Journal: PLoS ONE

Article Title: The MicroRNA and MessengerRNA Profile of the RNA-Induced Silencing Complex in Human Primary Astrocyte and Astrocytoma Cells

doi: 10.1371/journal.pone.0013445

Figure Lengend Snippet: A hierarchical heatmap comparing global mRNA levels to RISC-IP mRNA levels in U-87 astrocytoma and primary astrocytes. MRNAs included in the heatmap had a fold change >1.4 and were significantly expressed (p<0.01).

Article Snippet: Gene expression microarray analyses of global mRNA and RISC-immunoprecipitated mRNA in primary human astrocytes and U-87 astrocytoma cells were outsourced to LC Sciences who are partnered with an Affymetrix® Authorized Service Provider, SeqWright DNA Technology Services (Houston, TX).

Techniques:

Journal: PLoS ONE

Article Title: The MicroRNA and MessengerRNA Profile of the RNA-Induced Silencing Complex in Human Primary Astrocyte and Astrocytoma Cells

doi: 10.1371/journal.pone.0013445

Figure Lengend Snippet: RISC-immunoprecipitated mRNA compared to global cellular mRNA in U-87 astrocytoma cells and primary astrocytes with a fold change > ±1.8 (p <0.01).

Article Snippet: Gene expression microarray analyses of global mRNA and RISC-immunoprecipitated mRNA in primary human astrocytes and U-87 astrocytoma cells were outsourced to LC Sciences who are partnered with an Affymetrix® Authorized Service Provider, SeqWright DNA Technology Services (Houston, TX).

Techniques: RNA Binding Assay, Sequencing

Journal: PLoS ONE

Article Title: The MicroRNA and MessengerRNA Profile of the RNA-Induced Silencing Complex in Human Primary Astrocyte and Astrocytoma Cells

doi: 10.1371/journal.pone.0013445

Figure Lengend Snippet: ( A ) MRNA microarray validation with qRT-PCR analysis in grouped RISC-IP U-87 astrocytoma and primary astrocytes samples. Grouped RISC-IP data were compared to the grouped global mRNA from U-87 astrocytoma and primary astrocytes samples. Eight mRNAs were selected from the grouped mRNA microarray dataset and examined by qRT-PCR. Fold change from the mRNA microarray are given by log2 values (left y-axis, light grey bars). Fold change from the qRT-PCR was determined using the 2 -ΔΔCt method and all mRNA expression values were normalized to the beta-actin endogenous control (right y-axis, dark grey bars). Error bars represent the standard deviation of the mean (SD). Importantly, the fold change (y-axis) cannot be directly compared between assays due to differences in calculation methods, but the general trend of up-regulation and down-regulation can be compared. ( B ) MRNAs in RISC compared to the global cellular milieu in U-87 astrocytoma cells. MRNA expression in U-87 astrocytoma cells were normalized to primary astrocytes mRNA expression. All mRNAs had a fold change >2.5 and were significantly expressed (p<0.01). Green and red arrows indicate decreased and increased levels respectively.

Article Snippet: Gene expression microarray analyses of global mRNA and RISC-immunoprecipitated mRNA in primary human astrocytes and U-87 astrocytoma cells were outsourced to LC Sciences who are partnered with an Affymetrix® Authorized Service Provider, SeqWright DNA Technology Services (Houston, TX).

Techniques: Microarray, Quantitative RT-PCR, Expressing, Standard Deviation

Journal: PLoS ONE

Article Title: The MicroRNA and MessengerRNA Profile of the RNA-Induced Silencing Complex in Human Primary Astrocyte and Astrocytoma Cells

doi: 10.1371/journal.pone.0013445

Figure Lengend Snippet: RISC-immunoprecipitated mRNA in human U-87 astrocytoma cells compared to RISC-immunoprecipitated mRNA in primary human astrocytes with a fold change >±2.6 (p <0.01).

Article Snippet: Gene expression microarray analyses of global mRNA and RISC-immunoprecipitated mRNA in primary human astrocytes and U-87 astrocytoma cells were outsourced to LC Sciences who are partnered with an Affymetrix® Authorized Service Provider, SeqWright DNA Technology Services (Houston, TX).

