From d029d5d7f8ead1f1de8d318045004a4a6f68f5fb Mon Sep 17 00:00:00 2001
From: Bonface
Date: Fri, 9 Feb 2024 09:41:28 -0600
Subject: Update dataset RTF Files.

---
 general/datasets/BR_U_1203_M/platform.rtf | 14 ++++++++++++++
 1 file changed, 14 insertions(+)
 create mode 100644 general/datasets/BR_U_1203_M/platform.rtf

(limited to 'general/datasets/BR_U_1203_M/platform.rtf')

diff --git a/general/datasets/BR_U_1203_M/platform.rtf b/general/datasets/BR_U_1203_M/platform.rtf
new file mode 100644
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+<p><strong>Affymetrix U74Av2 GeneChip:</strong> The expression data were generated using 97 U74Av2 arrays. The chromosomal locations of U74Av2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6) assembly. This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see <a class="fs14" href="http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&amp;org=mouse">http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&amp;org=mouse</a>). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possiible to confirm the BLAT alignment results yourself simply by clicking on the <strong>Verify</strong> link in the Trait Data and Editing Form (right side of the <strong>Location</strong> line).</p>
+
+<p>Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is <strong>at</strong>. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:</p>
+
+<ul>
+	<li><strong>f_at (sequence family)</strong>: Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.</li>
+	<li><strong>s_at (similarity constraint)</strong>: All Probes in this probe set target common sequences found in transcripts from several genes.</li>
+	<li><strong>g_at (common groups)</strong>: Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.</li>
+	<li><strong>r_at (rules dropped)</strong>: Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.</li>
+	<li><strong>i_at (incomplete)</strong>: Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).</li>
+	<li><strong>st (sense target)</strong> : Designates a sense target; almost always generated in error.</li>
+</ul>
+
+<p>Descriptions for the probe set extensions were taken from the Affymetrix<a class="fs14" href="./dbdoc/data_analysis_fundamentals_manual.pdf"> GeneChip Expression Analysis Fundamentals</a>.</p>
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