diff --git a/wiki/pages/engineering-learn.html b/wiki/pages/engineering-learn.html index bd53489fe56fafa7b47e2ea6c5d9705377effc59..8233ba1ed90f5f441529ae6312e01e91ce45da9b 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>