MULTI-seq: Universal sample multiplexing for single-cell RNA sequencing using lipid-tagged indices

We report the development of MULTI-seq: a scRNA-seq and snRNA-seq sample multiplexing approach using lipid- or cholesterol-modified oligonucleotides. We demonstrate MULTI-seq utility in the following scRNA-seq and snRNA-seq contexts: (1) Live HEKs and HMECs with and without stimulation with TGF-β, (2) Purified nuclei from HEKs, MEFs, and Jurkats stimulated for 0-24 hrs with ionomycin and PMA, (3) 96 unique HMEC cultures (with one technical replicate), and (4) human metastases and mouse immune cells isolated from cryopreserved primary tissue samples dissected from a patient-derived xenograft mouse model of triple-negative breast cancer at progressive stages of metastasis to the lung. Single-cell or single-nucleus gene expression profiles for (1) HEKs and HMECs, (2) HEKs, MEFs, and Jurkats, (3) HMECs in distinct culture conditions, and (4) Human metastases and mouse immune cells from PDX mice.