Total RNA was prepared from three pools of dissected E10.25 control (Tbx3 fl/+) and Tbx3;PrxCre mutant forelimbs using the RNAeasy Micro Kit (Qiagen 74004). The microarray and genomic analysis and bioinformatics core facilities at the University of Utah performed Agilent mouse whole-genome expression arrays and array image data analysis using Agilent Feature Extraction software. Subtle intensity-dependent bias was corrected with LOWESS normalization, with no background subtraction. Statistical analysis of normalized log-transformed data was performed in GeneSifter (www.genesifter.net ). Differentially expressed transcripts were defined (adjusted for multiple testing using the Benjamini and Hochberg method) as p<0.05. The results presented in Supplementary file 1 show transcripts that were statistically differentially expressed +/-1.3 fold in the mutant limb buds; yellow highlighting indicates changes that were replicated by RNA-Seq.
Agilent mouse whole genome expression arrays
Manufactured by Agilent Technologies
The Agilent mouse whole-genome expression arrays are high-density oligonucleotide microarrays designed to analyze the expression of mouse genes across the entire genome. These arrays provide comprehensive coverage of the mouse transcriptome, enabling researchers to measure the expression levels of thousands of genes simultaneously.
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Lab products found in correlation
2 protocols using agilent mouse whole genome expression arrays
1
Microarray Analysis of Forelimb Development
2
Microarray Analysis of Mouse Transcriptome
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The experiments were run in quadruplicate on Agilent mouse whole-genome expression arrays. The array image data were quantitated using Agilent Feature Extraction software (version 9.5.1.1). Subtle intensity-dependent bias was corrected with LOWESS normalization, with no background subtraction. Statistical analysis of normalized log-transformed data was performed in Gene Sifter (www.genesifter.net). Differentially expressed transcripts were defined (adjusted for multiple testing using the Benjamini and Hochberg method) as P<0.05. Spots with an intensity below background were removed prior to statistical analysis. Heat maps were generated using Heatmapper (www.heatmapper.ca).
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