human whole genome onearray v6.1 microarray  (Phalanx Biotech)

Journal: Cancer & Metabolism

Article Title: FOXO3a/miR-4259-driven LDHA expression as a key mechanism of gemcitabine sensitivity in pancreatic ductal adenocarcinoma

doi: 10.1186/s40170-025-00377-3

Figure Lengend Snippet: miR-4259 targets the LDHA 3’UTR and inhibits LDHA-mediated gemcitabine resistance in PDAC. ( A ) The miR-4259 expression (left) and LDHA -3’UTR luciferase activity (right) in PANC-1 and PANC-1/GEM cells was measured by RT-qPCR and a luciferase reporter assay, respectively. The RT-qPCR data were normalized to the level of U47 RNA in each individual sample. ( B ) A schematic diagram representing the predicted miR-4259-binding sequences or the mutated versions of the miRNA (left). The luciferase reporter activity (right) of the LDHA -3’UTR wild-type (+ 1 ~ + 937) and LDHA -3’UTR mutant reporters (mutant sites: 498, 498/518 and 498/518/818) were measured by a dual-luciferase reporter assay in HEK-293T cells transfected with miR-4259 and a reporter at different ratios. ( C ) The luciferase reporter activity of the LDHA -3’UTR wild-type and LDHA -3’UTR mutant reporters (triple-mutant sites, 498/518/818) in PANC-1/GEM and SUIT-2 cells and their expression of miR-4259. ( D ) The LDHA and miR-4259 expression (left) of PANC-1/GEM cells transfected with the indicated plasmids were analyzed by Western blotting and RT-qPCR, respectively. The cell viability (right) of these transfectants in the presence of gemcitabine treatment was measured by the MTT assay. ( E ) The LDHA and miR-4259 expression (left) of PANC-1 cells were analyzed by Western blotting and RT-qPCR, respectively. The cell viability ( right ) of these transfectants in the presence of gemcitabine treatment was measured by the MTT assay. The results are presented as the means ± s.e.m. of three independent experiments. * P < 0.05, ** P < 0.01, *** P < 0.001 and n.s. not significant (two-tailed Student’s t -test)

Article Snippet: Five micrograms of total RNA obtained from PANC-1 and PANC-1/GEM cells were labeled and hybridized on miRNA microarrays (using the Human miRNA OneArray ® v2 (Phalanx Biotech Group, San Diego, CA, USA).

Techniques: Expressing, Luciferase, Activity Assay, Quantitative RT-PCR, Reporter Assay, Binding Assay, Mutagenesis, Transfection, Western Blot, MTT Assay, Two Tailed Test

Journal: International Journal of Molecular Sciences

Article Title: MicroRNA Signature in an In Vitro Keratinocyte Model of Diabetic Wound Healing

doi: 10.3390/ijms251810125

Figure Lengend Snippet: Differentially expressed miRNAs with significant variances under high-glucose and hypoxic environment.

Article Snippet: Small RNAs (<200 nucleotides) were enriched using cutoff concentrators (Sartorius, Gottingen, Germany). miRNAs were labeled with Cy5 dye (ULS ® microRNA Labeling Kit, Kreatech Diagnostics, Amsterdam, Netherlands) and hybridized to human miRNA OneArray ® 4.1 microarray chips (Phalanx Biotech Group, Hsinchu, Taiwan).

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: MicroRNA Signature in an In Vitro Keratinocyte Model of Diabetic Wound Healing

doi: 10.3390/ijms251810125

Figure Lengend Snippet: Differential expression of miRNAs in HaCaT cells under high-glucose/hypoxia versus normal conditions. ( A ) Heat map and cluster dendrogram of 143 differentially expressed miRNAs. Columns represent miRNA expression at 24 h and 48 h under normal (24 hr1 and 48 hr1) and high-glucose/hypoxia (24 hr4 and 48 hr4) conditions. ( B ) Heat map and cluster dendrogram of 11 miRNAs with the highest changes on the expression levels at 24 and 48 h post-wounding (labeled with red asterisks in ( A )). This heat map shows miRNA changes after the normalization of the high-glucose/hypoxia condition over the normal condition. Subsequent qRT-PCR verification on these miRNAs is shown in .

Article Snippet: Small RNAs (<200 nucleotides) were enriched using cutoff concentrators (Sartorius, Gottingen, Germany). miRNAs were labeled with Cy5 dye (ULS ® microRNA Labeling Kit, Kreatech Diagnostics, Amsterdam, Netherlands) and hybridized to human miRNA OneArray ® 4.1 microarray chips (Phalanx Biotech Group, Hsinchu, Taiwan).

