Journal: BMC Ophthalmology

Article Title: MiRNAs regulate oxidative stress related genes via binding to the 3′ UTR and TATA-box regions: a new hypothesis for cataract pathogenesis

doi: 10.1186/s12886-017-0537-9

Figure Lengend Snippet: Heatmap shows differentially expressed mRNAs in cataractous lens samples compared with transparent lens samples. Six separate microarray assays were performed to determine the genome-wide mRNA expression in the central epithelium of transparent and cataractous human lenses. Microarray data were processed by CapitalBio Corporation. Heatmap shows differentially expressed mRNAs in cataractous lens samples compared with transparent lens samples. Relative expression value from high to low was shown by gradient of red to green in the heatmap. Colors indicate relative mRNA expression. Red and green indicate higher or lower expression of mRNAs relative to those in transparent lens samples, respectively. FDR (false discovery rate) adjusted p -value <0.05

Article Snippet: Microarray data were processed by CapitalBio Corporation.

Techniques: Microarray, Genome Wide, Expressing

Journal: Genomics Data

Article Title: An integrative approach to analyze microarray datasets for prioritization of genes relevant to lens biology and disease

doi: 10.1016/j.gdata.2015.06.017

Figure Lengend Snippet: Workflow of microarray design, data pre-processing and analysis of differentially expressed genes.

Article Snippet: Microarray data processing and analysis was performed under the ‘R’ statistical environment ( http://www.r-project.org /) using lumi package for Illumina microarray data, available through Bioconductor ( www.bioconductor.org ).

Techniques: Microarray

Journal: Genomics Data

Article Title: An integrative approach to analyze microarray datasets for prioritization of genes relevant to lens biology and disease

doi: 10.1016/j.gdata.2015.06.017

Figure Lengend Snippet: Selection of mutant stage for lens microarray analysis. Light microscopy based grid imaging of lenses from (A) control and (B) Mafg −/−: Mafk +/− compound mutant mice demonstrates no opacities at post-natal stage (P)60 or 2 months (2 mo.). High-resolution scanning electron microscopy (SEM) analysis of lenses from (A’) control and (B’) Mafg −/−: Mafk +/− compound mutant mice confirm the absence of overt abnormalities in mutant fiber cells at stage 2 mo. However, grid imaging analysis at age 7 months (7 mo.) demonstrates that while (C) control mice have transparent lenses, (D) Mafg −/−: Mafk +/− compound mutant mice exhibit lens opacities (asterisk). SEM analysis at age 7 months demonstrates that while (C’) Control lenses have normal fiber cells, (D’) Mafg −/−: Mafk +/− compound mutant mice exhibit severe fiber cell defects (asterisk). Based on this analysis, the age P60 (2 mo.), when Mafg −/−: Mafk +/− compound mutant mice do not exhibit overt lens defects, was selected as the stage to perform microarrays. This is based on the consideration that microarrays at P60 will increase the likelihood of detecting gene expression changes that reflect primary alterations prior to the manifestation of overt defects that occur with age. Scale bar in B’ and D’ is 10 μm.

Article Snippet: Microarray data processing and analysis was performed under the ‘R’ statistical environment ( http://www.r-project.org /) using lumi package for Illumina microarray data, available through Bioconductor ( www.bioconductor.org ).

Techniques: Selection, Mutagenesis, Microarray, Light Microscopy, Imaging, Control, Electron Microscopy, Gene Expression

Journal: Genomics Data

Article Title: An integrative approach to analyze microarray datasets for prioritization of genes relevant to lens biology and disease

doi: 10.1016/j.gdata.2015.06.017

Figure Lengend Snippet: Microarray expression data quality assessment plots. Comparisons of raw unprocessed and normalized processed expression intensities between arrays of mutant and control datasets. PCA plots from (A) raw and (B) processed datasets. Histograms for (C) raw and (D) processed datasets. Boxplot for (E) raw and (F) processed datasets. Key to samples in each type of analysis is given below.

Article Snippet: Microarray data processing and analysis was performed under the ‘R’ statistical environment ( http://www.r-project.org /) using lumi package for Illumina microarray data, available through Bioconductor ( www.bioconductor.org ).

Techniques: Microarray, Expressing, Mutagenesis, Control