198c9b8daecc44fbda6a6494c566c723920f030a
lrnassar
  Wed Mar 11 18:25:21 2026 -0700
Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.

diff --git src/hg/makeDb/trackDb/human/encodeYaleMASPlacRNATars.html src/hg/makeDb/trackDb/human/encodeYaleMASPlacRNATars.html
index 5604ae5fc46..3545dfdd1d0 100644
--- src/hg/makeDb/trackDb/human/encodeYaleMASPlacRNATars.html
+++ src/hg/makeDb/trackDb/human/encodeYaleMASPlacRNATars.html
@@ -1,89 +1,89 @@
 <H2>Description</H2>
 <P>
 This track shows the locations of forward (+) and reverse (-) strand 
 transcriptionally-active regions (TARs)/transcribed fragments 
 (transfrags), for human NB4 cell total RNA and for
 human placenta Poly(A)+ RNA, hybridized to the Yale 
 Maskless Array Synthesizer (MAS) ENCODE oligonucleotide microarray, 
 transcription mapping design #1. This array has 36-mer oligonucleotide probes 
 approximately every 36 bp (<em>i.e.</em> end-to-end) covering all the 
 non-repetitive DNA sequence of the ENCODE regions ENm001 - ENm012. See 
 NCBI GEO accession 
 <A HREF="https://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GPL2105"
 TARGET=_blank>GPL2105</A> for details of this array design.</P> 
 <P>
 These TARs/transfrags are based on a transcript map combining 
 hybridization intensities from three biological replicates, each with at 
 least two technical replicates. Arrays were hybridized using either
 Nimblegen standard protocol, or the protocol described in Bertone 
 <em>et al</em>. (2004). The label of each subtrack in this annotation 
 indicates the specific protocol used for that particular data set.</P>
 
 <H2>Methods</H2>
 <P>
 A score was assigned to each oligonucleotide probe position by combining 
 two or more technical replicates and by using a sliding window 
 approach. Within a sliding window of 160 bp (corresponding to 5 
 oligos), the hybridization intensities for all replicates of each 
 oligonucleotide probe were compared to their respective array median 
 intensity. Within the window and across all the replicates, the number 
 of probes above and below their respective median was counted. Using 
 the sign test, a one-sided P-value was then calculated and a score 
 defined as score=-log(<i>p-value</i>) was assigned to the oligo in the 
 center of the window.</P>
 <P>
 Three independent biological replicates were generated, and each was 
 hybridized to at least two different arrays (technical replicates). 
 Transcribed regions (TARs/transfrags) were then identified using a score 
 threshold of 95th percentile as well as a maximum gap of 80 bp and a 
 minimum run of 50 bp (between oligonucleotide positions), effectively 
 allowing a gap of one oligo and demanding the TAR/transfrag to 
 encompass at least 3 oligos.</P>
 
 <H2>Verification</H2>
 <P>
 Transcribed regions (TARs/transfrags), as determined by individual biological 
 samples, were compared to ensure significant overlap.</P>
 
 <H2>Credits</H2>
 <P>
-These data were generated and analyzed by the the labs of Michael Snyder, 
+These data were generated and analyzed by the labs of Michael Snyder, 
 Mark Gerstein and Sherman Weissman at Yale University.</P>
 
 <H2>References</H2>
 <P>
 Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SP, 
 Gingeras TR,
 <A
 HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11988577&query_hl=5"
     TARGET=_blank>
 Large-scale transcriptional activity in chromosomes 21 and 22</A>, 
 <i>Science</i>. 2002 May 3;296(5569):916-9.
 
 <BR><BR>
 Rinn JL, Euskirchen G, Bertone P, Martone R, Luscombe NM, Hartman S, 
 Harrison PM, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M, 
 <A 
 HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12600945&query_hl=1"
     TARGET=_blank>
 The transcriptional activity of human Chromosome 22</A>, 
 <i>Genes Dev</i>, 2003 Feb 15;17(4):529-40.
 
 <BR><BR>
 Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, 
 Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M,
 <A
 HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15539566&query_hl=7"
     TARGET=_blank>
 Global identification of human transcribed sequences with genome tiling arrays</A>, 
 <i>Science</i>. 2004 Dec 24;306(5705):2242-6. Epub 2004 Nov 11.
 
 <BR><BR>
 Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, 
 Stern D, Tammana H, Helt G, Sementchenko V, Piccolboni A, Bekiranov S, 
 Bailey DK, Ganesh M, Ghosh S, Bell I, Gerhard DS, Gingeras TR,
 <A
 HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15790807&query_hl=5"
     TARGET=_blank>
 Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution</A>, 
 <i>Science</i>. 2005 May 20;308(5725):1149-54. Epub 2005 Mar 24.