Research
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
| Featured projects | Duration |
|---|---|
|
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 |
|
Quantitative transcriptome analysis (CAGE) Genome Innovation Hub Collaborative Project (UQ infrastructure) |
2019 |
|
Genome-wide CRISPR screening for modifiers of diverse cellular phenotypes Genome Innovation Hub Collaborative Project (UQ infrastructure) |
2019 |
|
Spatial genomics technologies to study cancer and genetic diseases in tissue contexts Genome Innovation Hub Collaborative Project (UQ infrastructure) |
2019 |
Pages
Publications & pre-prints
Sushma Marla, Sally Mortlock, Sohye Yoon, Joanna Crawford, Stacey Andersen, Michael D. Mueller, Brett McKinnon, Quan Nguyen, Grant W. Montgomery
Cells, Volume 12, Issue 13 (2023); https://doi.org/10.3390/cells12131736
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)
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
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
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
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
