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: Journal of Cancer

Article Title: Modulation of Wnt Activity and Cell Physiology by Butyrate in LT97 Microadenoma Cells

doi: 10.7150/jca.8569

Figure Lengend Snippet: Venn diagrams of microarray data. (A) Venn diagram for “within treatment” comparison of differentially expressed genes in mock or butyrate treatments across cell lines (>3Fold, 9,096 probes). 99 intersection probes are differentially expressed in opposite directions. 2,685 intersection probes are differentially expressed in the same direction. (B) Venn diagram for “within cell lines” comparison of differentially expressed genes in mock treated control (Ctrl) vs. butyrate (NaB) treatments of two cell lines (>3Fold, 8,335 probes). 165 intersection probes are differentially expressed in opposite directions. 1,986 intersection probes are differentially expressed in the same direction.

Article Snippet: After treatment with or without 5 mM butyrate for 17.5 hr, cells were washed with 1 x PBS, scraped into PBS and pelleted; the pellets were snap frozen in liquid nitrogen and sent to Genus Biosystems for RNA extraction and microarray analyses, utilizing the Agilent human whole genome oligo microarray.

Techniques: Microarray, Comparison, Control

Journal:

Article Title: Gene expression profiling in autoimmune non-infectious uveitis disease

doi:

Figure Lengend Snippet: Scatter plot analysis of gene expression profiling on uveitis patients demonstrates differential gene expression. cDNA microarray analysis on 50 RNA samples from uveitis patients and 1 pooled sample from controls was performed. After normalization on house-keeping genes, e.g, GAPDH and beta-2-microglobulin (B2M), the final scores of each of the genes of all arrays were compared to those from the control array. The scatter plot was acquired as described in the Materials and Methods. The Y-axis represents log scores from uveitis patients (group 2) and the X-axis represents log scores from normal controls (group 1). Each symbol represents one gene with red-colored ones represent 2-fold higher expressed in uveitis patients (group 2), green-colored ones represent 2-fold lower expressed in uveitis patients and the black-colored ones represent within 2-fold cut-off threshold.

Article Snippet: Probes were hybridized to a pathway-specific cDNA microarray chip (Inflammatory and autoimmune GEArray; SuperArray Inc., Gaithersburg, MD).

Techniques: Gene Expression, Microarray, Control

Journal:

Article Title: Gene expression profiling in autoimmune non-infectious uveitis disease

doi:

Figure Lengend Snippet: Clustergram analysis of gene expression revealed 4 distinct gene expression profiles. cDNA microarray was performed as described above and clustergram analysis on microarray data was described in the Materials & Methods section. X-axis represents all genes listed in the cDNA microarray chip and Y-axis depicts gene expression profiles from all samples of uveitis patients normalized on normal controls. Each colored band represents expression of a single gene from one patient when compared to that from normal donors with higher expression in red and lower expression in green. Groups I, II, III and IV designate 4 sub-groups of gene expression profiles. Analysis of gene expression profiling among uveitis patients revealed 4 sets of genes designated as molecular signatures A, B, C and D that can be used to define the 4 sub-groups of gene expression profiles.

Article Snippet: Probes were hybridized to a pathway-specific cDNA microarray chip (Inflammatory and autoimmune GEArray; SuperArray Inc., Gaithersburg, MD).

Techniques: Gene Expression, Microarray, Expressing

Journal:

Article Title: Gene expression profiling in autoimmune non-infectious uveitis disease

doi:

Figure Lengend Snippet: Comparison of clustergram analysis of gene expression profiling of 2 male siblings (designated as patient A and patient B) with the same diagnosis of intermediate uveitis with that from normal controls (designated as NL). The cDNA microarray and clustergram analysis were performed as described above and in the Materials and Methods. The X-axis listed all the gene symbols in the cDNA microarray chips. The gene expression profiles from the 2 male siblings with the same diagnosis of intermediate uveitis (designated as patient A and patient B) were aligned with the profile from normal subjects (NL). As described above, each colored band represents expression of a single gene from either patient A or patient B or from normal subjects after normalization on house keeping genes, with higher expression in red and lower expression in green.

Article Snippet: Probes were hybridized to a pathway-specific cDNA microarray chip (Inflammatory and autoimmune GEArray; SuperArray Inc., Gaithersburg, MD).

Techniques: Comparison, Gene Expression, Biomarker Discovery, Microarray, Expressing