sirna ambion target finder software  (Thermo Fisher)

Journal: PLoS ONE

Article Title: Production of Cloned Pigs with Targeted Attenuation of Gene Expression

doi: 10.1371/journal.pone.0064613

Figure Lengend Snippet: (A) Synthetic siRNAs sequences (siRNA1, siRNA2 and siRNA3) targeting the porcine apoE mRNA. (B) Effect of the siRNAs on apoE transcripts levels in cultured porcine granulosa cells. The siRNAs were introduced into the cells by lipofection. Control cells were treated with the lipofection agent alone. Cells were harvested 48 h after treatment and apoE mRNA levels were analyzed by qRT-PCR. Values were normalized to the abundance of GAPDH mRNA. The inhibitory effect of each siRNA was compared to the control group. Values are shown as percent of the control value, as the means ± SEM (n = 3 replicates). Bars that do not share a common superscript are statistically different ( P <0.05).

Article Snippet: Three synthetic siRNAs (siRNA1, siRNA2 and siRNA3; ) targeting the porcine apoE mRNA (GI:311232) were designed using the siRNA Target Finder software from Ambion (Life Technologies Inc.).

Techniques: Cell Culture, Quantitative RT-PCR

Journal: PLoS ONE

Article Title: ShRNA-Targeted COMMD7 Suppresses Hepatocellular Carcinoma Growth

doi: 10.1371/journal.pone.0045412

Figure Lengend Snippet: COMMD7 shRNA sequences and Primer pairs for polymerase chain reaction.

Article Snippet: The sequence of short hairpin RNA (shRNA) targeting COMMD7 was designed by using shRNA Target Finder (Ambion, Austin, TX), including Bam H I and Hind III sites at its terminals, and described in .

Techniques: shRNA

Journal: PLoS ONE

Article Title: ShRNA-Targeted COMMD7 Suppresses Hepatocellular Carcinoma Growth

doi: 10.1371/journal.pone.0045412

Figure Lengend Snippet: (A) Stably-transfected HepG2 cells on fluorescence microscopy (×200). (B) qRT-PCR quantification and western blotting of COMMD7. (C) MTT assay were performed at indicated days to show the proliferative curve. ** P <0.01 vs sramble shRNA treatment.

Article Snippet: The sequence of short hairpin RNA (shRNA) targeting COMMD7 was designed by using shRNA Target Finder (Ambion, Austin, TX), including Bam H I and Hind III sites at its terminals, and described in .

Techniques: Stable Transfection, Transfection, Fluorescence, Microscopy, Quantitative RT-PCR, Western Blot, MTT Assay, shRNA

Journal: PLoS ONE

Article Title: Specific Silencing of the REST Target Genes in Insulin-Secreting Cells Uncovers Their Participation in Beta Cell Survival

doi: 10.1371/journal.pone.0045844

Figure Lengend Snippet: A . Left panel, immunoblotting of total proteins from INS-1E cells, 72 h after transfection with a negative siRNA (siNeg) or siRNAs against Cdk5r2 (siCdk5r2#1 and siCdk5r2#2). Right panel, quantification of the corresponding Cdk5r2 protein levels. Results are mean ± SEM of three independent experiments. ** P <0.01 versus values of siNeg-transduced INS-1E cells. B . Quantification of apoptotic nuclei in non-transfected INS-1E cells (NT) and INS-1E cells transfected with a negative siRNA (siNeg) or with siRNAs against Cdk5r2 (siCdk5r2#1 and siCdk5r2#2), treated 24 h with a mix of cytokines (black bars) or not (white bars). Results are mean ± SEM of six independent experiments. ** P <0.01 versus controls. C . Immunoblotting of total proteins from INS-1E cells transfected with a negative siRNA (siNeg) or siRNAs against Cdk5r2 (siCdk5r2#1 and siCdk5r2#2), treated 24 h with a mix of cytokines (Cyt) or not (Ctrl). The cleavage of caspase-9 and −3, induced by cytokines, is higher in siCdk5r2- than in siNeg-treated cells. D . Quantification of apoptotic nuclei in non-transfected INS-1E cells (NT) and INS-1E cells transfected with a negative siRNA (siNeg) or siRNAs against Cdk5r2 (siCdk5r2#1 and siCdk5r2#2), exposed 15 h to control medium (white bars) or palmitate (black bars). Results are mean ± SEM of six independent experiments. ** P <0.01 versus controls.

Article Snippet: Specific siRNAs against rat Cdk5r2 were selected using the siRNA Target Finder (Ambion, Austin, TX, USA).

Techniques: Western Blot, Transfection