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<p>All animals were raised at the Jackson Laboratory or at UTHSC in SPF facilities. All mice were killed by cervical dislocation. Whole brain dissections were performed at either Beth Israel Deaconess Medical Center by Glenn Rosen or at UTHSC by Lu Lu and colleagues. Neocortex samples were close to complete but are likely to include variable amounts of underlying white matter. Samples may also include parts of the pyriform cortex and subiculum.</p>
<p>A pool of dissected neocortical tissue from two to three naive adults of the same strain, sex, and age was collected in one session and used to generate RNA samples. The great majority (75%) of animals were sacrificed between 9:30 AM and 11:30 AM. All animals were sacrificed between 9 AM and 5 PM during the light phase. All RNA samples were extracted at UTHSC by Zhiping Jia (CHECK LAST STATEMENT WITH LU).</p>
<p>All animals used in this study were between XX and XX days of age (average of XX days; see Table 1 below). All animals were sacrifice between 9 AM and 5 PM during the light phase.</p>
<p><strong>Sample Processing:</strong> Samples were processed by Lu Lu and colleagues in the Illumina Core at UTHSC between December 2007 and January 2008. All processing steps were performed by Feng Jiao. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8 to pass our quality control (QC). The majority of samples had values between 1.9 and 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using the Ambion/Illumina (http://www.ambion.com/catalog/CatNum.php?AMIL1791) TotalPrep RNA amplication kit (Cat#IL1791). The biotin labeled cRNA was then evaluated using both the 260/280 ratio (values of 2.0-2.3 are acceptable) using a NanoDrop ND-1000 (http://www.nanodrop.com/nd-1000-overview.html). Those samples that passed QC steps (1-3% failed and new RNA samples had to be acquired and processed) were immediately used on Mouse-6 v 1.1 slide. The slides were hybridized and washed following standard Illumina protocols.</p>
<p><strong>Replication and Sample Balance:</strong> We obtained a male sample pool and female sample pool from as many strains as possible. However, a number of strains are represented by samples from a single sex (see figure at bottom of page).</p>
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