Cluster analysis of C (blue), N (red) and CN (grey) expression profiles where all samples were median-centred and treated as they were independent experiments

<p><b>Copyright information:</b></p><p>Taken from "Non-coding antisense transcription detected by conventional and single-stranded cDNA microarray"</p><p>http://www.biomedcentral.com/1471-2164/8/295</p><p>BMC Genomics 2007;8():295-295.</p><p>Published online 29 Aug 2007</p><p>PMCID:PMC2020490.</p><p></p> Minimum presence per cDNA clone was set to 7 out of 9 in each data set. Histogram of pair-wise Euclidean distances over all samples for IMAGE clones. For each IMAGE in 9 dimensions, i.e. hybridization 1–9, the Euclidean distance between C and N is √(Σi = 1 (C-N)) where Cand Nis the log2ratio for C and N probe respectively for hybridization i. Histogram of distances between C and N probes for all IMAGE for each hybridization

Strand-specific end modifications (amino-linkers) are incorporated into DNA by two parallel PCR reactions

<p><b>Copyright information:</b></p><p>Taken from "Non-coding antisense transcription detected by conventional and single-stranded cDNA microarray"</p><p>http://www.biomedcentral.com/1471-2164/8/295</p><p>BMC Genomics 2007;8():295-295.</p><p>Published online 29 Aug 2007</p><p>PMCID:PMC2020490.</p><p></p> After clean-up, the PCR product for each end-modified strand is printed separately onto the same microarray glass slide. The amino terminal groups are further coupled to the glass. The probes are digested with 5'-3' T7 gene 6 exonuclease and then immersed in boiling water. As a result of this treatment, only end-modifed strands remain attached to the surface. Hybridization of labelled transcribed RNA from the β-lactamase gene with β-lactamase single-stranded sense and antisense DNA capture probes. Control spots containing ds-DNA probes or amino-modified PCR primers alone were also included on the array (not shown). Both probes and controls were spotted in 10 × 10 replicates. Scatter plot showing the distribution of raw median pixel signal intensities from the hybridization performed in (b). Signals from all replicates are clearly discriminated according to the strand from which they originated (sense or antisense). Control spots for background intensities (printing buffer, PCR and amplification primers) demonstrate the specificity of the single stranded probes

Unsupervised hierarchical clustering based on our 2188-gene signature applied to external data sets.

<p>a) Clustering based on GSE4554 and b) Clustering based on the four largest batches of the TCGA RNAseqv2 data sets. MMR proficient tumors (green), microsatellite-low tumors (blue) and MMR deficient tumors (red) along the x-axis.</p

Up-regulated signaling pathways in FCCTX and Lynch syndrome tumors.

<p>Up-regulated signaling pathways in FCCTX and Lynch syndrome tumors.</p

Clinical characteristics of the colorectal cancer subsets.

<p>Clinical characteristics of the colorectal cancer subsets.</p

qRT-PCR analysis of 5 target genes in the four different colorectal cancer subsets.

<p>Differential expression of <i>MYC, NDUFA9</i>, <i>H2AFZ</i>, <i>AXIN2</i>, and <i>DNA2</i> was done for 12 representative samples (3 from each group) and qRT-PCR ratios were normalized to rRNA18S and median centered.</p

Graphene Growth and Transfer on Ultrathin Platinum Films

abstract: Graphene is a very strong two-dimensional material with a lot of potential applications in microelectromechanical systems (MEMS). In this research, graphene is being optimized for use in a 5 m x 5 m graphene resonator. To work properly, this graphene resonator must have a uniform strain across all manufactured devices. To reduce strain induced in graphene sheets grown for use in these resonators, evaporated platinum has been used in this investigation due to its relatively lower surface roughness compared to copper films. The final goal is to have the layer of ultrathin platinum (<=200 nm) deposited on the MEMS graphene resonator and used to grow graphene directly onto the devices to remove the manual transfer step due to its inscalability. After growth, graphene is coated with polymer and the platinum is then etched. This investigation concentrated on the transfer process of graphene onto Si/SiO2 substrate from the platinum films. It was determined that the ideal platinum etchant was aqua regia at a volumetric ratio of 6:3:1 (H2O:HCl:HNO3). This concentration was dilute enough to preserve the polymer and graphene layer, but strong enough to etch within a day. Type and thickness of polymer support layers were also investigated. PMMA at a thickness of 200 nm was ideal because it was easy to remove with acetone and strong enough to support the graphene during the etch process. A reference growth recipe was used in this investigation, but now that the transfer has been demonstrated, growth can be optimized for even thinner films

Copy number estimation using targeted sequencing data.

<p>(a) Whole genome plot of HCC1395 copy number variations derived from targeted sequencing data analyzed with CONTRA in comparison to segmented Affymetrix 6.0 copy number data for the same cell line. For the sequencing data, the black datapoints are the CONTRA adjusted mean log2 ratios, and red datapoints are the CONTRA/GLAD segmented copy log2 ratios. For the Affymetrix 6.0 data, blue datapoints are the segmented copy number data. Zoomed-in plots of three selected genes, (b) <i>CDKN2A</i> and (c) <i>PTEN</i> in HCC1395, and (d) <i>ERBB2</i> in HCC1954 (color codes are as above). (e) Representative correlation plot for one cell line, HCC1395, of segmented CONTRA copy number data versus Affymetrix 6.0 segmented copy number data (Pearson r = 0.89). Correlation plots for all cell lines are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144528#pone.0144528.s002" target="_blank">S2 Fig</a>.</p

Base replacements in coding regions versus non-coding regions.

<p>Forest plot indicating odds ratio (marker) and 95% confidence intervals (whiskers) for the frequency of indicated base replacements in coding regions (CDS) versus non-coding (non-CDS) regions. The dimensions of the squares are inversely proportional to the standard error (SE) of ln(odds ratio). * P = 0.024; *** P<0.0001 (Bonferroni adjusted).</p

Hierarchical clustering of 69 tumor samples with available gene expression data

Clustering was based on 364 genes from the intrinsic gene list published by Sørlie and colleagues [] that matched our cDNA clones. Colored boxes indicate classification of each tumor into subtypes/subgroups. Filled or open boxes indicate the percentage of cells in each tumor positive for the CD44/CD24and CD44/CD24phenotypes as determined by immunohistochemistry. SR, steroid receptor. Hu classification, Hu and colleagues [].<p><b>Copyright information:</b></p><p>Taken from "The CD44/CD24phenotype is enriched in basal-like breast tumors"</p><p>http://breast-cancer-research.com/content/10/3/R53</p><p>Breast Cancer Research : BCR 2008;10(3):R53-R53.</p><p>Published online 17 Jun 2008</p><p>PMCID:PMC2481503.</p><p></p