Techniques:

Journal: PLoS ONE

Article Title: The MicroRNA and MessengerRNA Profile of the RNA-Induced Silencing Complex in Human Primary Astrocyte and Astrocytoma Cells

doi: 10.1371/journal.pone.0013445

Figure Lengend Snippet: Bar charts display the relative number (-log(p-value)) of mRNAs with a fold change >2.5 and were considered significant (p<0.01). RISC-IP mRNA were indicated with dark blue bars and the global mRNA were indicated with light blue bars. The threshold (yellow lines) were set at p<0.01 and were calculated using Fischer's exact p-value test using IPA software.

Article Snippet: Gene expression microarray analyses of global mRNA and RISC-immunoprecipitated mRNA in primary human astrocytes and U-87 astrocytoma cells were outsourced to LC Sciences who are partnered with an Affymetrix® Authorized Service Provider, SeqWright DNA Technology Services (Houston, TX).

Techniques: Software

Journal: PLoS ONE

Article Title: The MicroRNA and MessengerRNA Profile of the RNA-Induced Silencing Complex in Human Primary Astrocyte and Astrocytoma Cells

doi: 10.1371/journal.pone.0013445

Figure Lengend Snippet: Bar charts display the relative number (-log(p-value)) of mRNAs with a fold change >2.5 and were considered significant (p<0.01). RISC-IP mRNA were indicated with dark blue bars and the global mRNA were indicated with light blue bars. The threshold (yellow lines) were set at p<0.01 and were calculated using Fischer's exact p-value test using IPA software.

Article Snippet: Gene expression microarray analyses of global mRNA and RISC-immunoprecipitated mRNA in primary human astrocytes and U-87 astrocytoma cells were outsourced to LC Sciences who are partnered with an Affymetrix® Authorized Service Provider, SeqWright DNA Technology Services (Houston, TX).

Techniques: Software

Journal: PLoS ONE

Article Title: The MicroRNA and MessengerRNA Profile of the RNA-Induced Silencing Complex in Human Primary Astrocyte and Astrocytoma Cells

doi: 10.1371/journal.pone.0013445

Figure Lengend Snippet: Specific messenger RNA fold change linked to the increased levels of miR-34a in U-87 astrocytoma RISC.

Article Snippet: Gene expression microarray analyses of global mRNA and RISC-immunoprecipitated mRNA in primary human astrocytes and U-87 astrocytoma cells were outsourced to LC Sciences who are partnered with an Affymetrix® Authorized Service Provider, SeqWright DNA Technology Services (Houston, TX).

Techniques: Permeability, Migration, Expressing, Binding Assay, Isolation

Journal: PLoS ONE

Article Title: The MicroRNA and MessengerRNA Profile of the RNA-Induced Silencing Complex in Human Primary Astrocyte and Astrocytoma Cells

doi: 10.1371/journal.pone.0013445

Figure Lengend Snippet: Specific messenger RNA fold change linked to increased levels of miR-195 in U-87 astrocytoma RISC.

Article Snippet: Gene expression microarray analyses of global mRNA and RISC-immunoprecipitated mRNA in primary human astrocytes and U-87 astrocytoma cells were outsourced to LC Sciences who are partnered with an Affymetrix® Authorized Service Provider, SeqWright DNA Technology Services (Houston, TX).

Techniques: Transduction

Journal: International Journal of Ophthalmology

Article Title: Homocysteine mediates transcriptional changes of the inflammatory pathway signature genes in human retinal pigment epithelial cells

doi: 10.18240/ijo.2017.05.06

Figure Lengend Snippet: Classification of genes identified through gene microarray analysis after Hcy exposure

Article Snippet: We analyzed ARPE-19 cells to find out the molecular changes at the transcriptional level post exposure to the Hcy treatment and obtained readouts specific for the inflammatory genomic signatures employing a microarray and bioinformatics based suite using the human gene expression microarray platform (GEArray; SA Biosciences, Frederic, MD, USA) that can profile expression of 113 key cytokines and chemokines genes involved in the inflammatory immune responses.

