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: 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