Single-cell ID-seq identifies BMP signaling as a driver of a late stage epidermal differentiation program

We developed a single cell application of the sequencing-based immunodetection method ID-seq which makes it possible to multiplex measurements of many different epitopes from proteins and phosphoproteins in a high throughput setting. A FACS sort step was implemented to allow sorting of single cells in 96 well plates. With these DNA-tagged antibodies and dedicated sample preparation protocol adapted for single cells, we studied the studied the changes of 70 (phospho-)proteins in primary human skin cells compared to a subpopulation with low ITGB1 protein expression. Given that ITGB1 is a skin stem cell marker, we indeed found that the ITGB1 low cells are differentiated and we found a role for BMP signaling in this process. We present an single cell immuno-detection sequencing assay for multiplexed protein detection, based on next-generation sequencing (NGS) of barcoded DNA-tags coupled to antibodies. Sequencing samples contain reads with antibody specific DNA-tag sequences. Using the antibody and sample index files and the indicated processing pipeline from github.com/jessievb/IDseq, one will obtain a count table of tags per sample.