ProtoplastsAim

The aim of this project is to implement and optimize single cell RNA-seq and ATAC-seq (scRNA-seq and scATAC-seq) profiling methods in plant cells and associated bioinformatics data analysis pipelines to enable future discoveries in plant biology and agriculture across the large UQ plant biology research community.

Brief project outline

The Project consist of three aims/phases:

Aim 1: Generate scRNA-seq and scATAC-seq from Arabidopsis leaf protoplasts and, in comparison to the existing bulk RNA-seq and ATAC-seq data (Tanurdzic lab), determine cell type-specific gene expression and chromatin remodelling responses to the plant hormone strigolactone.

Aim 2: Compare scRNA-seq profiles obtained from isolated single nuclei to scRNA-seq data obtained from single plant protoplasts or to bulk RNA-seq data from the same organs/experiments.

Aim 3: Establish and evaluate the performance of the joint transcriptome and chromatin accessibility profiling method based on a splint adapter (as implemented in sci-CAR and SNARE-seq).

Genomics-based innovative aspect of proposal

Transcriptional and chromatin profiling of single plant cells/nuclei is in its infancy. While great technical and analytical strides have been made in the field of single cell profiling, and the GIH has been at the forefront of these development, little to none of this capability has been translated to plant single cell profiling. This is the main goal of this proposal: enabling single cell plant functional genomics and systems biology across a variety of plant species (both model organisms like Arabidopsis as well as crops, e.g. wheat), research questions, and UQ units. At the same time, we are proposing establishment of new methods for simultaneous transcriptome and chromatin accessibility profiling that would be of use across the wider genomics community (taxon-agnostic).

Broad applicability of the technique

Single cell profiling of transcriptomes and chromatin has a wide appeal. Its applications to plant cells is in its infancy and the implementation of the techniques and protocols in this proposal would place plant molecular biology researchers across UQ at an important advantage. Tanurdzic and GIH team will, therefore, work with UQ colleagues to share the expertise gained during the GIH project and share molecular biology protocols and bioinformatics analysis pipelines to facilitate adoption into the community of UQ genomics researchers.

 

 

Project members


Research collaborators

Dr Milos Tanurdzic

Dr Milos Tanurdzic

Senior Lecturer
School of Biological Sciences, Faculty of Science
Dr Elizabeth Dun

Dr Elizabeth Dun

UQ Amplify Associate Lecturer
School of Biological Sciences, Faculty of Science

Jazmine Lee Humphreys

PhD candidate
School of Biological Sciences, Faculty of Science
Dr Franziska Fichtner

Dr Franziska Fichtner

Laureate Fellow Postdoctoral Research
School of Biological Sciences, Faculty of Science

Genome Innovation Hub

Stacey Andersen

Stacey Andersen

Senior Research Assistant
Genome Innovation Hub
Senior Research Assistant
IMB Sequencing Facility
Dr Sohye Yoon

Dr Sohye Yoon

Research Assistant
Genome innovation Hub
Jun Xu

Jun Xu

Research Assistant
Genome Innovation Hub