Australia Partnering Award: International pooling for advanced cereal science - IPAC
Lead Research Organisation:
University of Dundee
Department Name: School of Life Sciences
Abstract
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Organisations
- University of Dundee (Lead Research Organisation)
- Australian National University (ANU) (Collaboration)
- La Trobe University (Collaboration, Project Partner)
- Commonwealth Scientific and Industrial Research Organisation (Collaboration)
- Australian National University (Project Partner)
- University of Adelaide (Project Partner)
| Description | The Generation Gap - Mechanisms of maternal control on grain |
| Amount | £588,538 (GBP) |
| Funding ID | BB/W003074/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2021 |
| End | 09/2024 |
| Description | 3D RNA-seq training workshop |
| Organisation | Australian National University (ANU) |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | We have carried out a 3D RNA-seq training workshop at the Australian National University. (https://www.eventbrite.com.au/e/3d-rna-seq-workshop-tickets-556207510637) |
| Collaborator Contribution | The participants have provided feedbacks on how to improve the 3D RNA-seq tool as well as the training. |
| Impact | not available yet |
| Start Year | 2023 |
| Description | Collaboration with Australian National University |
| Organisation | Australian National University (ANU) |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | Our team (Runxuan Zhang and Wenbin Guo) visited Dr. Eduardo Eryas' group at Australian National University (ANU) in February 2023. Our team conducted training sessions on our 3D RNA-seq transcriptomic pipeline (described in another collaboration/partner outcome provided by Runxuan Zhang). The team established the pipeline for using the computational tool developed in his group "rattle (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02715-w)" to process an sample nanopore sequencing dataset on barley RNAs. We also discussed about the future developments on RNA analysis. We also established contacts with other colleagues from ANU, including Ashley Jones (https://biology.anu.edu.au/people/professional-staff/ashley-jones) and Aude Fahrer (https://biology.anu.edu.au/people/academics/aude-fahrer). Runxuan Zhang also delivered a seminar talk entitled "Innovative advanced computational solutions for -omics data" |
| Collaborator Contribution | open invitation and arranged the visit |
| Impact | none yet |
| Start Year | 2023 |
| Description | Collaboration with La Trobe |
| Organisation | La Trobe University |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | Our team (Runxuan Zhang and Wenbin Guo) visited La Trobe University and conducted training sessions on our 3D RNA-seq transcriptomic pipeline. Runxuan Zhang also delivered a talk with a title "Computational solutions for tools and resources for accurate transcriptomics". Connections have been established with colleagues at La Trobe, including Monika Doblin (https://scholars.latrobe.edu.au/mdoblin), Tony Bacic (https://scholars.latrobe.edu.au/tbacic), Ricarda Jost (https://scholars.latrobe.edu.au/rjost), Oliver Berkowitz (https://scholars.latrobe.edu.au/oberkowitz) and Quentin Gouil (https://www.wehi.edu.au/people/matthew-ritchie/239/matthew-ritchie-lab-team) |
| Collaborator Contribution | Our team learned about the exciting single cell and cannabis work carried out at La Trobe. |
| Impact | Open invitation to visit and explore ways to develop spatial transcriptomics |
| Start Year | 2023 |
| Description | Collaboration with the Australian Commonwealth Scientific and Industrial Research Organization (CSIRO) |
| Organisation | Commonwealth Scientific and Industrial Research Organisation |
| Country | Australia |
| Sector | Public |
| PI Contribution | Our team of Runxuan Zhang and Wenbin Guo visited Commonwealth Scientific and Industrial Research Organization (CSIRO) Canberra on March 7th and 9th and met with data analysis group headed by Shannon Dillon. Runxuan Zhang delivered a presentation of our transcriptomics work. |
| Collaborator Contribution | Our team learned about work carried out at CSIRO including Phenomics, genome to phenomes, integrated analytics and crop breeding data science. |
| Impact | New connections with Australian researchers at CSIRO |
| Start Year | 2023 |
| Description | 3D RNA-seq Training at La Trobe University at Melbourne, Australia |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | 12 PhD students and postdocs at La Trobe University in Melbourne Australia have attend the 3D RNA-seq training workshop, which equipped them with analysis skill for RNA-seq data. An anonymous survey shows that 100% of participants would recommend the training course and the 3D RNA-seq tool to others. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.eventbrite.com.au/e/3d-rna-seq-app-a-flexible-and-powerful-tool-for-analysis-of-rna-seq-... |
| Description | Deliver 3D RNA-seq training workshop at Australian National University |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Wenbin and I have undertaken a two-day workshop about their software 3D RNA-seq (https://3drnaseq.hutton.ac.uk/app_direct/3DRNAseq/) for the analysis of transcriptomics data. Sessions are available to attend on the following dates and times: Wednesday 1 March 2023, 9:00am to 12:00 noon, Seminar Rooms 1 & 2 Thursday 2 March 2023, 9:00am to 12:00 noon, Seminar Rooms 1 & 2 |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.eventbrite.com.au/e/3d-rna-seq-workshop-tickets-556207510637 |