general/datasets/Hc_u_0304_r/experiment-design.rtf


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<p>About amplification and hybridization:</p>

<p>Total RNA was quantified using RiboGreen and split into equal aliquots of approximately 10 ng, representing RNA from approximately 10,000 cells, and labeled using a total of three rounds of RNA amplification, exactly as described previously (Scherer et al. <a class="normal" href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=12661160&amp;dopt=Abstract" target="_blank">2003</a>). Labeled cRNA was fractionated and hybridized to the U74Av2 microarray following standard Affymetrix protocols.</p>

<p>About the chromosome and megabase position values:</p>

<blockquote>The chromosomal locations of probe sets and gene markers were determined by BLAT analysis using the Mouse Genome Sequencing Consortium Oct 2003 Assembly (see <a class="normal" href="http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&amp;org=mouse">http://genome.ucsc.edu/</a>). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.</blockquote>