Single-cell and short read sequencing

The Genome Innovation Hub continually develops a number of protocols and procedures while undertaking our collaborative projects. Below are a selection of detailed developments useful to researchers undertaking Single-cell and Short read sequencing procedures in the laboratory.

Developments

Cap analysis of gene expression (CAGE)

CAGE (cap analysis gene expression) is highly sensitive and accurate quantitative transcriptome analysis which utilizes a cap structure on 5’ end of RNA. This feature enables high-throughput identification of transcription start sites and ability to infer promoters and transcription factor binding motifs. 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. This protocol produces comparable results to the commercial kit while introducing savings in reagent costs and time.

scSplit tool: genotype-free demultiplexing of pooled single-cell RNA-seq

A variety of methods have been developed to demultiplex pooled samples in a single cell RNA sequencing (scRNA-seq) experiment which either require hashtag barcodes or sample genotypes prior to pooling. We introduce scSplit which utilizes genetic differences inferred from scRNA-seq data alone to demultiplex pooled samples. scSplit also enables mapping clusters to original samples. Using simulated, merged, and pooled multi-individual datasets, we show that scSplit prediction is highly concordant with demuxlet predictions and is highly consistent with the known truth in cell-hashing dataset.

Featured projects	Duration
Optimised bioinformatics and validation pipeline for genome-wide CRISPR screening data Genome Innovation Hub Collaborative Project (UQ infrastructure)	2021
RNA velocity quantification of single-cell transcriptomics Genome Innovation Hub Collaborative Project (UQ infrastructure)	2021
Expanding the scope of multimodal single cell sequencing Genome Innovation Hub Collaborative Project (UQ infrastructure)	2021
HTS single cell CRISPR technology for experimental validation of population genetics and functional genomics discovery Genome Innovation Hub Collaborative Project (UQ infrastructure)	2021
Understanding host-pathogen interactions through development of new co-transcriptomic single cell RNA sequencing technologies Genome Innovation Hub Collaborative Project (UQ infrastructure)	2020
Single-cell transcriptome and chromatin profiling in plant cells Genome Innovation Hub Collaborative Project (UQ infrastructure)	2020
Combining novel scSLAM-seq technology with 10x Genomics Chromium to track microchanges in newly synthesised RNA Genome Innovation Hub Collaborative Project (UQ infrastructure)	2020
Simultaneous identification of RNA-chromatin interactions and transcriptomes in single cells Genome Innovation Hub Collaborative Project (UQ infrastructure)	2020
Genome-wide CRISPR screening for modifiers of diverse cellular phenotypes Genome Innovation Hub Collaborative Project (UQ infrastructure)	2019
Quantitative transcriptome analysis (CAGE) Genome Innovation Hub Collaborative Project (UQ infrastructure)	2019

Publications & pre-prints

Genotype-free demultiplexing of pooled single-cell RNA-seq

Jun Xu, Caitlin Falconer, Quan Nguyen, Joanna Crawford, Brett D. McKinnon, Sally Mortlock, Anne Senabouth, Stacey Andersen, Han Sheng Chiu, Longda Jiang, Nathan J. Palpant, Jian Yang, Michael D. Mueller, Alex W. Hewitt, Alice Pébay, Grant W. Montgomery, Joseph E. Powell & Lachlan J.M Coin

Genome Biology volume 20, Article number: 290 (2019)

A Deep Learning Model for Molecular Label Transfer that Enables Cancer Cell Identification from Histopathology Images

Andrew Su, HoJoon Lee, Xiao Tan, Carlos J. Suarez, Noemi Andor, Quan Nguyen, Hanlee P. Ji

bioRxiv 2021.03.18.436004; doi: https://doi.org/10.1101/2021.03.18.436004

Spatially resolved transcriptome profiles of mammalian kidneys illustrate the molecular complexity of functional nephron segments, cell-to-cell interactions and genetic variants

Arti M. Raghubar, Duy T. Pham, Xiao Tan, Laura F. Grice, Joanna Crawford, Pui Yeng Lam, Stacey B. Andersen, Sohye Yoon, Monica S.Y. Ng, Siok Min Teoh, Samuel E. Holland, Anne Stewart, Leo Francis, Alexander N. Combes, Andrew J. Kassianos, Helen Healy, Quan Nguyen, Andrew J. Mallett

bioRxiv 2020.09.29.317917; doi: https://doi.org/10.1101/2020.09.29.317917

Spatial analysis of ligand-receptor interactions in skin cancer at genome-wide and single-cell resolution.

