News

We are now excited to officially announce our new collaborative projects and lead researchers for 2022! We look forward to starting these projects soon and all the genomic and genetic developments that will arise from these diverse research areas.

Welcome to the first edition of the GIH newsletter for 2022. In this issue we are excited to announce the recipients of 2022 External Projects! We also highlight one of our collaborative projects, a novel method for plant epigenetic profiling, as well as our latest publications and new developments.

Of note is that March is worldwide Endometriosis month. In support we shine a spotlight on one of our GIH project leaders, Dr Brett McKinnon, a UQ research fellow working in this area. In this edition we also feature "a day in the life" in one of our latest collaborative UQ facilities, BASE, who bio-manufactures RNA/DNA for vaccine development.

The Genome Innovation Hub team are honoured to be the recipients of the 2021 Award For Team Excellence. This award recognises the significant and outstanding performance of a team within the Research and Innovation Portfolio. 

The members of the GIH team are honoured for our nominations for UQ's Deputy Vice-Chancellor's 2021 Research and Innovation staff awards! We'd like to thank all our nominators, collegues and our 100+ research collaborators sharing their exciting genomic and genetic project ideas with us!

The M. jansenii genome has been used as a model for testing sequencing methods using a wide range of long read sequencing techniques. Here, we report a chromosome level genome assembly, generated using a combination of Pacific Biosciences sequencing and Hi-C, comprising 14 pseudo-molecules, with a N50 of 52 Mb and a total genome assembly size of 758 Mb of which 56% is repetitive.

Happy Holidays from the Genome Innovation Hub research team.
We hope your holidays will be filled with joy and laughter through the New Year!
Thank you to all our fantastic collaborators, amazing colleagues and super supporters for being part of another great year of innovative genomic and genetic research at The University of Queensland!

The Institute for Molecular Bioscience (IMB) Impact Awards provide an opportunity for the Institute to acknowledge and celebrate the outstanding achievements and successes of their fellow staff and students. GIH's sequencing expert Stacey Andersen and lead bioinformatician Jun Xu, have both been nominated in the 2021 IMB Impact Awards in recognition of their efforts in collaborative IMB-based projects. 

To all applicants for an External Project with the Genome Innovation Hub (GIH) at The University of Queensland we appreciate the time you have taken to prepare your application and thank you for your interest in collaborating with The Genome Innovation Hub team.

Welcome to the fourth edition of the GIH newsletter for 2021. Firstly, in this issue we are pleased to introduce our new Deputy Director, Dr Allan McCrae.

We also announce our 2022 External Project call, the GIH team's nomination for the UQ Staff Excellence Awards and congratulate GIH's collaborators and committee members on recent NHMRC grant success. We highlight one of our collaborative projects, our latest publications and seminars. We shine a spotlight on one of project leaders, Dr Denuja Karunakaran as well as our collaborative computing facility QCIF Bioinformatics

The GIH team is proud to be nominated for the 2021 UQ Awards for Excellence!
We've had a great year working with all our colleagues including everyone within our collaborative projects and would like to thank our nominators, supporters and researchers for contributing to our success!

In this recorded webinar, GIH collaborator, Dr Peter Crisp, a DECRA Research Fellow and Lecturer who leads a research group in the School of Agriculture and Food Science, describes their recently developed approach that uses DNA methylation profiling of a single tissue (eg a leaf) to distill a genome down to the relatively small fraction of regions that are functionally valuable for trait variation throughout development.

Application closing date 26th November 2021.
Collaborating research groups with proposals for innovative genomic projects will be again sought for 2022. For successful applications, GIH staff and potential funding toward GIH consumables will support each project to develop cutting-edge technology breakthroughs (methods and pipelines).

Through our GIH funded collaborative project “Dual guide screening” and in association with the Queensland Facility for Advanced Genome Editing (QFAGE) and the Transgenic Animal Service of Queensland (TASQ) , we have built a workflow for high efficient CRISPR knockout using optimised triple guide RNA design. This workflow was utilised by GIH team member Dr Di Xia for the research within this publication by Harriet P. Lo, et al, where Di contributed to both the genome editing required to create both the Cavin4 Knockout mouse model and Cavin4 Knockout C2C12 cells.

