Journal: International Journal of Biological Sciences

Article Title: Rat Mitochondrion-Neuron Focused Microarray (rMNChip) and Bioinformatics Tools for Rapid Identification of Differential Pathways in Brain Tissues

doi:

Figure Lengend Snippet: High quality rMNChip microarray . (A) Representative microarray image of rMNChip. This pseudo-colored image represents an rMNChip microarray hybridized with the Cy5-labeled target cDNA reverse-transcribed from a rat brain RNA sample. Eight printing pinss were used to print 8 sub-arrays of rMNChip and each element was printed as a spot of technical triplicates adjacent to each other. The pixel intensities on spotted probes reflect abundances of hybridized target cDNA. (B) The inset shows details of spots morphologies of 12 genes (36 spots) with signal intensities ranging from high, to low and undetectable. (C) A table summarizes information of the genes and spots in the negative controls, positive controls, mtDNA- and nDNA-encoded test genes. The differences between the negative control and the others were highly significant (p<0.0001) while the difference between the positive control and the test spots were not statistically significant ( p >0.05), as expected.

Article Snippet: Microarray labeling and hybridization, image scanning and processing : RNA samples of rat brain tissues were purchased from Zyagen (San Diego, California).

Techniques: Microarray, Labeling, Reverse Transcription, Negative Control, Positive Control

Journal: International Journal of Biological Sciences

Article Title: Rat Mitochondrion-Neuron Focused Microarray (rMNChip) and Bioinformatics Tools for Rapid Identification of Differential Pathways in Brain Tissues

doi:

Figure Lengend Snippet: Consistency of the rMNChip microarrays and data normalization. (A) The consistency in gene expression levels between the intra and inter rMNChip microarrays hybridized with the same RNA sample. A scatter plot and fitted line of signal intensities of 1,465 informative genes between two sets of genes on Array 1 and Array 2 on Slide 1 (left panel) and Array 4 and Array 5 on Slide 2 (middle panel), and between two different rMNChip microarrays (right panel). Each array was hybridized with Cy5-labeled cDNA sample synthesized from the same RNA samples via parallel microarray experiments. The normalized (but not log-transformed) signal intensities of 1,465 informative genes from one were plotted against those of the other. The strong linear relationship (y = ax + b) and the positive coefficient of determination (r 2 ) were computed from the scatter plots and indicated in each comparison. “x”: signal intensity of a spot on one microarray, “y”: signal intensity of the corresponding spot on the other microarray. ( B) Box plots of expression data before and after normalization. The quantile normalization algorithms were used to adjust the values of the background-subtracted mean pixel intensities of each and every set of 4,395 spots across intra- and inter- rMNChip microarrays hybridized with Cy5-labeled RNA samples indicated. In contrast to the boxplot of pre-normalization data (top panel), the post-normalized data distributes in the same intervals with the same density center, indicating successful adjustment of data. The post-normalized data were used for further analysis. Ln: the natural logarithm, Tis: brain tissue, Exp: microarray experiments including technical and experimental triplicates, CL: cerebellum, CR: cerebrum, FC: frontal cortex, HC: hippocampus, and HT: hypothalamus.

Article Snippet: Microarray labeling and hybridization, image scanning and processing : RNA samples of rat brain tissues were purchased from Zyagen (San Diego, California).

Techniques: Gene Expression, Labeling, Synthesized, Microarray, Transformation Assay, Comparison, Expressing

Journal: PLoS Genetics

Article Title: Diverse Splicing Patterns of Exonized Alu Elements in Human Tissues

doi: 10.1371/journal.pgen.1000225

Figure Lengend Snippet: RT-PCR analysis of Alu-derived exons whose Exon array probe intensities correlate with overall gene expression levels.

Article Snippet: Total RNA samples from rhesus macaque tissues (brain, skeletal muscle, pancreas) were purchased from Biochain Inc (Hayward, CA).

Techniques: Expressing, Sequencing, Binding Assay, Activation Assay, Activity Assay, Protein Binding

Journal: PLoS Genetics

Article Title: Diverse Splicing Patterns of Exonized Alu Elements in Human Tissues

doi: 10.1371/journal.pgen.1000225

Figure Lengend Snippet: Detection of tissue-specific splicing in candidate Alu-derived exons selected from Exon array analysis and published literature.

Article Snippet: Total RNA samples from rhesus macaque tissues (brain, skeletal muscle, pancreas) were purchased from Biochain Inc (Hayward, CA).

Techniques: Binding Assay, Sequencing, Activity Assay, Activation Assay