2e3c89f43f3bb9d386178270200d0acce9fc8050
lrnassar
  Fri Nov 22 17:47:13 2024 -0800
Giving the UI link cronjob some love by fixing all the 301 redirects. These are the bulk of the items listed on the cron. No RM.

diff --git src/hg/makeDb/trackDb/allenBrainAli.html src/hg/makeDb/trackDb/allenBrainAli.html
index f79be40..23218d8 100644
--- src/hg/makeDb/trackDb/allenBrainAli.html
+++ src/hg/makeDb/trackDb/allenBrainAli.html
@@ -1,35 +1,35 @@
 <H2>Description</H2>
 <P>
 This track provides a link into the 
 <A HREF="http://portal.brain-map.org/" TARGET=_blank> Allen Brain Atlas</A> (ABA)
 images for this probe.  The ABA is an extensive
 database of high resolution in-situ hybridization images of adult
 male mouse brains covering the majority of genes.</P>
 
 <H2>Methods</H2>
 <P>
 The ABA created a platform for high-throughput <em>in situ</em> hybridization 
 (ISH) that allows a highly systematic approach to analyzing gene expression in 
 the brain. ISH is a technique that allows the cellular localization of mRNA 
 transcripts for specific genes. Labeled antisense probes, specific to a 
 particular gene, are hybridized to cellular (sense) transcripts and subsequent 
 detection of the bound probe produces specific labeling in those cells 
 expressing the particular gene. This method involves tagged nucleotides 
 detected by colorimetric methods.</P>
 
 <P>The platform used for the ABA utilizes this non-isotopic approach, with 
 digoxigenin-labeled nucleotides incorporated into a riboprobe produced by <em>in
 vitro</em> transcription. This method produces a label that fills the cell body,
 in contrast to autoradiography that produces scattered silver grains surrounding
 each labeled cell. To enhance the ability to detect low level expression, the 
 ABA has incorporated a tyramide signal amplification step into the protocol that
 greatly increases sensitivity. The specific methodology is described in detail 
-within the <A HREF="http://help.brain-map.org/display/mousebrain/Documentation"
+within the <A HREF="https://community.brain-map.org/c/how-to/mouse-atlas/22"
 TARGET=_blank>ABA Data Production Processes document</A>.</P>
 
 <H2>Credits</H2>
 <P>
 Thanks to the <A HREF="https://alleninstitute.org/" TARGET=_blank>Allen 
 Institute for Brain Science</A> in general, and Susan 
 Sunkin in particular, for coordinating with UCSC on this annotation.</P>