Hosted by Australian BioCommons. As part of this launch, you’ll hear what’s possible from some of the early adopters including Prof Sandie Degnan and Prof Bernard Degnan, who have utilised the Apollo platform to provide the framework for their muti-omic browser in the GIH collaboratative project "Developing a scalable genome browser and repository for complex multi-omic datasets". Wednesday, 29 September 2021:12:00 pm 1:00 pm

Through the collaborative project “Dual guide screening” and in association with QFAGE and Agilent, we have generated a workflow for high efficient CRISPR knockout using optimised multiple guide RNA design. This workflow was utilised by GIH team member Dr Di Xia for the research within this publication by Meredith A. Redd, et al, where Di prepared the method for the genome editing strategy design, supervised the CRISPR transfection, troubleshooting and analysis to generate the Asic1a knock-out iPSCs, along with training members of the QFAGE in the procedure.

As one of the sucessful outcomes from the GIH funded collaborative project Simultaneous identification of RNA-chromatin interactions and transcriptomes in single cells, contributing author and team member of both GIH and the UQ Sequencing Facilty, Stacey Andersen, performed sequencing on the NextSeq of the Illumina libraries and reviewed the manuscript.

Welcome to the third edition of the GIH newsletter for 2021. In this issue we highlight the RNAscope Hiplex assay, introduce the GIH project Genome Phaser and mention our latest collaborative publications, workshops, software, seminars and news. We also shine a spotlight on one of project leaders, Dr CX Chan as well as three partner UQ facilities: Australian Centre for Ecogenomics, Genomic Research Services and the newly formed Viral Vector Core.

Acknowledgment: The Authors noted that the work was supported by funding from the Genome Innovation Hub.
They are part of the GIH collaborative project "Simultaneous identification of RNA-chromatin interactions and transcriptomes in single cells, January 2020"

As an update to our GIH collaborative publication "Comparison of long-read methods for sequencing and assembly of a plant genome", GigaScience journal's sister journal, GigaByte, has just published the followup publication "Improvements in the sequencing and assembly of plant genomes" as its first ever Update article!
Congratulations to everyone involved in these two publications.  

As a follow on from the GIH funded project "Assembly of complex genome (Macadamia) using single molecule sequencing", Dual GIH and QCIF team member Valentine Murigneux contributed to this publication through her involvement in the conceptualization, data curation, funding aquisition and drafting of the manuscript.

Register for this great Galaxy tutorial by QCIF and GIHs Valentine Murigneux! 

Acknowledgement: The authors thanked the University of Queensland Genome Innovation Hub for continuing support. They are part of the GIH collaborative project "Simultaneous identification of RNA-chromatin interactions and transcriptomes in single cells, January 2020"

Dear Colleagues,
Welcome to the second edition of the GIH newsletter for 2021.
In this issue we highlight some of our new developments, project updates and news. We also shine a spotlight on some of our collaborators and one of our partner facilities.
The next edition of this newsletter will be distributed in August 2021.
Professor Grant Montgomery, Director

Acknowledgment: The Authors noted that the work was supported by funding from the Genome Innovation Hub external project grants. They are part of the GIH collaborative project "Spatial genomics technologies to study cancer and genetic diseases in tissue contexts,
January 2019".

Thanks to AGRF's new "Live & On Demand" webinar series, you can find out more about the AGRF-UQ PacBio Sequel II service by watching a webinar featuring talks by our GIH collaborator, Dr CX Chan, the UQ IMB sequencing Facility Manager, Angelika Christ, as well as representatives from UQ Research Infrastructure, AGRF and PacBio.

Dear Colleagues,
Welcome to the first edition of the newsletter for 2021. 
In this issue we highlight some of our recent achievements, new developments and project updates. We are also proud to announce our new collaborative projects for 2021. 
The next edition of this newsletter will be distributed in May 2021.

As a successful outcome of the GIH funded project "Assembly of complex genome (Macadamia) using single molecule sequencing", Dual GIH and QCIF team member Valentine Murigneux performed Illumina, Oxford Nanopore Technology (ONT) and PacBio assemblies and assembly evaluation. Valentine also wrote the manuscript draft with input from all authors. GIH team member Dr Subash Rai performed the ONT library preparation and sequencing. 

