Team:AMU-Poznan/Project

From 2014.igem.org

(Difference between revisions)
Line 58: Line 58:
<h1>Standard Parts</h1>
<h1>Standard Parts</h1>
-
</br></br>
+
</br>
 +
We are creating a particle which can be inserted into plasmid built by Standard parts from Registry of Standard Biological Parts.
 +
<img src="https://static.igem.org/mediawiki/2014/b/bb/Shmir-STANDARD.png" width="60%"></br>
<h1>User Guide</h1>
<h1>User Guide</h1>
</br></br>
</br></br>
Line 68: Line 70:
</br></br>
</br></br>
<h1>Releases (re-use of 2013iGEM software)</h1>
<h1>Releases (re-use of 2013iGEM software)</h1>
-
</br></br>
+
</br>sh-miR designer v1.0 </br>
 +
First version of the program presented on iGEM 2013 by our team. The user have to provide siRNA sequence (one or both strands). The miRNA database includes 5 miRNAs. </br>
 +
sh-miR designer v1.1 </br>
 +
Strand discrimination functionality was added based on miRbase.  </br>
 +
extended miRNA database </br>
 +
sh-miR designer v2.0 </br>
 +
siRNA prediction algorithm was added to functionality (the input is NCBI transcript number) </br>
 +
user can choose GC content of siRNA molecule, maximal off-target, if he/she wants immunostimulatory sequences inside the molecule and to choose if he/she wants to include all or chosen scaffold </br>
 +
extended miRNA database</br>
 +
 +
What we are working on: </br>
 +
strand discrimination based on therodynamics of siRNA ends; </br>
 +
preparing construct with flanking restriction enzymes </br>
 +
providing plasmids with parts from standard parts </br>
<h1>Unit Tests</h1>
<h1>Unit Tests</h1>
</br></br>
</br></br>
Line 74: Line 89:
</br></br>
</br></br>
<h1>Test cases</h1>
<h1>Test cases</h1>
-
</br></br>
+
</br>1) ATXN3 - therapeutic sh-miR against SCA3 disease</br>
 +
transcript number: NM_001164782.1 </br>
 +
GC content: default </br>
 +
Off-target: 10 </br>
 +
scaffold: ALL </br>
 +
immunostimulatory: NO</br>
 +
2) P54 - therapeutic sh-miR against cancer</br>
 +
transcript number: NM_000546.5 </br>
 +
GC content: default </br>
 +
Off-target: 10 </br>
 +
scaffold: ALL </br>
 +
immunostimulatory: YES</br>
 +
3) biological function analysis, PARP1, we have miR-30a in our lab</br>
 +
transcript number: NM_001618.3 </br>
 +
GC content: default </br>
 +
Off-target: 0 </br>
 +
scaffold: miR-30a </br>
 +
immunostimulatory: no_difference (default) </br>
 +
4) biological function, PARP1, we have miR-30a in our laboratory and have immune cells</br>
 +
transcript number: NM_001618.3 </br>
 +
GC content: default </br>
 +
Off-target: 0 </br>
 +
scaffold: miR-30a </br>
 +
immunostimulatory: NO</br>
 +
5) biological function, PARP1 and have immune cells</br>
 +
transcript number: NM_001618.3 </br>
 +
GC content: default </br>
 +
Off-target: 0 </br>
 +
scaffold: ALL </br>
 +
immunostimulatory: NO</br>
<h1>References</h1>
<h1>References</h1>
-
</br></br>
+
</br>
 +
1. Boudreau RL, Monteys AM, Davidson BL. Minimizing variables among hairpin-based RNAi
 +
vectors reveals the potency of shRNAs. RNA. 2008 Sep;14(9):1834-44. Epub 2008 Aug 12.</br>
 +
2. Chang K, Elledge SJ, Hannon GJ. Lessons from Nature: microRNA-based shRNA libraries. Nat
 +
Methods. 2006 Sep;3(9):707-14.</br>
 +
3. Dow LE, Premsrirut PK, Zuber J, Fellmann C, McJunkin K, Miething C, Park Y, Dickins RA,
 +
Hannon GJ, Lowe SW. A pipeline for the generation of shRNA transgenic mice. Nat Protoc.
 +
2012 Feb 2;7(2):374-93. doi: 10.1038/nprot.2011.446.</br>
 +
4. Fahim M, Larkin PJ. Designing Effective amiRNA and Multimeric amiRNA Against Plant
 +
