Journal: Frontiers in Pharmacology

Article Title: Pharmacogenomic Characterization and Isobologram Analysis of the Combination of Ascorbic Acid and Curcumin—Two Main Metabolites of Curcuma longa —in Cancer Cells

doi: 10.3389/fphar.2017.00038

Figure Lengend Snippet: Dendrograms and cluster image map of curcumin obtained by hierarchical cluster analysis of mRNA expression of 40 genes in the NCI cell line panel as analyzed by the Novartis microarray platform . The dendrogram on the left shows the clustering of cell lines and the dendrogram on the top shows the clustering of genes. The cluster image map shows each single mRNA expression value obtained by microarray analysis. The expression values have been normalized and color-coded.

Article Snippet: In the present investigation, we focused only on the Novartis microarray platform for the comparison of curcumin and vitamin C and to reduce the degree of complexity.

Techniques: Expressing, Microarray

Journal: Frontiers in Pharmacology

Article Title: Pharmacogenomic Characterization and Isobologram Analysis of the Combination of Ascorbic Acid and Curcumin—Two Main Metabolites of Curcuma longa —in Cancer Cells

doi: 10.3389/fphar.2017.00038

Figure Lengend Snippet: Dendrograms and cluster image map of vitamin C obtained by hierarchical cluster analysis of mRNA expression of 40 genes in the NCI cell line panel as analyzed by the Novartis microarray platform . The dendrogram on the left shows the clustering of cell lines and the dendrogram on the top shows the clustering of genes. The cluster image map shows each single mRNA expression value obtained by microarray analysis. The expression values have been normalized and color-coded.

Article Snippet: In the present investigation, we focused only on the Novartis microarray platform for the comparison of curcumin and vitamin C and to reduce the degree of complexity.

Techniques: Expressing, Microarray

Journal: Frontiers in Immunology

Article Title: Gill and Liver Transcript Expression Changes Associated With Gill Damage in Atlantic Salmon ( Salmo salar )

doi: 10.3389/fimmu.2022.806484

Figure Lengend Snippet: Overview of the field trial and the microarray experimental design. (A) Abiotic and biotic stressors potentially contributing to gill damage of farmed Atlantic salmon. (B) Common reference design microarray experiment. Arrows represent microarrays with the numbers of biological replicates shown next to the arrows. The base of the arrow shows the Cy3-labeled sample (i.e., common reference pool), and the arrowhead shows the Cy5-labeled sample (i.e., experimental sample). This figure was constructed using BioRender ( https://biorender.com/ ).

Article Snippet: The consortium for Genomic Research on All Salmonids Project (cGRASP)-designed Agilent 44K salmonid oligonucleotide microarray platform ( ) was utilized in the current transcriptome profiling.

Techniques: Microarray, Labeling, Construct

Journal: Frontiers in Immunology

Article Title: Gill and Liver Transcript Expression Changes Associated With Gill Damage in Atlantic Salmon ( Salmo salar )

doi: 10.3389/fimmu.2022.806484

Figure Lengend Snippet: Primers used in the gill either in the preliminary qPCR or the microarray validation experiment, including comparison between microarray Rank Products and qPCR fold-change results for Atlantic salmon transcripts responsive in moderately damaged gill.

Article Snippet: The consortium for Genomic Research on All Salmonids Project (cGRASP)-designed Agilent 44K salmonid oligonucleotide microarray platform ( ) was utilized in the current transcriptome profiling.

Techniques: Microarray, Sequencing, Amplification, Binding Assay

Journal: Frontiers in Immunology

Article Title: Gill and Liver Transcript Expression Changes Associated With Gill Damage in Atlantic Salmon ( Salmo salar )

doi: 10.3389/fimmu.2022.806484

Figure Lengend Snippet: Bar plot of gill transcripts related to gill remodeling and wound healing (panel A–U ). On the lower right side, Panel (V) shows a scatterplot of log 2 fold-change from Rank Products microarray data vs . qPCR log 2 fold-change. Different letters indicate a significant difference between groups using one-way ANOVA. Asterisk (*) shows significance (p< 0.05) between GS0 and GS2 using t-test. Gene symbols followed by a dagger (†) are associated with p-values between 0.05 and 0.10 using either t-test (GS0 vs GS2; i.e., mmp19 ) or one-way ANOVA (i.e., tnnt2 ).

Article Snippet: The consortium for Genomic Research on All Salmonids Project (cGRASP)-designed Agilent 44K salmonid oligonucleotide microarray platform ( ) was utilized in the current transcriptome profiling.