Techniques: Microarray

Journal: International Journal of Molecular Sciences

Article Title: ANGPTL4 Induces TMZ Resistance of Glioblastoma by Promoting Cancer Stemness Enrichment via the EGFR/AKT/4E-BP1 Cascade

doi: 10.3390/ijms20225625

Figure Lengend Snippet: Effect of specificity protein (Sp)4 on ANGPTL4 and GBM. ( A ) The protein expression of Sp1, 2, 3, and 4 in normal brain tissue and a brain tumor was validated by Western blotting. Normal brain tissue lysate: GTX27918 (Genetex); Brain tumor tissue: SF268 (Human Glioblastoma, Origene). ( B ) Left panel: heatmap of Sp4-regulated cell movement-related genes. Right panel: The results of microarray analysis after Ingenuity Pathway Analysis (IPA)-mediated function annotation. ( C ) After Sp4 knockdown for 3 days, the protein expression of ANGPTL4 and Sp4 was validated by Western blotting. ( D ) Sp4-regulated genes in which Sp4 associates with the promoter region revealed by chromatin immunoprecipitation coupled with sequencing (ChIP-Seq). ( E ) The defined promoter region of ANGPTL4 and the binding regions of Sp4 determined by ChIP-seq. ( F ) After transfection with the indicated plasmid and pGL2-ANGPTL4 promoter for 2 days, the promoter activity of ANGPTL4 were measured by a reporter assay. Data were expressed as the relative luciferase activity mean ± SEM. (*** p < 0.001). ( G ) After Sp4 overexpression for 48 h, the protein expression was validated by Western blotting. The experiments were performed three times independently, and quantitative results were expressed as the mean ± SEM (* p < 0.05).

Article Snippet: Total RNA was extracted using TRIzol reagent (15596026, Thermo Fisher Scientific) from U87MG cells following control or Sp4 siRNA knockdown for 48 h. Gene expression analysis was performed using a SurePrint G3 Human Gene Expression 8 × 60K Microarray by Welgene Biotech Co., Ltd. (Taipei, Taiwan).

Techniques: Expressing, Western Blot, Microarray, Knockdown, Chromatin Immunoprecipitation, Sequencing, ChIP-sequencing, Binding Assay, Transfection, Plasmid Preparation, Activity Assay, Reporter Assay, Luciferase, Over Expression

Journal: Journal of Cellular and Molecular Medicine

Article Title: Screening differential circular RNA expression profiles reveals the regulatory role of circMARS in anti‐tuberculosis drug‐induced liver injury

doi: 10.1111/jcmm.17157

Figure Lengend Snippet: Study flow chart. First, the difference of circRNA expression profiles between anti‐tuberculosis drug‐induced liver injury (ADLI) and non‐ADLI patients were explored. Then, a differentially expressed circRNA was selected for verification in a cohort of 300 patients. Finally, the function of this circRNA was verified in a self‐controlled cohort of 35 patients based on the results of the experimental study

Article Snippet: The circRNAs in the discovery cohort were profiled using the CapitalBio Technology CircRNA Human Gene Expression Microarray v2.0 (CapitalBio Technology, Beijing, China).

Techniques: Expressing

Journal: Journal of Cellular and Molecular Medicine

Article Title: Screening differential circular RNA expression profiles reveals the regulatory role of circMARS in anti‐tuberculosis drug‐induced liver injury

doi: 10.1111/jcmm.17157

Figure Lengend Snippet: Identification of circRNA expression profiles in ADLI. (A) The scatter plots of circRNAs expression variations in the ADLI patients and in vitro assays. The red and green points in the plot indicate the upregulated and downregulated circRNAs. (B) Venn diagrams of the co‐expression circRNAs in the serum and cells. Two drugs: cells with Isoniazid (INH) + Rifampicin (RFP); three drugs: cells with INH + RFP + Pyrazinamide (PZA)

Article Snippet: The circRNAs in the discovery cohort were profiled using the CapitalBio Technology CircRNA Human Gene Expression Microarray v2.0 (CapitalBio Technology, Beijing, China).

Techniques: Expressing, In Vitro