26ad7e5fe96a1b5070432af743fda80a385d52e8 lrnassar Wed Apr 29 13:28:42 2020 -0700 Moving the track desc page down to the wuhCor1 level refs #25458 diff --git src/hg/makeDb/trackDb/targets.html src/hg/makeDb/trackDb/targets.html deleted file mode 100644 index 1ed3a9f..0000000 --- src/hg/makeDb/trackDb/targets.html +++ /dev/null @@ -1,28 +0,0 @@ -<H2>Description</H2> -<P> -<p>This track shows data from Braun et al, 2020,<a target=_blank href = "https://www.medrxiv.org/content/10.1101/2020.04.17.20061440v1.full.pdf+html">"Presence of SARS-CoV-2 reactive T cells in COVID-19 patients and healthy donors"</a> -<p>The authors stimulated PBMCs with two sets (M1 and M2) of overlapping SARS-CoV peptide pools. -Importantly these are SARS-Cov peptides that have experimental support as putative MHC-II epitopes for SARS-CoV, but note they do not all 100% match SARS-Cov-2 sequence. -Using these peptide sets, the authors "demonstrate the presence of S-reactive CD4+ 52 T cells in 83% of COVID-19 patients, 53 as well as in 34% of SARS-CoV-2 seronegative healthy donors (HD), albeit at lower frequencies." - -<h2>Display Conventions and Configuration</h2> -<p> -Two tracks are available: -</p> -<ul> -<li>M1_peptides: The more N-terminal peptide library -<li>M2 peptides: The more C-terminal peptide library -</ul> - -<p> The annotated interval represents the alignment of the peptide to the viral -genome. The sequence displayed in the name is SARS-CoV peptide sequence (which -is the actual sequence which was used in the paper, but not necessarily -identical to the SARS-CoV-2 peptide).</p> - -<h2>Methods</h2> -<p>Table S1 contains the peptide sequences (SARS-CoV sequence) used. This table was downloaded and tblastn was used to align the identified the SARS-CoV peptides to the SARS-CoV-2 genome. -<p>A small number of peptides were not found or reported erroneous hits, in which the coordinates were identified by manually blat-ing the SARS-CoV-2 sequence from the alignments reported in Fig S1. -<p> - -<h2>References</h2> -Braun et al, 2020<a target=_blank href = "https://www.medrxiv.org/content/10.1101/2020.04.17.20061440v1.full.pdf+html">"Presence of SARS-CoV-2 reactive T cells in COVID-19 patients and healthy donors"</a>