Journal: RNA

Article Title: Codon optimality controls differential mRNA translation during amino acid starvation

doi: 10.1261/rna.058180.116

Figure Lengend Snippet: tRNA isoacceptors decoding rare codons are selectively enriched in translating ribosomes during amino acid starvation. ( A ) Representative tRNA microarray results obtained from HEK293 cells with or without amino acid starvation. ( B ) Heatmap showing enrichment of specific tRNAs associated with translating ribosomes during amino acid starvation. The isoacceptors for each tRNA are arranged in the decreasing order of their frequency from top to bottom . The signal obtained for each tRNA during starvation is normalized to the control. The heatmap plots the log 2 of normalized tRNA enrichment values. The color change from green to red signifies an increased association with the ribosome. This heatmap is representative of two biological replicates ( Supplemental Fig. S4C ). ( C ) Scatter plot showing the correlation between tRNA isoacceptor signals after starvation and the codon usage fraction. tRNAs without isoacceptors are not included in this analysis. The Pearson correlation coefficient is shown in the plot. ( D ) tRNA charging levels of tRNA isoacceptors in control and starvation conditions. The assay used for this qRT-PCR-based analysis was adapted from . Primers used for qPCR are described in Materials and Methods. Error bar, ±SD; (*) P < 0.05, (**) P < 0.01, (***) P < 0.001.

Article Snippet: Briefly, the labeled tRNA sample was first dissolved in microarray hybridization buffer (Sigma-Aldrich) containing 20 μg of salmon sperm DNA and 10 μg of poly(A).

Techniques: Microarray, Quantitative RT-PCR

Journal: Virus research

Article Title: Differential gene expression related to Nora virus infection of Drosophila melanogaster

doi: 10.1016/j.virusres.2013.03.021

Figure Lengend Snippet: Genes identified by cDNA microarray analysis as up-regulated by 1.5 fold or greater in Nora virus infected flies as compared to uninfected flies with a p -value of less than 0.01. The fold change was determined based on the average results of 3 microarrays and the gene names, gene ID #, and gene biological functions were identified using Flybase and NCBI GenBank.

Article Snippet: Fragmented probes were added to 40 µl of Ambion Microarray Hybridization Buffer II and denatured by heat at 95 °C for 5 min and kept at 60 °C until hybridization.

Techniques: Microarray, Infection, Activity Assay, Binding Assay

Journal: Virus research

Article Title: Differential gene expression related to Nora virus infection of Drosophila melanogaster

doi: 10.1016/j.virusres.2013.03.021

Figure Lengend Snippet: Genes identified by cDNA microarray analysis as down-regulated by 1.5 fold or greater in Nora virus infected flies as compared to uninfected flies with a p -value of less than 0.01. The fold change was determined based on the average results of 3 microarrays and the gene names, gene ID #, and gene biological functions were identified using Flybase and NCBI GenBank.

Article Snippet: Fragmented probes were added to 40 µl of Ambion Microarray Hybridization Buffer II and denatured by heat at 95 °C for 5 min and kept at 60 °C until hybridization.

Techniques: Microarray, Infection, Activity Assay, Binding Assay

Journal: Virus research

Article Title: Differential gene expression related to Nora virus infection of Drosophila melanogaster

doi: 10.1016/j.virusres.2013.03.021

Figure Lengend Snippet: Initial validation of microarray data by qRT-PCR analysis of one up-regulated (Cp16) and one down-regulated (TpnC4) gene. The light gray bars represent the mRNA levels quantified by cDNA microarray and the black bars represent the mRNA levels quantified by qRT-PCR analysis. The data from both analyses is consistent. The error bars represent the standard error of the mean and n = 3.

Article Snippet: Fragmented probes were added to 40 µl of Ambion Microarray Hybridization Buffer II and denatured by heat at 95 °C for 5 min and kept at 60 °C until hybridization.

Techniques: Microarray, Quantitative RT-PCR

Journal: Virus research

Article Title: Differential gene expression related to Nora virus infection of Drosophila melanogaster

doi: 10.1016/j.virusres.2013.03.021

Figure Lengend Snippet: Independent infection experiment to validate microarray data by qRT-PCR analysis of three up-regulated (Cp16, Fcp3c, and BtbVII) and two down-regulated (TpnC4 and CG6639) genes. The light gray bars represent the mRNA levels quantified by cDNA microarray and the black bars represent the mRNA levels quantified by qRT-PCR analysis. Cp16 and TpnC4 are shown first because they were used in the initial validation and in this experiment to provided consistency and direct data comparison. The data from the cDNA microarray and qRT-PCR analyses is consistent, as are the results between the initial validation and this subsequent experiment. The error bars represent the standard error of the mean and n = 3.

Article Snippet: Fragmented probes were added to 40 µl of Ambion Microarray Hybridization Buffer II and denatured by heat at 95 °C for 5 min and kept at 60 °C until hybridization.

Techniques: Infection, Microarray, Quantitative RT-PCR