Journal: Aging (Albany NY)

Article Title: Calycosin stimulates the proliferation of endothelial cells, but not breast cancer cells, via a feedback loop involving RP11-65M17.3, BRIP1 and ERα

doi: 10.18632/aging.202641

Figure Lengend Snippet: The effects of calycosin treatment on lncRNA profiles in HUVECs.

Article Snippet: Labeled cDNA was subjected to hybridization using the Human lncRNA OneArray Plus microarray (Phalanx Biotech Group, Taiwan), followed by scanning using an Agilent scanner (Agilent Technologies, USA).

Techniques:

Journal: Frontiers in Immunology

Article Title: Resolvin D1 Reduces Lung Infection and Inflammation Activating Resolution in Cystic Fibrosis

doi: 10.3389/fimmu.2020.00581

Figure Lengend Snippet: RvD1 regulates select genes related to microbial clearance and inflammatory signaling in CF MΦ and epithelial cells. (A) Homozygous ΔF508 peripheral blood monocyte-derived MΦ (0.5–1 × 10 6 cells/plate) and CFBEC (2.5 × 10 6 cells/plate) were treated with RvD1 (10 nM) or vehicle (0.01% EtOH) for 15 min at 37°C and infected with RP73 P. aeruginosa (∼7.5 × 10 6 CFU/plate). Medium was removed after 3 h, and total RNA was used for microarray analysis. Shown here are heat map view (Cluster 3.0, TreeView, Stanford University Labs) and scatter plots of gene expression patterns (mean from five different donors). (B) IPA findings of biological functions associated with RvD1-regulated genes in MΦ and CFBEC. (C) Top RvD1-regulated genes and associated functions identified by IPA. Blue symbols, upregulated genes; yellow symbols, downregulated genes; blue dotted lines, expression leading to activation; yellow dotted lines, expression leading to inhibition; gray dotted lines, expression leading to unpredictable effect of function; blue boxes, activated functions; yellow boxes, inhibited functions.

Article Snippet: Total RNA extracted from CFBEC and MΦ cells was linearly amplified, labeled with Cy3/5, and hybridized on HOA_007 Human Whole Genome OneArray Microarray V7 (29,264 probes; Phalanx Biotech, San Diego, CA, United States) analyzed as in ref. ( ).

Techniques: Derivative Assay, Infection, Microarray, Gene Expression, Expressing, Activation Assay, Inhibition

Journal: Journal of molecular biology

Article Title: Proteomic Analysis of Ribosomes: Translational Control of mRNA populations by Glycogen Synthase GYS1

doi: 10.1016/j.jmb.2011.04.064

Figure Lengend Snippet: Microarray profiling of polysomal fractions isolated from control siRNA- and GYS1 siRNA-treated cells. (A) HeLa cells were transfected with siRNAs and separated on gradients as shown in Figure 4B. Sucrose gradient fractions 8–9, 10–11, and 12–13 were pooled and are indicated as light, medium and heavy polysomes, respectively (see Figure 4B). PolyA-selected RNA was prepared from the gradient input fraction and the various polysomal fractions. Human whole genome oligonucleotide arrays were performed in triplicate on each sample and normalized and averaged on OneArray platforms, performed by Phalanx Biotech. (Palo Alto, CA). Samples from cells transfected with GYS1 siRNAs were compared to samples from cells transfected with control siRNAs. Cluster analysis of genes with a differential p-value of <0.1 was performed. The scale of the heat-map is presented as log2 fold-change. RNAs were categorized into four classes: (1) mRNA whose abundance was diminished in both input and polysomal samples, (2) mRNA whose abundance was diminished in the input sample, but enhanced in heavy polysomal samples, (3) mRNA whose abundance was enhanced in the input sample, but diminished in heavy polysomal fraction, (4) mRNA whose abundance was enhanced in both input and polysomal samples. Several mRNAs displaying significant changes within each of those four classes were chosen for further analysis. (B) Quantitation of selected mRNAs. Changes in total mRNA abundance of selected mRNAs by Northern blot analysis (red bars), compared to the microarray results (blue bars) of the input sample are shown.

Article Snippet: RNA was pelleted and washed as above and RNA amplification and microarrays were performed in triplicate by Phalanx Biotech (Palo Alto, CA) using OneArray oligonucleotide arrays.

Techniques: Microarray, Isolation, Control, Transfection, Quantitation Assay, Northern Blot