Journal: EMBO Molecular Medicine

Article Title: LIMT is a novel metastasis inhibiting lnc RNA suppressed by EGF and downregulated in aggressive breast cancer

doi: 10.15252/emmm.201606198

Figure Lengend Snippet: RNA from the samples presented in Fig B was converted into cDNA, and levels of the indicated lncRNAs were measured using real‐time qPCR. RNA was collected at 0, 20, 40, 60, 120, 240, and 480 min after stimulation with EGF (10 ng/ml). Expression values are presented as log2 fold change relative to time zero, and they are normalized to beta‐2‐microglobulin's mRNA. Each panel depicts expression profiles determined using both microarrays (see Fig ; black) and qPCR (gray). The lncRNAs are allocated into four clusters according to their expression profile: downregulation, upregulation, transient downregulation, and transient upregulation.

Article Snippet: For Oslo2, expression was measured using SurePrint G3 Human GE 8x60K one‐color microarrays (Agilent Technologies), according to the manufacturer's protocol.

Techniques: Expressing

Journal: EMBO Molecular Medicine

Article Title: LIMT is a novel metastasis inhibiting lnc RNA suppressed by EGF and downregulated in aggressive breast cancer

doi: 10.15252/emmm.201606198

Figure Lengend Snippet: Shown are levels of two EGF‐regulated lncRNAs: the EGF‐downregulated lncRNA called LIMT (left) and the upregulated lncRNA called LOC388796 (right). RNA abundance was determined using microarrays (red) and real‐time qPCR (blue) and presented as fold change relative to time zero. Beta‐2‐microglobulin was used for normalization. Shown are Kaplan–Meier plots of overall survival and relapse‐free survival for the EGF‐regulated lncRNA called LIMT. To obtain the data, we overlapped the list of EGF‐regulated lncRNAs with the METABRIC clinical dataset (Illumina platform; left panel) and the KM‐plotter dataset (Affymetrix platform; right panel). The red and blue lines of the left panel correspond to high and low expressors, respectively (each shows one‐third of the population; 1129 out of a total of 1,693 patients). The same applies to the right panel, except that the population was divided into two equal size groups ( N = 1,660 patients). Coding potentials of clinically significant lncRNAs were calculated using CPAT, and they are individually presented along with the mean coding probabilities of control groups of protein‐coding RNAs and lncRNAs (in blue). Note that two variants of LINC00472 and LINC00652 are presented. Evolutionary conservation of the primary nucleotide sequences of the clinically significant EGF‐regulated lncRNAs was calculated using PhyloP across 100 vertebrates. Individual conservation scores are presented along with that of control groups of protein‐coding RNAs and noncoding RNAs (in blue).

Article Snippet: For Oslo2, expression was measured using SurePrint G3 Human GE 8x60K one‐color microarrays (Agilent Technologies), according to the manufacturer's protocol.

Techniques:

Journal: EMBO Molecular Medicine

Article Title: LIMT is a novel metastasis inhibiting lnc RNA suppressed by EGF and downregulated in aggressive breast cancer

doi: 10.15252/emmm.201606198

Figure Lengend Snippet: A, B Using Agilent microarrays, the expression of LIMT was assayed in all breast cancer specimens of the Oslo2 study ( N = 381). The log2 expression of LIMT in patients was plotted against the log2 expression of its neighboring coding genes, RHOF (A) and SETD1B (B). Pearson correlation values are indicated. C LIMT was stably overexpressed or transiently knocked down (using siRNAs) in MCF10A cells. RNA was processed and hybridized to Affymetrix gene expression microarrays. Shown are expression levels of 48 selected genes, which showed a significant fold change of at least 1.5 under at least one of the conditions. Genes are presented in two clusters according to their response to manipulation of LIMT (OX, overexpression; KD, knockdown). Highlighted are genes that have previously been implicated in cancer progression or regulation of cell migration.

Article Snippet: For Oslo2, expression was measured using SurePrint G3 Human GE 8x60K one‐color microarrays (Agilent Technologies), according to the manufacturer's protocol.

Techniques: Expressing, Stable Transfection, Over Expression, Migration

Journal: Oncotarget

Article Title: Analysis of region specific gene expression patterns in the heart and systemic responses after experimental myocardial ischemia

doi: 10.18632/oncotarget.17955

Figure Lengend Snippet: A. Venn diagram showing up-regulated genes with significant changes in all three areas of myocardium 24h after induction of acute myocardial infarction compared to control myocardium (CZ). Infarct core zone (IZ, n = 2483); border zone (BZ, n = 285); remote myocardium zone (RZ, n = 135). B. Venn diagram showing downregulated genes with significant changes in all three areas of myocardium 24h after induction of acute myocardial infarction compared to control myocardium (CZ). Infarct core zone (IZ, n = 6420); border zone (BZ, n = 71); remote myocardium zone (RZ, n = 78). C. Principal Component Analysis displaying mRNA expression data of the different areas of infarcted hearts and untreated healthy hearts. Infarct core zone (IZ, red dots); border zone (BZ, orange dots); remote myocardium (RZ, grey dots); control zone (CZ, blue dots). D. Validation of microarray results by RT-PCR. mRNA levels of nine selected genes were quantified by RT-PCR. Shown are mean ± SD of log FC values. RT-PCR data were normalized to beta-actin.

Article Snippet: To produce Cy3-labeled cRNA, the RNA samples were amplified and labelled using the Agilent Whole Porcine Genome Oligo Microarray (one-color).

Techniques: Expressing, Microarray, Reverse Transcription Polymerase Chain Reaction