Journal article

A simple, scalable approach to building a cross-platform transcriptome atlas

Paul W Angel, Nadia Rajab, Yidi Deng, Chris M Pacheco, Tyrone Chen, Kim-Anh Le Cao, Jarny Choi, Christine A Wells

PLOS COMPUTATIONAL BIOLOGY | PUBLIC LIBRARY SCIENCE | Published : 2020

Abstract

Gene expression atlases have transformed our understanding of the development, composition and function of human tissues. New technologies promise improved cellular or molecular resolution, and have led to the identification of new cell types, or better defined cell states. But as new technologies emerge, information derived on old platforms becomes obsolete. We demonstrate that it is possible to combine a large number of different profiling experiments summarised from dozens of laboratories and representing hundreds of donors, to create an integrated molecular map of human tissue. As an example, we combine 850 samples from 38 platforms to build an integrated atlas of human blood cells. We a..

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Grants

Awarded by Australian Research Council


Awarded by National Health and Medical Research Council (NHMRC) Career Development fellowship


Awarded by NHMRC


Funding Acknowledgements

Stemformatics was established through Australian Research Council Funding to Stem Cells Australia (SRI110001002)and to CAW (Future Fellowship FT150100330) (https://www.arc.gov.au).KALC was supported by the National Health and Medical Research Council (NHMRC) Career Development fellowship (GNT1159458). PWA and JR are funded by NHMRC (GNT1181327) and (APP1186371) to CAW (https://www.nhmrc.gov.au).NR is funded by the Centre for Stem Cell Systems (https://biomedicalsciences.unimelb.edu.au/departments/anatomy-and-neuroscience/engage/cscs) and the CSIRO Synthetic Biology Future Science Platform (https://research.csiro.au/synthetic-biology-fsp/).The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.The authors thank Matthew Rutar for early discussions on blood annotations, Jack Bransfield and Isha Nagpal for front end development of the Stemformatics server. This research was undertaken with the assistance of resources from the National Computational Infrastructure (NCI Australia), an NCRIS enabled capability supported by the Australian Government.