Techniques: Microarray

Journal: Frontiers in Immunology

Article Title: Gill and Liver Transcript Expression Changes Associated With Gill Damage in Atlantic Salmon ( Salmo salar )

doi: 10.3389/fimmu.2022.806484

Figure Lengend Snippet: Results of principal component analysis (PCA) plotted on two dimensions (Panel A ) for the gill differentially expressed microarray log 2 ratio (Cy5/Cy3). PC1 explained 50.72%, PC2 explained 25.49%, and PC3 explained 7.46% of the variability. Panel (B) Bar-plot of the percentage of the explained variance for each PC (dimension). Panel (C) PCA plotted on three dimensions for the gill differentially expressed microarray log 2 ratio (Cy5/Cy3) data.

Article Snippet: The consortium for Genomic Research on All Salmonids Project (cGRASP)-designed Agilent 44K salmonid oligonucleotide microarray platform ( ) was utilized in the current transcriptome profiling.

Techniques: Microarray

Journal: Oncogene

Article Title: Stem cell-like transcriptional reprogramming mediates metastatic resistance to mTOR inhibition

doi: 10.1038/onc.2016.427

Figure Lengend Snippet: mTORC1 activity concurrent with enhanced metastatic potential. ( a ) Left panels, representative immunohistochemical scores (0, negative, to 3, highest expression) of pS6 staining in the tissue microarray (TMA) of primary breast tumors. Right panel, results for the association between pS6 staining and distant metastasis. ( b ) Increased expression of mTORC1 pathway components with enhanced metastatic potential of MDA-MB-231 cells. The loading control (α-tubulin, TUBA) is shown. Bottom panel, graph showing quantifications of protein levels relative to parental and TUBA (per sample). ( c ) Increased pS6 expression in lung metastases developed by LM2 cells. The arrows mark magnified fields. Right panel, box-and-whisker plots for the quantification (pixels/area, p/a) of pS6 intensity; three mice and three similar lung metastases were analyzed in each setting. The P -value of the two-tailed Mann–Whitney test is shown. ( d ) Left panel, graph showing the in vivo photon flux quantification in mice injected with LM2 and treated with DMSO or everolimus. Representative images from bioluminescence in lungs from DMSO- or everolimus-treated mice are shown. The scale bar depicts the range of photon flux values as a pseudo-color display, with red and blue representing high and low values, respectively. Right top panels, quantification of lung colonization (total metastasis area normalized per total lung area, based on HE). Right bottom panels, representative immunohistochemical results for pS6 and quantification of normalized intensities.

Article Snippet: The RNAs were amplified using the Ribo-SPIA system (NuGEN Technologies Inc., San Carlos, CA, USA) and subsequently hybridized on the Human Genome U219 microarray platform (Affymetrix, Santa Clara, CA, USA; IRB Core Facility, Barcelona, Spain).

Techniques: Activity Assay, Immunohistochemical staining, Expressing, Staining, Microarray, Whisker Assay, Two Tailed Test, MANN-WHITNEY, In Vivo, Injection

Journal: Oncogene

Article Title: Stem cell-like transcriptional reprogramming mediates metastatic resistance to mTOR inhibition

doi: 10.1038/onc.2016.427

Figure Lengend Snippet: EVI1 couples stemness, metastatic potential and resistance to mTOR inhibition. ( a ) TCGA network of significant co-expression (PCC P -values <0.05) between EVI1 and signatures derived from stem cell-like cells and/or metastatic settings . ( b ) Distributions of PCCs between EVI1 and the commonly overexpressed 79 genes across the studied models or the complete microarray gene list as background control. The P -value of the Mann–Whitney test for the comparison of the distributions is shown. ( c ) Reduced pS6 levels with EVI1 depletion in cell models. The quantification of pS6/S6 signal ratios is show at the bottom (relative to siControl). ( d ) Ectopic overexpression of GFP-EVI1 in MCF7 (left panels) and HCC1937 (right panels) cells provides higher viability upon exposure to everolimus, relative to GFP-only overexpression. Also shown are the western blot results for defined markers across the drug-exposed cell cultures. The quantification of pS6/S6 signal ratios is show at the bottom (relative to TUBA per sample). ( e ) Increased EVI1 binding at predicted target promoters/gene loci with adaptation to everolimus. The fold changes are relative to the immunoglobulin control and the promoter gene targets are shown in the X axis. ( f ) Relative overexpression of RAPTOR and/or RHEB with adaptation to everolimus in MCF7 and HCC1937 cells. The quantification is show at the bottom (relative to untreated and TUBA per sample). ( g ) Relative reduction of RAPTOR and RHEB expression following EVI1 depletion, in particular in the everolimus-adapted setting.

Article Snippet: The RNAs were amplified using the Ribo-SPIA system (NuGEN Technologies Inc., San Carlos, CA, USA) and subsequently hybridized on the Human Genome U219 microarray platform (Affymetrix, Santa Clara, CA, USA; IRB Core Facility, Barcelona, Spain).

Techniques: Inhibition, Expressing, Derivative Assay, Microarray, MANN-WHITNEY, Over Expression, Western Blot, Binding Assay