Techniques: Quantitative Proteomics, Expressing, Labeling, Quantitative RT-PCR

Journal: International Journal of Molecular Sciences

Article Title: MicroRNA Signature in an In Vitro Keratinocyte Model of Diabetic Wound Healing

doi: 10.3390/ijms251810125

Figure Lengend Snippet: Verification of the expression patterns of the cDNA microarray by qRT-PCR. ( A ) Differentially expressed miRNAs at 24 h post-wounding. ( B ) Differentially expressed miRNAs at 48 h post-wounding. A total of 11 miRNAs were selected for further verification by qRT-PCR in this study. In the figures, the relative miRNA expression levels are all expressed on a log2 scale, with data from the cDNA microarray shown in blue, and data from three independent experiments of qRT-PCR shown in red.

Article Snippet: Small RNAs (<200 nucleotides) were enriched using cutoff concentrators (Sartorius, Gottingen, Germany). miRNAs were labeled with Cy5 dye (ULS ® microRNA Labeling Kit, Kreatech Diagnostics, Amsterdam, Netherlands) and hybridized to human miRNA OneArray ® 4.1 microarray chips (Phalanx Biotech Group, Hsinchu, Taiwan).

Techniques: Expressing, Microarray, Quantitative RT-PCR

Journal: International Journal of Molecular Sciences

Article Title: MicroRNA Signature in an In Vitro Keratinocyte Model of Diabetic Wound Healing

doi: 10.3390/ijms251810125

Figure Lengend Snippet: Effects of miR-3138 mimic and miR-3679-5p inhibitor transfection on keratinocyte migration. The present experiments were performed under normal ( A – C ) and high-glucose/hypoxic conditions ( D – F ). ( A , D ) Relative miR-3138 and miR-3679-5p levels post-transfection. ( B , E ) Representative images of keratinocyte migration after the transfection with miRNA mimic and inhibitor. ( C , F ) Average wound closure percentages from three independent experiments after the transfection with miRNA mimic and inhibitor. Different letters labeled at the top of columns indicate statistically significant differences ( p < 0.05).

Article Snippet: Small RNAs (<200 nucleotides) were enriched using cutoff concentrators (Sartorius, Gottingen, Germany). miRNAs were labeled with Cy5 dye (ULS ® microRNA Labeling Kit, Kreatech Diagnostics, Amsterdam, Netherlands) and hybridized to human miRNA OneArray ® 4.1 microarray chips (Phalanx Biotech Group, Hsinchu, Taiwan).

Techniques: Transfection, Migration, Labeling

Journal: International Journal of Molecular Sciences

Article Title: MicroRNA Signature in an In Vitro Keratinocyte Model of Diabetic Wound Healing

doi: 10.3390/ijms251810125

Figure Lengend Snippet: Bioinformatic prediction of the target genes for miR-3138 ( A ) and miR-3679-5p ( B ). Venn diagrams show overlapped target numbers predicted by TargetScan (red), miRDB (green), and DIANA (blue) databases. The pairing patterns between the sequences of target gene 3’UTR and miRNA are shown below each diagram.

Article Snippet: Small RNAs (<200 nucleotides) were enriched using cutoff concentrators (Sartorius, Gottingen, Germany). miRNAs were labeled with Cy5 dye (ULS ® microRNA Labeling Kit, Kreatech Diagnostics, Amsterdam, Netherlands) and hybridized to human miRNA OneArray ® 4.1 microarray chips (Phalanx Biotech Group, Hsinchu, Taiwan).

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: MicroRNA Signature in an In Vitro Keratinocyte Model of Diabetic Wound Healing

doi: 10.3390/ijms251810125

Figure Lengend Snippet: Primers used in this study.

Article Snippet: Small RNAs (<200 nucleotides) were enriched using cutoff concentrators (Sartorius, Gottingen, Germany). miRNAs were labeled with Cy5 dye (ULS ® microRNA Labeling Kit, Kreatech Diagnostics, Amsterdam, Netherlands) and hybridized to human miRNA OneArray ® 4.1 microarray chips (Phalanx Biotech Group, Hsinchu, Taiwan).

Techniques: Sequencing

Journal: Journal of Biomedical Science

Article Title: The RNA-binding protein KSRP aggravates malignant progression of clear cell renal cell carcinoma through transcriptional inhibition and post-transcriptional destabilization of the NEDD4L ubiquitin ligase

