From 49ef490e2bc70da27ef482a9e76d9597e4d40872 Mon Sep 17 00:00:00 2001
From: Arya Ajit Gohad <aryagohad21@gmail.com>
Date: Fri, 16 Dec 2022 18:32:42 +0000
Subject: [PATCH] Update wiki/pages/engineering-learn.html
---
wiki/pages/engineering-learn.html | 21 +++++----------------
1 file changed, 5 insertions(+), 16 deletions(-)
diff --git a/wiki/pages/engineering-learn.html b/wiki/pages/engineering-learn.html
index bd53489..8233ba1 100644
--- a/wiki/pages/engineering-learn.html
+++ b/wiki/pages/engineering-learn.html
@@ -119,22 +119,11 @@ How to bring experimental results and OSTIR predictions (both dimensionless numb
<h2>NuPack Analysis</h2>
<hr>
<ul>
- <li>Syn 2e, 2d and 2g have similar F/OD in our experiment. Their last 9 nucleotides are
-GAGGAGAAA. There is no structural correlation that can be found from NuPACK
-alone. In the paper reported in literature (Viegas et al.), they give 4-5 fold better
-expression. In our experiment they did not perform well with respect to the control.
-</li><li>U9 and U10 give similar F/OD in our test. Their last nine nucleotides are GAATGTACC.
-Their expression is way better than the U13 UTR. The last 9 nucleotides of U13 are
-different- GAATGTACA
-</li><li>csPF is only 9 nucleotides long and gives the best F/OD value in our experiments. This
-gives us evidence that only 9 nucleotides can improve the F/OD by approximately
-30%. We further correlate these with the findings of OSTIR tupple data run.
-</li><li>csPH gives a F/OD value that is different from csPF as reported in our experimental
-data. The last nine nucleotides of csPF are GGAATTTTT whereas of csPH are
-GGAATTTGT
-</li><li>Now, we plan to order all the truncated UTRs having just the last 9 nucleotides. With
-the interpretations of OSTIR we also do a site directed mutagenesis of the best
-performing csPF UTR for our next experimental cycle.</li>
+ <li>Syn2e, Syn2d and Syn2h were found to have similar F/OD values in both our strains. Their last 9 nucleotides are GAGGAGAAA. There is no structural correlation that can be found from NuPACK alone. In the paper reported in literature (Viegas et al.), they give 4-5-fold better expression. In our experiment, however, they did not perform well in either strain with respect to the control.
+</li><li>U9 and U10 give similar F/OD in our test. Their last nine nucleotides are GAATGTACC. Their expression is much better than the U13 UTR whose last 9 nucleotides of U13 are different- GAATGTACA.
+</li><li>cspF is only 9 nucleotides long and gives the best F/OD value for DH5alpha strain in our experiments. This gives us evidence that only 9 nucleotides can improve the F/OD by approximately 30%. We further correlate these with the findings of OSTIR tuple data run.
+</li><li>cspH gives a F/OD value that is different from cspF as reported in our experimental data. The last nine nucleotides of csPF are GGAATTTTT whereas of csPH are GGAATTTGT.
+</li><li>We ordered all the truncated UTRs having just the last 9 nucleotides. With the interpretations of OSTIR we conducted a site directed mutagenesis of the best performing as well as interesting UTR: cspF, for our next experimental cycle.</li>
</ul>
</p>
--
GitLab