Journal: Pediatric Research

Article Title: DNA methylation of IFI44L as a potential blood biomarker for childhood-onset systemic lupus erythematosus

doi: 10.1038/s41390-024-03135-1

Figure Lengend Snippet: Childhood-onset SLE distinct mRNA expression signature.

Article Snippet: In this study, we obtained mRNA expression microarray (GSE65391) and genome-wide DNA methylation data (GSE118144) related to cSLE from the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/ ) database in the National Center for Biotechnology Information (NCBI).

Techniques: Expressing

Journal: International Journal of Clinical and Experimental Pathology

Article Title: Long non-coding RNA P4713 contributes to the malignant phenotypes of oral squamous cell carcinoma by activating the JAK/STAT3 pathway

doi:

Figure Lengend Snippet: Analysis of long non-coding RNAs (lncRNAs) in oral squamous cell carcinoma (OSCC). A: Heat map, volcano plot, and log-log scatter plot showing differentially expressed lncRNAs between four OSCC samples and paired adjacent normal tissues (fold change > 2.0, P < 0.05). B: The expression of lncRNA P4713 was detected by quantitative real-time PCR (qRT-PCR) in 22 OSCC tissues and adjacent non-cancerous tissues. The results are expressed as log10 (2-ΔΔCt). A log2 fold change ≥ +2 or ≤ -2 was considered significant upregulation or downregulation (dotted lines). C: Relative P4713 expression in OSCC cell lines was measured by qRT-PCR. Columns represent the mean of three independent experiments; bars, the s.d; *P < 0.05; **P < 0.01. D: Confocal microscopic fluorescent in situ hybridization images and qRT-PCR results. Scale bar = 10 µm. E: Genome location analysis of human P4713 by the UCSC Genome Browser. F: Representative fluorescent images of at least three independent experiments. Scale bar = 10 µm. G: Relative levels of GFP expression by Western blot.

Article Snippet: The OSCC lncRNA/mRNA microarray analysis was performed by CapitalBio Corporation (Beijing, China).

Techniques: Expressing, Real-time Polymerase Chain Reaction, Quantitative RT-PCR, In Situ Hybridization, Western Blot

Journal: International Journal of Clinical and Experimental Pathology

Article Title: Long non-coding RNA P4713 contributes to the malignant phenotypes of oral squamous cell carcinoma by activating the JAK/STAT3 pathway

doi:

Figure Lengend Snippet: The effects of P4713 on oral squamous cell carcinoma cell proliferation in vitro. A: The relative expression of P4713 was examined by qRT-PCR in HSC-3 and UM1 cells. B: Cell proliferation was measured by CCK-8 assay. C: Detection for colony-formation assays after knockdown of P4713. D: Cell cycle analysis using propidium iodide staining. E: Western blot analysis of cyclin D1, CDK4, and CDK6 after P4713 knockdown.

Article Snippet: The OSCC lncRNA/mRNA microarray analysis was performed by CapitalBio Corporation (Beijing, China).

Techniques: In Vitro, Expressing, Quantitative RT-PCR, CCK-8 Assay, Knockdown, Cell Cycle Assay, Staining, Western Blot

Journal: International Journal of Clinical and Experimental Pathology

Article Title: Long non-coding RNA P4713 contributes to the malignant phenotypes of oral squamous cell carcinoma by activating the JAK/STAT3 pathway

doi:

Figure Lengend Snippet: Silencing of P4713 suppressed the migration and invasion of oral squamous cell carcinoma (OSCC) cells. A: Inhibition of migration in HSC-3 and UM1 cells after P4713 knockdown. B: A Matrigel invasion assay was performed using an invasion chamber after treatment with si-P4713. C: In vitro migration was assessed by wound healing experiments. D: E-cadherin, N-cadherin, and vimentin were analyzed by western blotting.

Article Snippet: The OSCC lncRNA/mRNA microarray analysis was performed by CapitalBio Corporation (Beijing, China).

Techniques: Migration, Inhibition, Knockdown, Invasion Assay, In Vitro, Western Blot

Journal: International Journal of Clinical and Experimental Pathology

Article Title: Long non-coding RNA P4713 contributes to the malignant phenotypes of oral squamous cell carcinoma by activating the JAK/STAT3 pathway

doi:

Figure Lengend Snippet: The relationship between P4713 and the JAK/STAT3 pathway. (A) Hierarchically clustered heatmaps of mRNAs altered in oral squamous cell carcinoma (OSCC; fold change > 2, P < 0.05). (B) The lncRNA-P4713 subnetwork in the OSCC co-expression network. (C) The top twenty GO terms of upregulated and downregulated mRNAs in OSCC cases (P < 0.05). (D) Significantly enriched pathways of the indicated gene sets. (E) qRT-PCR and (F) western blotting were used to measure the JAK/STAT3 pathway affected by P4713. (G) Representative fluorescent images of the location of STAT3. Scale bar = 10 µm.

Article Snippet: The OSCC lncRNA/mRNA microarray analysis was performed by CapitalBio Corporation (Beijing, China).

Techniques: Expressing, Quantitative RT-PCR, Western Blot

Journal: JMA Journal

Article Title: Hepatocyte-like Cells Derived from Human Pluripotent Stem Cells Can Be Enriched by a Combination of Mitochondrial Content and Activated Leukocyte Cell Adhesion Molecule

doi: 10.31662/jmaj.2018-0042

Figure Lengend Snippet: Separation of hepatocyte-like cells and cardiomyocytes from human ESC-derived EBs. (A) FACS separation of human ESC-derived EB cells by TMRM and ALCAM labeling with the antibody. (B) Signal differences between P1 and P2 in representative hepatic and cardiac gene expression in mRNA microarray analysis. (C) Confirmation of hepatic and cardiac genes by quantitative real-time PCR in presorted-cells (Pre) and sorted cells (P1, P2, P3, and P4). All data are represented as mean ± standard deviation (SD) (n = 3). Statistical analyses were conducted via one-way ANOVA and Tukey–Kramer test. *: p < 0.05. (D) Immunohistochemical detection of α-actinin, ALCAM, and AFP in cultured P1 and P2 cells. Scale bars represent 100 μm.

Article Snippet: Total RNA of each group was extracted and applied to the comparative mRNA microarray analysis (Toray Industries, Inc., Tokyo, Japan; Chip name: Human 25k ver2.10).

Techniques: Derivative Assay, Labeling, Gene Expression, Microarray, Real-time Polymerase Chain Reaction, Standard Deviation, Immunohistochemical staining, Cell Culture

Journal: Nucleic Acids Research

Article Title: ChIP-BIT: Bayesian inference of target genes using a novel joint probabilistic model of ChIP-seq profiles

doi: 10.1093/nar/gkv1491

Figure Lengend Snippet: TF knockdown experiments for target gene validation. ( A ) Western blot of NOTCH3 protein expression after transfecting MCF-7 breast cancer cells with siRNA of NOTCH3 and scramble (SCR) for 48 h, including full length (FL), transmembrane form (TM) and intracellular domain (ICD); ( B ) mRNA expression levels of PBX1 and NOTCH3 across siRNA samples; ( C ) mRNA expression pattern of functional PBX1-NOTCH3 co-regulated target genes, which is shown in terms of the fold change (log2) of expression level for each TF knockdown experiment.

Article Snippet: We then performed microarray mRNA profiling by using Illumina HumanHT-12 v4 Expression BeadChip before and after siNOTCH3 is introduced to the cells.

Techniques: Knockdown, Biomarker Discovery, Western Blot, Expressing, Functional Assay

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