doi: 10.1186/s12929-023-00949-9

Figure Lengend Snippet: KH-type splicing regulatory protein (KSRP) negatively regulates neural precursor cell-expressed developmentally downregulated 4 like (NEDD4L) mRNA stability via inducing miR-629-5p upregulation and targeting AU-rich elements (AREs) of the 3' untranslated region (3’UTR). A Decay rate of NEDD4L mRNA after treatment with 5 μg/mL actinomycin D for the indicated times in Caki-1 cells with or without KSRP-knockdown. B Flowchart for identifying miRNA induced by KSRP. The left part shows that TCGA miRNA sequencing data were retrieved from UCSC Xena. TCGA KIRC patients with low expression of miRNA (> 10% patients with reads per million mapped reads (RPM) of < 1) were excluded. The remaining 401 miRNAs were used to perform a differentially expressed (DE)-miRNA analysis between tumor ( n = 241) and normal tissues ( n = 70). Forty miRNAs were identified as upregulated miRNAs (with fold change (FC) of > 2 and a false discovery rate (FDR) of < 0.01) in KIRC tumor tissues. Right part shows 29 miRNAs with an FC of < 0.5 as identified in KSRP-depleted Caki-1 cells. By intersecting miRNAs upregulated in TCGA KIRC tissues with miRNAs induced by KSRP in ccRCC cells, miR-629-5p was identified as a critical candidate. C Real-time qPCR analysis of miR-629-5p in Caki-1 cells transfected with a KSRP shRNA, pEGFP-KSRP, or their corresponding control vector. D, E Caki-1 cells were transfected with an miR-629-5p mimic ( D ) or miR-629-5p inhibitor ( E ) for 24 h. NEDD4L protein levels and invasive ability of cells were respectively determined by Western blot (WB) (left panel) and Matrigel invasion (right panel) assays. F Expressions of KSRP and NEDD4L (left panel) and invasive ability of cells (right panel) were determined in Caki-1 cells transfected with pEGFP-KSRP with or without an miR-629-5p inhibitor. G Correlation between miR-629-5p and NEDD4L expression in TCGA KIRC patients as demonstrated in dot plots. Correlation coefficients and p values were evaluated by a Pearson correlation analysis. H GSEA of TCGA KIRC patients with high (top 5%) versus low (bottom 5%) expressions of miR-629-5p. A gene set of the epithelial-mesenchymal transition (EMT) derived from HALLMARK was used. The normalized enrichment score (NES) and FDR are shown in the enrichment plot. I Correlations of miR-629-5p expression with EMT markers were demonstrated in a correlation plot using miRNA sequencing data of TCGA KIRC patients. Correlation coefficients and p values were evaluated by a Pearson correlation analysis. J WB analysis of E-cadherin, N-cadherin, and vimentin expressions in Caki-1 and 786-O cells transfected with an miR-629-5p mimic. K Left panel, Schematic of the human NEDD4L-3' untranslated region (3'UTR) inserted in the luciferase reporter vector. Positions of AU-rich elements (AREs) are indicated by two gray oblongs, and the corresponding sequences are shown underneath. Right panel, Relative luciferase activities of Caki-1 cells transfected with the NEDD4L luciferase 3’UTR reporter vector containing wild-type or mutant ARE domains with or without KSRP shRNA. Values are presented as the mean ± SD of three independent experiments. ** p < 0.01, compared to the respective control groups

Article Snippet: To identify which miRNAs are regulated by KSRP, a high-throughput and specific miRNA microarray (human miRNA OneArray ® miRNA profiling chip) using Caki-1 cells with/without KSRP-KD was conducted by the Phalanx Biotech Group (Hsinchu, Taiwan).

Techniques: Knockdown, Sequencing, Expressing, Transfection, shRNA, Control, Plasmid Preparation, Western Blot, Derivative Assay, Luciferase, Mutagenesis

Journal: Frontiers in Pharmacology

Article Title: β-elemene Isopropanolamine Derivative LXX-8250 Induces Apoptosis Through Impairing Autophagic Flux via PFKFB4 Repression in Melanoma Cells

doi: 10.3389/fphar.2022.900973

Figure Lengend Snippet: Effects of LXX-8250 on PFKFB4 expression. (A) Heatmap for the representative downregulated genes in LXX-8250 (14.6 μM) treated cells compared with control cells, as evaluated by microarray analyses (fold change>1.5, p < 0.05). (B) The relative PFKFB4 mRNA expression levels in SKCM data from TCGA combined with Skin data from GTEx data. Tumor, 469 cases; Normal, 557 cases. (C,D) Real time PCR analyses for the cells treated with LXX-8250 14.6 μM, (C) ; 22.8 µΜ, (D) . (E,F) Western blot analysis for the cells treated with LXX-8250 14.6 μM, (E) ; 22.8 µΜ, (F) for the indicated times. The quantification results of the band density were labeled above the bands. Data represent mean ± SD. ** p < 0.01, *** p < 0.001.

Article Snippet: Gene microarray analyses were performed by Phalanx Biotech Group using the Human OneArray ® V7.1 microarray.

Techniques: Expressing, Control, Microarray, Real-time Polymerase Chain Reaction, Western Blot, Labeling