Team:SYSU-Software/Collaborations

SYSU-Software:Project

OVERVIEW

  • We collaborated with NJU-China, SYSU-CHINA during our project.

  • For NJU-China, we developed a tool for searching and selecting shRNAs from given mRNAs.

  • Collaborating with SYSU-CHINA, we held 2016 CCiC in Sun Yat-sen University,

  • and nearly 30 teams participated in this ceremony.

WITH NJU-CHINA WITH SYSU-CHINA

WITH NJU-CHINA

  • A shRNA Automatic Design

  • and Selection Tool

  •    During their project, 2016 wet-lab team NJU-China needed a tool that can automatically design shRNA sequence

  • and select the most appropriate ones according to the given target DNA or mRNA sequence.

  •    Our collaboration can also be seen in the Collaboration site of NJU-China

  • Demands: In their experiment, they needed to design a shRNA for K-ras in A549. They needed a small tool to design

  • shRNA with given DNA or mRNA sequence and select the most appropriate ones. The design of shRNA should fulfill

  • the following 19 requirements.

  • 1. content of G and C should range from 30% to 52%

  • 2. 15th to 19th bases in sense chain should contain at least three A/Us

  • 3. the 19th base in sense chain should be A

  • 4. the 3rd base in sense chain should be A

  • 5. the 10th base in sense chain should be U

  • 6. the 19th base in sense chain should not be G or C

  • 7. the 13th base in sense chain should not be G

  • 8. do not have inverted repeat sequence

  • 9. 5’ end of antisense chain should be A or U

  • 10. 5’ end of sense chain should be G or C

  • 11. first 7 bases of 5’ end in antisense chain should have at least 5 A/Us

  • 12. GC bases should not repeat continuously over 9 times

  • 13. content of A/U in first 3 bases of 3’ end and 5’ end in sense chain should be asymmetric

  • 14. the 1st base in sense chain should be G or C

  • 15. the 6th base in sense chain should be A

  • 16. the 19th base in sense chain should be A or U

  • 17. the 1st base in sense chain should not be U

  • 18. the 19th base in sense chain should not be G

  • 19. number of A/U in first three bases of 3’ end should be at least one more than that of 5’ end

  • Most importantly, the design shRNA must satisfy at least two points in 14, 15 and 16.

  • Solution: We wrote a small program with C++. This program asked the user to input their mRNA sequence and it

  • would generate a series of shRNA sequences with length between 21nt and 23nt. Then the program would check

  • these sequences how many requirements they satisfied, and ranked them by this number. Download the tool.

  • Result: NJU-China used our tool and generated the sequence of shRNA targeting to K-ras gene. The predicted se-

  • quence and its structure was shown in Fig. 1. Their experiment also proved this shRNA could significantly impress

  • the expression of K-ras in A549 (Fig. 2)

Fig.1 The predicted sequence and structure of this shRNA

Fig. 2 The experiment validate that the designed shRNA performs well

Fig. 3 The result of western blot also expressed shRNA impressed K-ras

WITH SYSU-CHINA

  • Central China

  • iGEM Consortium

  •    From September 2nd to 4th, we helped SYSU-CHINA for their organization of 2016 Sun Yat-sen University Central

  • China iGEM Consortium in Hedanqing Lecture Hall. 28 iGEM teams around this country and professors from School of

  • Life Sciences participated in this consortium.

  •    SYSU-CHINA was mainly responsible for this consortium, which consisted of presentation and poster sections, aiming

  • at simulating the Giant Jamboree. Prof. Yan Zhang and Prof. Junjiu Huang present the opening speech, giving us sincerely

  • wishes and strengthon our future competition. Senior Haoqian Zhang also shared his experience on iGEM competition

  • and provide precious advise to us.

  •    During the whole consortium, every iGEM team shared their ideas in their 20 minutes presentation, and their ideas

  • would be questioned and exchanged in the left 10 minutes by professors and audiences.

  •    For more details please see SYSU-CHINA.

  • Interlab

  • Collaboration

  •    We shared iGEM interlab kits and iGEM plate kits with SYSU-CHINA. During their experiment, their Interlab plasmid

  • (Device I) can not be transformed well in bacterial culture medium, so we provided our plasmids for them to finish their

  • Interlab project. SYSU-CHINA also helped us when we used up one of our plate kits (B0015 terminator), and their kindly

  • help ensured us Interlab project. Reference can be seen in the Collaboration site of SYSU-CHINA