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diff --git a/general/group_infofiles/BXD.html b/general/group_infofiles/BXD.html index 295090c..b96028d 100644 --- a/general/group_infofiles/BXD.html +++ b/general/group_infofiles/BXD.html @@ -1,11 +1,10 @@ - -<Blockquote><P> +<P> The BXD family of recombinant inbred (<A HREF="http://www.complextrait.org/archive/2001/HTML/silverbook/frame1.1.shtml" target="_blank" class="fs14">RI</A>) strains were derived by crossing C57BL/6J (B6) and DBA/2J (D2) and inbreeding progeny for 20 or more generations. This genetic reference panel is a remarkable resource because data for thousands of phenotypes and nearly 100 gene, protein, and metabolite expression data sets have been acquired over a nearly a 40-year period. Another advantage of the BXD family is that the both parents have been sequenced (C57BL/6J as part of a public effort, and DBA/2J by Celera Genomics, by the UTHSC group and by Sanger). Based on our analysis of the sequence data, these two strains differ at approximately 4.8 million SNPs. Variants (mostly single nucleotide polymorphisms and about 500,000 insertion-deletions) that produce interesting phenotypes can be located efficiently. The zoomable physical maps in GeneNetwork can display the positions of B versus D-type SNPs at high resolution. </P> Our DBA/2J sequence data (from Wang et al. 2016) have been used to generate a virtual genome for this strain using a C57BL/6J framework. In other words, all SNPs and small DBA/2J indels have inserted in place of original C57BL/6J sequence. -</BLOCKQUOTE> + <P> <DIR> @@ -14,7 +13,7 @@ Our DBA/2J sequence data (from Wang et al. 2016) have been used to generate a vi <DIR><P><SMALL><B>Legend:</B> Photo gallery of BXD strains</SMALL></P> </DIR> -<BLOCKQUOTE> + <P><B>EPOCH DIFFERENCES or "Batch Effect" among BXD strains</B>. BXD strains (1 through 103) were produced as at least four separate groups or subfamilies. BXD1 through BXD30 were produced by Benjamin A. Taylor starting in about 1971, with the first publication using early generation BXD lines at F7 to F10 in 1973 (<A HREf="http://www.ncbi.nlm.nih.gov/pubmed/4719448">Taylor et al., 1973</A> <A HREF="/images/upload/Taylor_1973.pdf"> Full text</A>, 1975 (<A HREf="http://www.ncbi.nlm.nih.gov/pubmed/807855">Taylor et al., 1975</A>, <A HREf="http://www.ncbi.nlm.nih.gov/pubmed/1203051">Womack et al., 1975</A>). A distinction is made between an RI line, which is not necessarily fully inbred (<20 F generations of inbreeding, and an RI strain, which should be the progeny of 20 or more sequential sib matings). @@ -108,5 +107,3 @@ Users of the expanded BXD panel should take this epoch substructure into account <P>For more details on the history, generation, and use of RI strains as genetic reference populations for systems genetics please see Silver <A HREF="http://www.complextrait.org/archive/2001/HTML/silverbook/frame1.1.shtml" target="_blank" class="fs14">(1995)</A>. Additional useful literature links are provided in the <B>References</B> link at the top center of this page. </P> - -</Blockquote> |