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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.

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.

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.