M Tran, S Yoon, M Teoh, S Andersen, PY Lam, P Purdue, A Raghubar, SJ Hanson, K Devitt, K Jones, S Walters, ZK Tuong, A Kulasinghe, J Monkman, HP Soyer, I Frazer, Q Nguyen.

https://doi.org/10.1101/2020.09.10.290833

stLearn: integrating spatial location, tissue morphology and gene expression to find cell types, cell-cell interactions and spatial trajectories within undissociated tissues

Duy Pham, Xiao Tan, Jun Xu, Laura F. Grice, Pui Yeng Lam, Arti Raghubar, Jana Vukovic, Marc J. Ruitenberg, Quan Nguyen
bioRxiv 2020.05.31.125658; doi: https://doi.org/10.1101/2020.05.31.125658

SpaCell: integrating tissue morphology and spatial gene expression to predict disease cells.

Xiao Tan, Andrew Su, Minh Tran, Quan Nguyen
Bioinformatics, Volume 36, Issue 7, 1 April 2020, Pages 2293–2294

Stacey Andersen

Senior Research Assistant

Genome Innovation Hub
Senior Research Assistant

IMB Sequencing Facility
Dr Tim Bruxner

Sequencing Specialist

Institute for Molecular Bioscience
Joanna Crawford

Senior Research Assistant

Institute for Molecular Bioscience
Dr Elizabeth Dun

UQ Amplify Associate Lecturer

School of Biological Sciences, Faculty of Science
Dr Emily Goodall

Research Officer

Institute for Molecular Bioscience
Professor Ian Henderson

Director

Institute for Molecular Bioscience
Affiliate Professor

UQ Centre for Clinical Research, Faculty of Medicine
Affiliate Professor

School of Chemistry and Molecular Biosciences, Faculty of Science
Jazmine Lee Humphreys

PhD candidate

School of Biological Sciences, Faculty of Science
Dr Ronan Kapetanovic

Senior Research Officer

Institute for Molecular Bioscience
Dr Denuja Karunakaran

IMB Fellow

Institute for Molecular Bioscience
Professor Grant Montgomery

Director

Genome Innovation Hub (GIH)
Professorial Research Fellow - GL

Institute for Molecular Biosciences (IMB)
Affiliate Professorial Research Fellow

Queensland Brain Institute (QBI)
Affiliate Professorial Research Fellow

Office of the Pro-Vice-Chancellor (Research Infrastructure)
Valentine Murigneux

Senior research assistant

Genome Innovation Hub
Bioinformatician

QCIF Facility for Advanced Bioinformatics
Dr Minh-Duy Phan

Postdoctoral Research Fellow

School of Chemistry and Molecular Biosciences, Faculty of Science
Dr Divya Ramnath

Research Officer

Institute for Molecular Bioscience
Dr Elizabeth Ross

Research Fellow

Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation
Dr Rebecca San Gil

FightMND Research Fellow

Queensland Brain Institute
Professor Matt Sweet

Professorial Research Fellow - GL

Institute for Molecular Bioscience
Affiliated Professor

School of Chemistry and Molecular Biosciences
Dr Milos Tanurdzic

Senior Lecturer

School of Biological Sciences, Faculty of Science
Jessica von Pein

PhD candidate

Institute for Molecular Bioscience
Dr Adam Walker

Ross Maclean Fellow

Queensland Brain Institute
Isabel Warner

PhD candidate

Institute for Molecular Bioscience
Dr Sohye Yoon

Research Assistant

Genome innovation Hub
Dr Qiongyi Zhao

Research Fellow

Queensland Brain Institute

Research

Single-cell and short read sequencing

Developments

Cap analysis of gene expression (CAGE)

scSplit tool: genotype-free demultiplexing of pooled single-cell RNA-seq

Publications & pre-prints