Acknowledgement: The authors thanked the University of Queensland Genome Innovation Hub for continuing support. They are part of the GIH collaborative project "Simultaneous identification of RNA-chromatin interactions and transcriptomes in single cells, January 2020"

***NOTE THAT APPLICATIONS HAVE CLOSED FOR 2021 EXTERNAL PROJECTS***

As a successful follow-on from the GIH funded project "Spatial genomics technologies to study cancer and genetic diseases in tissue contexts", contributing author and team member of both GIH and the IMB Sequencing Facilty, Stacey Andersen, assisted with library preparation and sequencing on the  NextSeq500 (Illumina) instrument for data utilised in this publication. Dr Sohye Yoon supported the experimental set up including sample preparation of histology sections and imaging.

As one of the sucessful outcomes from the GIH funded collaborative project "Spatial genomics technologies to study cancer and genetic diseases in tissue contexts", GIH team member Dr Sohye Yoon, as the first co-author of the paper, conducted RNAscope Hiplex and droplet digital PCR assays. Sohye also contributed to drafting the manuscript including the work-flow illustration. Contributing author and team member of both GIH and the IMB Sequencing Facilty, Stacey Andersen, performed the NextSeq sequencing with the ST libraries. Stacey also contributed to sample preparation and performed droplet digital PCR experiments. Contributing author and team member Dr Brooke Purdue assisted with initial microscopy and imaging.

This project established the availability of CAGE through development of an optimized, cost -efficient in-house protocol, benchmarked against a commercially available ‘gold standard’ kit.

As one of the sucessful outcomes from the GIH funded collaborative project "Spatial genomics technologies to study cancer and genetic diseases in tissue contexts", GIH team member Jun Xu helped to conceive the experiments, develop the algorithms, write the software, conduct the experiments and analyse the data. He also helped to write the manuscript. GIH team member Dr Sohye Yoon conducted the RNAscope Hiplex assays. Sohye also contributed to drafting the manuscript. 

This webinar will present a comparison of three long read sequencing technologies applied to the de novo assembly of a plant genome, Macadamia jansenii.
GIH Collaborative Project.
Hosted by Australian BioCommons.

Thursday, July 2, 2020, 12:00 PM 1:00 PM

In this webinar, Professor Lachlan Coin will talk about his recent study with the Genome Innovation Hub at The University of Queensland for de novo assembly of the genome of Australia’s vulnerable plant species, Macadamia jansenii. In this study several long read sequencing technologies, including MGI’s unique single-tube Long Fragment Read (stLFR), are compared for the same sample.
GIH Collaborative Project.
Hosted by MGI

A new tool for visualising TraDIS (Transposon Directed Insertion Site Sequencing ) data. Search for your gene of interest via our new web browser developed with Professor Ian Henderson at the Institute of Biomolecular Sciences (IMB), Dr Dom Gorse at the Queensland Facility for Advanced Bioinformatics (QFAB Bioinformatics) in collaboration with the Genome Innovation Hub (GIH) at the University of Queensland.

Acknowledgement: The authors have acknowledged that the research for this publication was supported by GIH funding. They are part of the GIH collaborative project "Spatial genomics technologies to study cancer and genetic diseases in tissue contexts, 2019".

Here we introduce a simple, accurate, and efficient tool, mainly for droplet-based scRNA-seq, called "scSplit", which uses a hidden state model approach to demultiplex individual samples from mixed scRNA-seq data with high accuracy. Our approach does not require genotype information from the individual samples to demultiplex them, which also makes it suitable for applications where genotypes are unavailable or difficult to obtain. scSplit uses existing bioinformatics tools to identify putative variant sites from scRNA-seq data, then models the allelic counts to assign cells to clusters using an expectation-maximisation framework.

stLearn is designed to comprehensively analyse Spatial Transcriptomics (ST) data to investigate complex biological processes within an undissociated tissue.

A new method for demultiplexing pooled scRNA-seq data, which does not require a sample genotype, but uses genetic differences learnt from the data. Developed at The University of Queensland's Genome Innovation Hub (GIH) by Jon Xu with Professor Lachlan Coin (The University of Melbourne, Doherty Institute) and colleagues.