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Since 1999, the National Institute of Mental Health has financed an effort to create a brain map using the mouse genome, the Brain Molecular Anatomy Project, or B.M.A.P.
Total RNA isolated from embryonic stem cells or cardiomyocytes was screened using the mouse genome 430 2.0 array (Affymetrix).
Primers were chosen using the Primer3 software (http://www.broad.mit.edu/cgi-bin/primer/primer3_www.cgi) and the specificity of all primer pairs was tested with electronic PCR using the mouse genome and the mouse transcript database (http://www.ncbi.nlm.nih.gov/sutils/e-pcr/reverse.cgi).cgi
Mammalian Phenotype (MP) enrichment was determined using the Mouse Genome Informatics (MGI) database (Eppig et al., 2015).
The significance of the annotations was calculated using a hypergeometric statistical test with FDR p-value correction [ 113], using the mouse genome as reference.
Total RNA extracted using RNeasy Kit (QIAGEN) was subjected to gene expression profiling using the Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA).
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We used the Mouse Genome 430 2.0 array and compared two WT/dKO pairs from matched litters at 4 months of age.
Briefly, cDNA microarray analysis was performed using the Mouse Whole Genome OneArray® v2 (Phalanx Biotech).
The combined strategy is a hybrid of the Whole Genome Shotgun (WGS) approach used for the mouse genome and the hierarchical (BAC clone) approach used for the human genome.
This is the same library used by the Mouse Genome Sequencing Consortium to generate the B6 reference strain sequence.
These fosmid projects were improved to a sequence improvement standard similar to the one used by the mouse genome project (Mouse Genome Sequencing Consortium et al. 2002).
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