Viruses. Methods Mol Biol. 2013;942:357-77. doi: 10.1007/978-1-62703-119-6_19.</br>
 +
5. Fan ZD, Zhang L, Shi Z, Gan XB, Gao XY, Zhu GQ. Artificial microRNA interference targeting
 +
AT(1a) receptors in paraventricular nucleus attenuates hypertension in rats. Gene Ther. 2012
 +
Aug;19(8):810-7. doi: 10.1038/gt.2011.145. Epub 2011 Sep 29.</br>
 +
6. Fellmann C, Zuber J, McJunkin K, Chang K, Malone CD, Dickins RA, Xu Q, Hengartner MO,
 +
Elledge SJ, Hannon GJ, Lowe SW. Functional identification of optimized RNAi triggers using a
 +
massively parallel sensor assay. Mol Cell. 2011 Mar 18;41(6):733-46. Epub 2011 Feb 25.</br>
 +
7. Maczuga P, Lubelski J, van Logtenstein R, Borel F, Blits B, Fakkert E, Costessi A, Butler D, van
 +
Deventer S, Petry H, Koornneef A, Konstantinova P. Embedding siRNA sequences targeting
 +
Apolipoprotein B100 in shRNA and miRNA scaffolds results in differential processing and in
 +
vivo efficacy. Mol Ther. 2012 Oct 23. doi: 10.1038/mt.2012.160. [Epub ahead of print]</br>
 +
8. Maczuga P, Koornneef A, Borel F, Petry H, van Deventer S, Ritsema T, Konstantinova P.
 +
Optimization and comparison of knockdown efficacy between polymerase II expressed
 +
shRNA and artificial miRNA targeting luciferase and Apolipoprotein B100. BMC
 +
Biotechnol. 2012 Jul 24;12:42. doi: 10.1186/1472-6750-12-42.</br>
 +
9. Matveeva OV, Nazipova NN, Ogurtsov AY, Shabalina SA. Optimized models for design of
 +
efficient miR30-based shRNAs. Front Genet. 2012;3:163. Epub 2012 Aug 29.</br>
 +
10. McBride JL, Boudreau RL, Harper SQ, Staber PD, Monteys AM, Martins I, Gilmore BL, Burstein
 +
H, Peluso RW, Polisky B, Carter BJ, Davidson BL. Artificial miRNAs mitigate shRNA-mediated
 +
toxicity in the brain: implications for the therapeutic development of RNAi. Proc Natl Acad Sci
 +
U S A. 2008 Apr 15;105(15):5868-73. Epub 2008 Apr 8.</br>
 +
11. Schwab R, Ossowski S, Warthmann N, Weigel D. Directed gene silencing with artificial
 +
microRNAs. Methods Mol Biol. 2010;592:71-88.</br>
 +
12. Silva JM, Li MZ, Chang K, Ge W, Golding MC, Rickles RJ, Siolas D, Hu G, Paddison PJ, Schlabach
 +
MR, Sheth N, Bradshaw J, Burchard J, Kulkarni A, Cavet G,Sachidanandam R, McCombie WR, Cleary MA, Elledge SJ, Hannon GJ. Second-generation shRNA libraries
 +
covering the mouse and human genomes. Nat Genet. 2005 Nov;37(11):1281-8. Epub 2005
 +
Oct 2.</br>
 +
13. Stegmeier F, Hu G, Rickles RJ, Hannon GJ, Elledge SJ. A lentiviral microRNA-based system for
 +
single-copy polymerase II-regulated RNA interference in mammalian cells. Proc Natl Acad Sci
 +
U S A. 2005 Sep 13;102(37):13212-7. Epub 2005 Sep 1.</br>
 +
14. Wang X, Yang Y, Zhou J, Yu C, Cheng Y, Yan C, Chen J.Two-step method for constructing
 +
Arabidopsis artificial microRNA vectors. Biotechnol Lett. 2012 Jul;34(7):1343-9. Epub 2012
 +
Mar 22.</br>
 +
15. Warthmann N, Ossowski S, Schwab R, Weigel D. Artificial MicroRNAs for Specific Gene
 +
Silencing in Rice. Methods Mol Biol. 2013;956:131-49. doi: 10.1007/978-1-62703-194-3_11.</br>
 +
16. Zeng Y, Cullen BR. Efficient processing of primary microRNA hairpins by Drosha requires
 +
flanking nonstructured RNA sequences. J Biol Chem. 2005 Jul 29;280(30):27595-603. Epub
 +
2005 Jun 1.</br>
 +
17. Zeng Y, Wagner EJ, Cullen BR. Both natural and designed micro RNAs can inhibit the
 +
expression of cognate mRNAs when expressed in human cells. Mol Cell. 2002 Jun;9(6):1327-
 +
33</br>
<h1>Judging Form</h1>
<h1>Judging Form</h1>
</br></br>
</br></br>

Revision as of 21:21, 14 October 2014

Retrieved from "http://2014.igem.org/Team:AMU-Poznan/Project"