Journal article

Targeted single-cell RNA sequencing of transcription factors enhances the identification of cell types and trajectories

Alexandra Pokhilko, Adam E Handel, Fabiola Curion, Viola Volpato, Emma S Whiteley, Sunniva Bostrand, Sarah E Newey, Colin J Akerman, Caleb Webber, Michael B Clark, Rory Bowden, M Zameel Cader

GENOME RESEARCH | COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT | Published : 2021

Abstract

Single-cell RNA sequencing (scRNA-seq) is a widely used method for identifying cell types and trajectories in biologically heterogeneous samples, but it is limited in its detection and quantification of lowly expressed genes. This results in missing important biological signals, such as the expression of key transcription factors (TFs) driving cellular differentiation. We show that targeted sequencing of ∼1000 TFs (scCapture-seq) in iPSC-derived neuronal cultures greatly improves the biological information garnered from scRNA-seq. Increased TF resolution enhanced cell type identification, developmental trajectories, and gene regulatory networks. This allowed us to resolve differences among n..

View full abstract

University of Melbourne Researchers

Grants

Awarded by EU/European Federation of Pharmaceutical Industries and Associations Innovative Medicines Initiative 2 Joint Undertaking (IM2PACT grant)


Awarded by EU/European Federation of Pharmaceutical Industries and Associations Innovative Medicines Initiative 2 Joint Undertaking (AIMS-2-TRIALS grant )


Awarded by Biotechnology and Biological Sciences Research Council (BBSRC) project


Awarded by European Research Council (ERC)


Awarded by Innovative Medicines Initiative Joint Undertaking


Awarded by Australian National Health and Medical Research Council (NHMRC) Early Career Fellowship


Awarded by EMBO Long Term Fellowship


Awarded by Wellcome Trust Research Training Fellowship


Awarded by Wellcome Trust


Funding Acknowledgements

This work was supported by a grant SFB646 from the EU/European Federation of Pharmaceutical Industries and Associations Innovative Medicines Initiative 2 Joint Undertaking (IM2PACT grant no. 807015 and AIMS-2-TRIALS grant agreement no. 777394) ; from National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC) ; from Biotechnology and Biological Sciences Research Council (BBSRC) project BB/S007938/1; from European Research Council (ERC) Grant Agreement 617670 and the Innovative Medicines Initiative Joint Undertaking under grant agreement no. 115439; from an Australian National Health and Medical Research Council (NHMRC) Early Career Fellowship (APP1072662 to M.B.C.) ; from an EMBO Long Term Fellowship (ALTF 864-2013 to M.B.C.) ; from Victorian State Government Operational Infrastructure Support and Australian Government NHMRC Independent Research Institutes Infrastructure Supports Scheme (IRIISS) . A.E.H. was supported by an NIHR Clinical Lectureship and Wellcome Trust Research Training Fellowship (100643/Z/12/Z) . Core funding to the Wellcome Centre for Human Genetics was provided by the Wellcome Trust (awards 090532/Z/09/Z and 203141/Z/16/Z) .