Lens RNA was extracted using the RNeasy Plus Kit (Qiagen, Valencia, CA) and subjected to microarray analysis using the MouseRef-8 v2.0 (1883 genes) Expression BeadChip Kit (Illumina, San Diego, CA) according to the manufacturers’ instructions and data were extracted, normalized, and summarized using the GenomeStudio Gene Expression (GX) Module (Illumina) as described [24 (link)]. The raw data were quality assessed by box-plot analysis (Supplementary Fig. 1 ) and the quantile normalized log2 signal data analyzed using R packages ‘lima’ and ‘gage’ with Bonferroni correction of p-values as described [24 (link)].
Genomestudio gene expression gx module
Manufactured by Illumina
The GenomeStudio Gene Expression (GX) Module is a software tool developed by Illumina for the analysis of gene expression data generated from Illumina microarray platforms. The core function of the GX Module is to provide a comprehensive suite of data visualization and analysis tools to assist researchers in interpreting their gene expression results.
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Lab products found in correlation
2 protocols using genomestudio gene expression gx module
1
Microarray Analysis of Lens RNA
2
Gene Expression Profiling Using Illumina Microarray
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Microarray analysis was performed at the University of Chicago Genomics Facility using Illumina HumanHT-12_V4_0 Expression BeadChip. Average signal and detection p values of Direct Hyb expression data was obtained using Illumina GenomeStudio Gene Expression (GX) Module (Illumina Inc.) and were imported into Arraystar expression analysis software version 15.0.1 (DNASTAR Inc.). Genes with average signal >10 were selected for determining differential expression and hierarchical clustering.
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