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: Oncotarget

Article Title: Integrative transcriptomics-based identification of cryptic drivers of taxol-resistance genes in ovarian carcinoma cells: Analysis of the androgen receptor

doi:

Figure Lengend Snippet: Upregulated genes in taxol resistant SKOV3/Tx600 cells and associated transactivators

Article Snippet: Fluorescent targets were hybridized to the Human Whole Genome OneArray v6.1 microarray, which contains 31, 741 DNA oligonucleotide probes (HOA6.1; Phalanx Biotech Group) with Phalanx OneArray Plus Hybridization Protocol.

Techniques: Microarray, Inhibition, Binding Assay, Activity Assay, Cell Surface Receptor Assay, Membrane, Transformation Assay

Journal: Cell Death & Disease

Article Title: p97/VCP is highly expressed in the stem-like cells of breast cancer and controls cancer stemness partly through the unfolded protein response

doi: 10.1038/s41419-021-03555-5

Figure Lengend Snippet: a Pathways affected by p97 inhibition in MDA-MB-231 cells. b Microarray analysis of the representative up and downregulated genes. c qPCR analysis of CEBPD mRNAs from the MDA-MB-231 cells treated with 2.5 μM Eer I or NMS-873. d , e Immunoblotting analysis of C/EBPδ from the MDA-MB-231 cells treated with increasing concentration of Eer I or NMS-873 and the MDA-MB-231 cells treated with 2.5 μM Eer I or NMS-873 from 1.5 to 24 h. GAPDH serves as a loading control. f Immunoblotting of C/EBPδ from the MDA-MB-231 cells with p97 silenced. GAPDH serves as a loading control. g Mammosphere formation of Eer I-treated MDA-MB-231 cells and with CEBPD silenced. Upper: the number of spheres under each treatment. Lower: representative images. Bar: 100 μm. h Immunoblotting of C/EBPδ and SOX2 from the Eer I-treated MDA-MB-231 cells with CEBPD silenced. Data were shown as mean + SD. * P < 0.05, ** P < 0.01, and *** P < 0.001.

Article Snippet: Total RNAs were isolated from Eer I- and NMS-873-treated MDA-MB-231 cells and analyzed by Human OneArray Plus Microarray (Zhuoli Biotech, Shanghai, China).

Techniques: Inhibition, Microarray, Western Blot, Concentration Assay, Control

Journal: Biochemistry and Biophysics Reports

Article Title: SOX2 suppresses the mobility of urothelial carcinoma by promoting the expression of S100A14

doi: 10.1016/j.bbrep.2016.06.016

Figure Lengend Snippet: SOX2 binds to and regulates the expression of the S100A14 mRNA in BFTC905. (A) Recombinant SOX2 was used as a bait protein to precipitate purified the total RNA from the BFTC905 cells in in vitro pull-down assays. GST served as the negative control. The RNA was purified from supernatant and precipitated fractions, followed by microarray analysis. The genes preferentially bound by SOX2 were indicated in red. (B) BFTC905/shLuc and BFTC905/shSOX2 cells were created by infecting the BFTC905 cells with shRNA-expressing lentiviral vectors. Suppression of SOX2 was confirmed by immunoblotting. (C) Massive parallel sequencing was performed to analyze the transcriptome of the BFTC905/shLuc and BFTC905/shSOX2 cells. The genes indicated in (A) was plotted against the expression change. Red color indicates more than 2-fold change in BFTC905/shSOX2. (D) The in vitro pull-down assay was performed using GST and SOX2 as the bait proteins. The level of the S100A14 mRNA in the input, supernatant, and precipitated fractions was determined by RT-PCR. DDIT3 serves as the non-enrichment negative control. (E) The CLIP assay was performed using either control IgG or anti-SOX2 antibodies. The RNA was recovered from the supernatant and the matrix, and the presence of the S100A14 transcript was detected by RT-PCR. and (F) The level of the S100A14 protein in the BFTC905/shLuc and BFTC905/shSOX2 cells was determined by immunoblotting. α-tubulin serves as the control.

Article Snippet: Purified RNA samples were amplified using the MessageAmp aRNA kit (Thermo Fisher) and analyzed using a whole genome DNA microarray (Human OneArray, Phalanx Biotech Group, HsinChu, Taiwan).

Techniques: Expressing, Recombinant, Purification, In Vitro, Negative Control, Microarray, shRNA, Western Blot, Sequencing, Pull Down Assay, Reverse Transcription Polymerase Chain Reaction