-transparent.png){kind=logo}
Molecular and functional variation in iPSC-derived sensory neurons. 2018
Jeremy Schwartzentruber, and
Stefanie Foskolou, and
Helena Kilpinen, and
Julia Rodrigues, and
Kaur Alasoo, and
Andrew J Knights, and
Minal Patel, and
Angela Goncalves, and
Rita Ferreira, and
Caroline Louise Benn, and
Anna Wilbrey, and
Magda Bictash, and
Emma Impey, and
Lishuang Cao, and
Sergio Lainez, and
Alexandre Julien Loucif, and
Paul John Whiting, and
, and
Alex Gutteridge, and
Daniel J Gaffney
Wellcome Trust Sanger Institute, Hinxton, UK. jeremys@ebi.ac.uk.
Induced pluripotent stem cells (iPSCs), and cells derived from them, have become key tools for modeling biological processes, particularly in cell types that are difficult to obtain from living donors. Here we present a map of regulatory variants in iPSC-derived neurons, based on 123 differentiations of iPSCs to a sensory neuronal fate. Gene expression was more variable across cultures than in primary dorsal root ganglion, particularly for genes related to nervous system development. Using single-cell RNA-sequencing, we found that the number of neuronal versus contaminating cells was influenced by iPSC culture conditions before differentiation. Despite high differentiation-induced variability, our allele-specific method detected thousands of quantitative trait loci (QTLs) that influenced gene expression, chromatin accessibility, and RNA splicing. On the basis of these detected QTLs, we estimate that recall-by-genotype studies that use iPSC-derived cells will require cells from at least 20-80 individuals to detect the effects of regulatory variants with moderately large effect sizes.
Related Publications
Jeremy Schwartzentruber, and
Stefanie Foskolou, and
Helena Kilpinen, and
Julia Rodrigues, and
Kaur Alasoo, and
Andrew J Knights, and
Minal Patel, and
Angela Goncalves, and
Rita Ferreira, and
Caroline Louise Benn, and
Anna Wilbrey, and
Magda Bictash, and
Emma Impey, and
Lishuang Cao, and
Sergio Lainez, and
Alexandre Julien Loucif, and
Paul John Whiting, and
, and
Alex Gutteridge, and
Daniel J Gaffney
March 2024,
Scientific reports,
Jeremy Schwartzentruber, and
Stefanie Foskolou, and
Helena Kilpinen, and
Julia Rodrigues, and
Kaur Alasoo, and
Andrew J Knights, and
Minal Patel, and
Angela Goncalves, and
Rita Ferreira, and
Caroline Louise Benn, and
Anna Wilbrey, and
Magda Bictash, and
Emma Impey, and
Lishuang Cao, and
Sergio Lainez, and
Alexandre Julien Loucif, and
Paul John Whiting, and
, and
Alex Gutteridge, and
Daniel J Gaffney
June 2022,
Toxicological sciences : an official journal of the Society of Toxicology,
Jeremy Schwartzentruber, and
Stefanie Foskolou, and
Helena Kilpinen, and
Julia Rodrigues, and
Kaur Alasoo, and
Andrew J Knights, and
Minal Patel, and
Angela Goncalves, and
Rita Ferreira, and
Caroline Louise Benn, and
Anna Wilbrey, and
Magda Bictash, and
Emma Impey, and
Lishuang Cao, and
Sergio Lainez, and
Alexandre Julien Loucif, and
Paul John Whiting, and
, and
Alex Gutteridge, and
Daniel J Gaffney
December 2023,
iScience,
Jeremy Schwartzentruber, and
