Journal: Frontiers in Genetics

Article Title: Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria

doi: 10.3389/fgene.2014.00191

Figure Lengend Snippet: World map showing genomic records for cyanobacteria generated using an interface powered by google maps, available on the Genomes Online Database (GOLD) website ( http://genomesonline.org/cgi-bin/GOLD/index.cgi ) . Red labels indicate the original location of a specifically sequenced strain. Labels direct the user to information on the organism, genome characteristics (i.e., GC content, size), sequencing method used, specific coordinates of the origin of the strain, as well as links to external databases (as shown for Prochlorococcus marinus NATL1A). The GOLD also describes the status of each record in tabular format.

Article Snippet: In the study of marine cyanobacteria, genome-level microarray analyses have frequently focused on limiting growth factors in oceans, such as iron (Thompson et al., ), nickel (Dupont et al., ), copper (Stuart et al., ), phosphate (Tetu et al., ; Ostrowski et al., ), and nitrogen (Su et al., ; Tolonen et al., ).

Techniques: Generated, Sequencing

Journal: Frontiers in Genetics

Article Title: Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria

doi: 10.3389/fgene.2014.00191

Figure Lengend Snippet: Publically available full genome sequences for cyanobacteria in various repositories as at April 2014 .

Article Snippet: In the study of marine cyanobacteria, genome-level microarray analyses have frequently focused on limiting growth factors in oceans, such as iron (Thompson et al., ), nickel (Dupont et al., ), copper (Stuart et al., ), phosphate (Tetu et al., ; Ostrowski et al., ), and nitrogen (Su et al., ; Tolonen et al., ).

Techniques:

Journal: Frontiers in Genetics

Article Title: Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria

doi: 10.3389/fgene.2014.00191

Figure Lengend Snippet: Pie chart showing records of expression data for different cyanobacteria that are currently available in the Gene Expression Omnibus (GEO) database ( http://www.ncbi.nlm.nih.gov/geo/ ) . The bias toward Synechocystis 6803 can be clearly seen in this species breakdown of transcriptomic data. Data from April 2014.

Article Snippet: In the study of marine cyanobacteria, genome-level microarray analyses have frequently focused on limiting growth factors in oceans, such as iron (Thompson et al., ), nickel (Dupont et al., ), copper (Stuart et al., ), phosphate (Tetu et al., ; Ostrowski et al., ), and nitrogen (Su et al., ; Tolonen et al., ).

Techniques: Expressing, Gene Expression

Journal: Frontiers in Genetics

Article Title: Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria

doi: 10.3389/fgene.2014.00191

Figure Lengend Snippet: Web-based analytical tools with a specific focus on cyanobacteria as at April 2014 .

Article Snippet: In the study of marine cyanobacteria, genome-level microarray analyses have frequently focused on limiting growth factors in oceans, such as iron (Thompson et al., ), nickel (Dupont et al., ), copper (Stuart et al., ), phosphate (Tetu et al., ; Ostrowski et al., ), and nitrogen (Su et al., ; Tolonen et al., ).

Techniques: Gene Expression

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