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/ucsfBrainMethyl.html src/hg/makeDb/trackDb/human/ucsfBrainMethyl.html index 0eb45a0b3c3..343e4258df2 100644 --- src/hg/makeDb/trackDb/human/ucsfBrainMethyl.html +++ src/hg/makeDb/trackDb/human/ucsfBrainMethyl.html @@ -80,31 +80,31 @@ distribution by spectrophotometry and Agilent DNA Bioanalyzer analysis. Four independent PCR reactions were performed to confirm enrichment for methylated and de-enrichment for unmethylated sequences, compared to input sonicated DNA. Visual inspection of extended coverage browser tracks confirmed expectations: lack of MeDIP signal in most 5' CpG island promoters and in regions devoid of CpG sites, as well as high MeDIP signal at known methylated sites (i.e. some imprinted regions). </p> <h3>MRE-seq</h3> <p> Each post-amplification library was QC'd for quantity, quality and size distribution by Nanodrop spectrophotometry and Agilent DNA Bioanalyzer analysis. Prior to high-throughput sequencing, a portion of each library was cloned into a sequencing vector and ~24 individual clones were Sanger sequenced to confirm the presence of MRE sites at the ends of each insert. Illumina sequencing reads were filtered to only -include those that map to MRE sites in the reference. MRE reads occured frequently in +include those that map to MRE sites in the reference. MRE reads occurred frequently in 5' CpG islands, which are often unmethylated and are enriched for the MRE recognition sequences relative to rest of the genome. </p> <h3>H3K4me3 ChIP-seq</h3> <p> Each post-amplification library was examined for quantity, quality and size distribution by Nanodrop spectrophotometry, Qubit fluoremetry and Agilent DNA Bioanalyzer. Fold H3K4me3 enrichment was confirmed by comparison to non-specific rabbit IgG enrichment. Visual inspection of the browser track of called peaks confirmed enrichment at a subset of annotated promoters. </p> <h3>RNA-seq and RNA-seq (SMART)</h3> <p>