Stefanie Foskolou, and
Helena Kilpinen, and
Julia Rodrigues, and
Kaur Alasoo, and
Andrew J Knights, and
Minal Patel, and
Angela Goncalves, and
Rita Ferreira, and
Caroline Louise Benn, and
Anna Wilbrey, and
Magda Bictash, and
Emma Impey, and
Lishuang Cao, and
Sergio Lainez, and
Alexandre Julien Loucif, and
Paul John Whiting, and
, and
Alex Gutteridge, and
Daniel J Gaffney
July 2018,
SLAS discovery : advancing life sciences R & D,
Jeremy Schwartzentruber, and
Stefanie Foskolou, and
Helena Kilpinen, and
Julia Rodrigues, and
Kaur Alasoo, and
Andrew J Knights, and
Minal Patel, and
Angela Goncalves, and
Rita Ferreira, and
Caroline Louise Benn, and
Anna Wilbrey, and
Magda Bictash, and
Emma Impey, and
Lishuang Cao, and
Sergio Lainez, and
Alexandre Julien Loucif, and
Paul John Whiting, and
, and
Alex Gutteridge, and
Daniel J Gaffney
January 2020,
Methods in molecular biology (Clifton, N.J.),
Jeremy Schwartzentruber, and
Stefanie Foskolou, and
Helena Kilpinen, and
Julia Rodrigues, and
Kaur Alasoo, and
Andrew J Knights, and
Minal Patel, and
Angela Goncalves, and
Rita Ferreira, and
Caroline Louise Benn, and
Anna Wilbrey, and
Magda Bictash, and
Emma Impey, and
Lishuang Cao, and
Sergio Lainez, and
Alexandre Julien Loucif, and
Paul John Whiting, and
, and
Alex Gutteridge, and
Daniel J Gaffney
March 2024,
Blood,
Jeremy Schwartzentruber, and
Stefanie Foskolou, and
Helena Kilpinen, and
Julia Rodrigues, and
Kaur Alasoo, and
Andrew J Knights, and
Minal Patel, and
Angela Goncalves, and
Rita Ferreira, and
Caroline Louise Benn, and
Anna Wilbrey, and
Magda Bictash, and
Emma Impey, and
Lishuang Cao, and
Sergio Lainez, and
Alexandre Julien Loucif, and
Paul John Whiting, and
, and
Alex Gutteridge, and
Daniel J Gaffney
April 2016,
Science translational medicine,
Jeremy Schwartzentruber, and
Stefanie Foskolou, and
Helena Kilpinen, and
Julia Rodrigues, and
Kaur Alasoo, and
Andrew J Knights, and
Minal Patel, and
Angela Goncalves, and
Rita Ferreira, and
Caroline Louise Benn, and
Anna Wilbrey, and
Magda Bictash, and
Emma Impey, and
Lishuang Cao, and
Sergio Lainez, and
Alexandre Julien Loucif, and
Paul John Whiting, and
, and
Alex Gutteridge, and
Daniel J Gaffney
July 2021,
Neurobiology of disease,
Jeremy Schwartzentruber, and
Stefanie Foskolou, and
Helena Kilpinen, and
Julia Rodrigues, and
Kaur Alasoo, and
Andrew J Knights, and
Minal Patel, and
Angela Goncalves, and
Rita Ferreira, and
Caroline Louise Benn, and
Anna Wilbrey, and
Magda Bictash, and
Emma Impey, and
Lishuang Cao, and
Sergio Lainez, and
Alexandre Julien Loucif, and
Paul John Whiting, and
, and
Alex Gutteridge, and
Daniel J Gaffney
May 2023,
Cells,
Jeremy Schwartzentruber, and
Stefanie Foskolou, and
Helena Kilpinen, and
Julia Rodrigues, and
Kaur Alasoo, and
Andrew J Knights, and
Minal Patel, and
Angela Goncalves, and
Rita Ferreira, and
Caroline Louise Benn, and
Anna Wilbrey, and
Magda Bictash, and
Emma Impey, and
Lishuang Cao, and
Sergio Lainez, and
Alexandre Julien Loucif, and
Paul John Whiting, and
, and
Alex Gutteridge, and
Daniel J Gaffney
April 2021,
Stem cell research,
