Cited by 119Single-cell and spatial transcriptomicsAdvanced Proteomics Techniques and ApplicationsMolecular Biology Techniques and Applications

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

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Gerlach, Jan. P., van Buggenum, Jessie A. G., Tanis, Sabine E. J., Hogeweg, Mark, Heuts, Branco M. H., Muraro, Mauro J., Elze, Lisa, Rivello, Francesca +5 more·2019·Scientific Reports

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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.

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Crossref · 10.1038/s41598-018-37977-7

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  • RAID enables correlation analysis of environmental stimuli with heterogeneous cellular responses.

    “RNA and immunodetection (RAID), a method developed for immunodetection of intracellular proteins or phosphorylated proteins together with mRNA profiling, enables correlation analysis of environmental stimuli with heterogeneous cellular responses77.”

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Authors
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.
Affiliations
  • Radboud University Nijmegen (NL)
  • Royal Netherlands Academy of Arts and Sciences (NL)
Corresponding author
Mulder, Klaas W.
Venue
Scientific Reports
Published
2019-02-06
Volume
9
Issue
1
Pages
1469-1469
ISSN
2045-2322 (ISSN-L)
OpenAlex
W2810689242
Cited by
104
References
35
Citations by year
2026: 10 · 2025: 11 · 2024: 13 · 2023: 21 · 2022: 15 · 2021: 20 · 2020: 8 · 2019: 5
FWCI
3.97
Type
journal article
Language
en
Open access
Locations
  • Scientific Reports (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • Europe PMC (PubMed Central) (publishedVersion, other-oa)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • KNAW research portal (Royal Academy of Art and Sciences (KNAW)) (publishedVersion, other-oa)
  • Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • Radboud Repository (Radboud University) (submittedVersion)
  • Radboud Repository (Radboud University) (submittedVersion, other-oa)
Funders
  • EC | European Research Council (339431)
  • Nederlandse Organisatie voor Wetenschappelijk Onderzoek (864.12.010)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Molecular Biology Techniques and Applications
Keywords
single-cell proteomics, phosphoproteomics, transcriptome, protein expression, keratinocytes, keratinocyte differentiation, focal adhesion kinase phosphorylation, stem cell markers, cellular heterogeneity, environmental stimuli
MeSH terms
Cell Differentiation, Cells, Cultured, Gene Expression Regulation, Humans, Phosphorylation, Quinazolines, Keratinocytes, Tissue Fixation, Tyrphostins, Gene Expression Profiling, Proteomics, Focal Adhesion Kinase 1, Single-Cell Analysis

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