Fig. 1

Overview of experimental workflows and cell purity tests. a. Schematic overview of the high-throughput transcriptomics and label-free proteomics workflows. b. Purity of SE-1-MACS-isolated liver sinusoidal endothelial cells (LSECs) and CD11b/c-MACS-isolated Kupffer cells (KCs). Cell isolates were analyzed by scanning electron microscopy (EM) (LSECs: n = 6, including all cell isolates for proteomics and RNA sequencing; KCs: n = 4, including all isolates for proteomics), and immune cytochemistry (KC: n = 4, LSEC: n = 3, including all cell isolates for proteomics). Results are presented as % of total cell count (mean ± standard deviation). Antibodies (Table 1) targeted either stabilin-2 (LSEC marker), SE-1/FcγRIIb2 (LSEC marker), CD11b/c (KC marker), or glial fibrillar acidic protein (GFAP, stellate cell marker). N.d., not determined. c-d. Scanning electron micrographs showing the typical morphology of MACS-isolated cells. Insert in c shows LSEC fenestrations (hallmark of LSECs), which were absent in KCs (d). e. Expression level of marker genes for LSECs, KCs, and hepatic stellate cells (HSC) in the KC and LSEC transcriptomes and proteomes. Expression values are given as RPKM (RNA-seq), and iBAQ (label-free proteomics), as described in Methods