Deakin University
Browse

File(s) under permanent embargo

A village in a dish model system for population-scale hiPSC studies

Version 2 2024-06-02, 22:57
Version 1 2023-07-18, 03:46
journal contribution
posted on 2024-06-02, 22:57 authored by DR Neavin, AM Steinmann, N Farbehi, HS Chiu, MS Daniszewski, H Arora, Y Bermudez, C Moutinho, CL Chan, M Bax, M Tyebally, V Gnanasambandapillai, CE Lam, U Nguyen, Damian HernandezDamian Hernandez, GE Lidgerwood, RM Graham, AW Hewitt, A Pébay, NJ Palpant, JE Powell
AbstractThe mechanisms by which DNA alleles contribute to disease risk, drug response, and other human phenotypes are highly context-specific, varying across cell types and different conditions. Human induced pluripotent stem cells are uniquely suited to study these context-dependent effects but cell lines from hundreds or thousands of individuals are required. Village cultures, where multiple induced pluripotent stem lines are cultured and differentiated in a single dish, provide an elegant solution for scaling induced pluripotent stem experiments to the necessary sample sizes required for population-scale studies. Here, we show the utility of village models, demonstrating how cells can be assigned to an induced pluripotent stem line using single-cell sequencing and illustrating that the genetic, epigenetic or induced pluripotent stem line-specific effects explain a large percentage of gene expression variation for many genes. We demonstrate that village methods can effectively detect induced pluripotent stem line-specific effects, including sensitive dynamics of cell states.

History

Journal

Nature Communications

Volume

14

Article number

3240

Pagination

1-12

Location

London, Eng.

ISSN

2041-1723

eISSN

2041-1723

Language

eng

Publication classification

C1.1 Refereed article in a scholarly journal

Issue

1

Publisher

Nature Research

Usage metrics

    Research Publications

    Categories

    No categories selected

    Exports

    RefWorks
    BibTeX
    Ref. manager
    Endnote
    DataCite
    NLM
    DC