Hogeweg, M. | Search bioRxiv

bioRxiv2018

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

Environmental stimuli often lead to heterogeneous cellular responses and transcriptional output. We developed single-cell RNA and Immunodetection (RAID) to allow combined analysis 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 heterogenenous cellular responses to environmental signals at the mRNA and phospho-proteome level.

genomics↗

bioRxiv2017

Immuno-Detection by sequencing (ID-seq) enables large-scale high-dimensional phenotyping in cells.

Cell-based small molecule screening is an effective strategy leading to new medicines. Scientists in the pharmaceutical industry as well as in academia have made tremendous progress in developing both large-scale and smaller-scale screening assays. However, an accessible and universal technology for measuring large numbers of molecular and cellular phenotypes in many samples in parallel is not available. Here, we present the Immuno-Detection by sequencing (ID-seq) technology that combines antibody-based protein detection and DNA-sequencing via DNA-tagged antibodies. We used ID-seq to simultaneously measure 84 (phospho-)proteins in hundreds of samples and screen the effects of ~300 kinase inhibitor probes on primary human epidermal stem cells to characterise the role of 225 kinases. Our work highlighted a previously unrecognized downregulation of mTOR signaling during differentiation and uncovered 13 kinases regulating epidermal renewal through distinct mechanisms.

genomics↗