copyright information:</b></p><p>Taken from "Optimization of cDNA microarrays procedures using criteria that do not rely on external standards"</p><p>http://www.biomedcentral.com/1471-2164/8/377</p><p>BMC Genomics 2007;8():377-377.</p><p>Published online 18 Oct 2007</p><p>PMCID:PMC2147032.</p><p></p

Characteristic patient features at the time of surgery.

<p>eGFR was calculated with the MDRD formula. The staging was performed based on the EAU Guidelines on renal cell carcinoma: 2014 update [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0149743#pone.0149743.ref043" target="_blank">43</a>].</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

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

Development of a candidate marker for ccRCC.

<p>(A) Expression values of <i>CA9</i> correctly classified 30 of 32 samples in our FFPE dataset. (B) Whisker plot of expression value distribution in our FFPE dataset for <i>CA9</i>. (C) Scatterplot for the expression values of <i>CA9</i> in our FFPE and in our RNAlater dataset. (D) <i>CA9</i> expression values correctly classify 139 out of 144 samples in a microarray dataset of ccRCC (GSE53757). (E) Distribution of <i>CA9</i> expression values for normal (NO) and ccRCC tumor samples (TU) in the GSE53757 dataset. (F) Stratification of the expression values of overexpressed <i>CA9</i> into all four stages of ccRCC [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0149743#pone.0149743.ref014" target="_blank">14</a>].</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

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

Gene network.

<p>The most differentially affected network with the central role of <i>TGFB1</i> in (A) FFPE samples and B) RNAlater data sets. <i>Proteins with cancer involvement are marked with purple outline</i>. <i>Red fill indicates overrepresentation of the gene in ccRCC</i>, <i>green indicates under-representation</i>. <i>Color intensity reflects range of fold change</i>.</p