Combined quantification of intracellular (phospho-)proteins and transcriptomics from fixed single cells

Jan P Gerlach; Jessie A G van Buggenum; Sabine E J Tanis; Mark Hogeweg; Branco M H Heuts; Mauro J Muraro; Lisa Elze; Francesca Rivello; Agata Rakszewska; Alexander van Oudenaarden; Wilhelm T S Huck; Hendrik G Stunnenberg; Klaas W Mulder

doi:10.1038/s41598-018-37977-7

Combined quantification of intracellular (phospho-)proteins and transcriptomics from fixed single cells

Jan P Gerlach, Jessie A G van Buggenum, Sabine E J Tanis, Mark Hogeweg, Branco M H Heuts, Mauro J Muraro, Lisa Elze, Francesca Rivello, Agata Rakszewska, Alexander van Oudenaarden, Wilhelm T S Huck, Hendrik G Stunnenberg, Klaas W Mulder

Hubrecht Institute

Research output: Contribution to journal/periodical › Article › Scientific › peer-review

59 Citations (Scopus)

Abstract

Environmental stimuli often lead to heterogeneous cellular responses and transcriptional output. We developed single-cell RNA and Immunodetection (RAID) to allow combined analysis of the transcriptome and intracellular (phospho-)proteins from fixed single cells. RAID successfully recapitulated differentiation-state changes at the protein and mRNA level in human keratinocytes. Furthermore, we show that differentiated keratinocytes that retain high phosphorylated FAK levels, a feature associated with stem cells, also express a selection of stem cell associated transcripts. Our data demonstrates that RAID allows investigation of heterogeneous cellular responses to environmental signals at the mRNA and phospho-proteome level.

Original language	English
Pages (from-to)	1469
Journal	Scientific Reports
Volume	9
Issue number	1
DOIs	https://doi.org/10.1038/s41598-018-37977-7
Publication status	Published - 06 Feb 2019

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Gerlach, J. P., van Buggenum, J. A. G., Tanis, S. E. J., Hogeweg, M., Heuts, B. M. H., Muraro, M. J., Elze, L., Rivello, F., Rakszewska, A., van Oudenaarden, A., Huck, W. T. S., Stunnenberg, H. G., & Mulder, K. W. (2019). Combined quantification of intracellular (phospho-)proteins and transcriptomics from fixed single cells. Scientific Reports, 9(1), 1469. https://doi.org/10.1038/s41598-018-37977-7

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title = "Combined quantification of intracellular (phospho-)proteins and transcriptomics from fixed single cells",

abstract = "Environmental stimuli often lead to heterogeneous cellular responses and transcriptional output. We developed single-cell RNA and Immunodetection (RAID) to allow combined analysis of the transcriptome and intracellular (phospho-)proteins from fixed single cells. RAID successfully recapitulated differentiation-state changes at the protein and mRNA level in human keratinocytes. Furthermore, we show that differentiated keratinocytes that retain high phosphorylated FAK levels, a feature associated with stem cells, also express a selection of stem cell associated transcripts. Our data demonstrates that RAID allows investigation of heterogeneous cellular responses to environmental signals at the mRNA and phospho-proteome level.",

author = "Gerlach, {Jan P} and {van Buggenum}, {Jessie A G} and Tanis, {Sabine E J} and Mark Hogeweg and Heuts, {Branco M H} and Muraro, {Mauro J} and Lisa Elze and Francesca Rivello and Agata Rakszewska and {van Oudenaarden}, Alexander and Huck, {Wilhelm T S} and Stunnenberg, {Hendrik G} and Mulder, {Klaas W}",

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Gerlach, JP, van Buggenum, JAG, Tanis, SEJ, Hogeweg, M, Heuts, BMH, Muraro, MJ, Elze, L, Rivello, F, Rakszewska, A, van Oudenaarden, A, Huck, WTS, Stunnenberg, HG & Mulder, KW 2019, 'Combined quantification of intracellular (phospho-)proteins and transcriptomics from fixed single cells', Scientific Reports, vol. 9, no. 1, pp. 1469. https://doi.org/10.1038/s41598-018-37977-7

TY - JOUR

T1 - Combined quantification of intracellular (phospho-)proteins and transcriptomics from fixed single cells

AU - Gerlach, Jan P

AU - van Buggenum, Jessie A G

AU - Tanis, Sabine E J

AU - Hogeweg, Mark

AU - Heuts, Branco M H

AU - Muraro, Mauro J

AU - Elze, Lisa

AU - Rivello, Francesca

AU - Rakszewska, Agata

AU - van Oudenaarden, Alexander

AU - Huck, Wilhelm T S

AU - Stunnenberg, Hendrik G

AU - Mulder, Klaas W

PY - 2019/2/6

Y1 - 2019/2/6

N2 - Environmental stimuli often lead to heterogeneous cellular responses and transcriptional output. We developed single-cell RNA and Immunodetection (RAID) to allow combined analysis of the transcriptome and intracellular (phospho-)proteins from fixed single cells. RAID successfully recapitulated differentiation-state changes at the protein and mRNA level in human keratinocytes. Furthermore, we show that differentiated keratinocytes that retain high phosphorylated FAK levels, a feature associated with stem cells, also express a selection of stem cell associated transcripts. Our data demonstrates that RAID allows investigation of heterogeneous cellular responses to environmental signals at the mRNA and phospho-proteome level.

AB - Environmental stimuli often lead to heterogeneous cellular responses and transcriptional output. We developed single-cell RNA and Immunodetection (RAID) to allow combined analysis of the transcriptome and intracellular (phospho-)proteins from fixed single cells. RAID successfully recapitulated differentiation-state changes at the protein and mRNA level in human keratinocytes. Furthermore, we show that differentiated keratinocytes that retain high phosphorylated FAK levels, a feature associated with stem cells, also express a selection of stem cell associated transcripts. Our data demonstrates that RAID allows investigation of heterogeneous cellular responses to environmental signals at the mRNA and phospho-proteome level.

U2 - 10.1038/s41598-018-37977-7

DO - 10.1038/s41598-018-37977-7

M3 - Article

C2 - 30728416

SN - 2045-2322

VL - 9

SP - 1469

JO - Scientific Reports

JF - Scientific Reports

IS - 1

ER -

Combined quantification of intracellular (phospho-)proteins and transcriptomics from fixed single cells

Abstract

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