Project title
Producing a haplotype-resolved germline Ig/TR reference assembly with high-fidelity whole genome sequencing in commonly-used laboratory mouse strains.
Collaborators and funding
Collaborators:
- Dr Katherine Jackson, Immunogenomics Lab, The Garvan Institute of Medical Research, Australia
- A/Prof Alexandra Sharland, Transplantation Immunobiology Group, Central Clinical School, The University of Sydney, Australia
- Shivanjali Ratnaseelan, Transplantation Immunobiology Group, Central Clinical School, The University of Sydney, Australia
- Martina Denkova, Transplantation Immunobiology Group, Central Clinical School, The University of Sydney, Australia
Bioinformatics support:
- Dr Ziad Al Bkhetan, Australian BioCommons
- Dr Georgina Samaha, Australian BioCommons, Bioinformatics Group, Sydney Informatics Hub, University of Sydney
Contact(s)
- Dr Katherine Jackson, k.jackson@garvan.org.au
- A/Prof Alexandra Sharland, alexandra.sharland@sydney.edu.au
- Shivanjali Ratnaseelan, srat5986@uni.sydney.edu.au
- Martina Denkova, mden0475@uni.sydney.edu.au
Project description and aims
We will perform high coverage whole genome sequencing on high molecular weight DNA extracted from BALB/c and B10.BR mouse kidney cells using PacBio Revio. We will then perform de-novo reference assembly, contig-alignment, and annotation to create a haplotype-resolved reference dataset of Immunoglobulin and T cell receptor germline genes.
How is ABLeS supporting this work?
This work is supported through the production bioinformatics scheme provided by ABLeS. The supports includes 4TB storage on scratch, 3 TB long-term storage and 50 KSUs allocation per quarter.
Expected outputs enabled by participation in ABLeS
Our work will result in haplotype-resolved Immunoglobulin and T cell receptor germline reference assemblies with minimal bias, covering lesser-documented common laboratory mouse strains, which we aim to publish on publicly available platforms such as OGRDB (the open germline receptor database) and in impactful journals such as Nature Communications.
These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.