0 array, and scanned as described previously (Steiner et al., 2004 and Wodicka et al., 1997). Gene expression profiles of the LPS- and LPS/Dex-treated human 3D co-cultures were compared to the ones of vehicle-treated

cells. Genes were considered changed, if they showed an at least 2 fold change (p ≤ 0.05, Student’s Pexidartinib molecular weight t-test) compared to vehicle treated cells upon LPS or LPS/Dex treatment. All treatments were performed in biological triplicates and each RNA sample was hybridized on a separate microarray. The original gene array data are available in Supplementary Fig. 3. For immunochistochemistry, 30-days-old human or 20-days-old rat 3D liver cells were washed in PBS and fixed in 4% paraformaldehyde (PAF)

for 30 min and washed three times with PBS. Cell permeabilization and blocking of the non-specific antibody-binding was performed in PBS containing 1% bovine serum albumin (BSA, Sigma) and 0.1% Triton X-100 (Fluka) for 1 h at RT. Permeabilized cells were incubated with primary antibodies against mouse albumin (1:100; cat #: A6684; Sigma), rat F4/80 (1:10; cat #: ab16911; Abcam), rabbit vimentin (1:50, cat #: 3932, Cell signaling), rabbit intercellular adhesion molecule 1 (ICAM-1) (1:100; cat #: HPA002126; Sigma) and goat dipeptidyl peptidase IV (DPPIV) (1:10; cat #: AF1180; R&D systems) overnight at 4 °C. The cells were then washed three times with PBS and incubated at RT for 1–2 h in the dark with the secondary antibodies: donkey anti-mouse Stem Cell Compound Library purchase IgG (H + L) AlexaFluor 568 (1:200; cat #: A10037; Invitrogen, Molecular probes), Sheep F(ab′)2 anti-rabbit IgG (H + L) (Cy3 ®) (1:50; cat #: ab50503; Abcam), rabbit anti-rat IgG AlexaFluor 594 (H + L) (1:200; cat #: A21211; Invitrogen, Molecular probes) and rabbit anti-goat AlexaFluor 568 (1:200;

cat #: A11079; Invitrogen, Molecular probes). After an additional washing with PBS, the nuclei were counterstained with 300 nM DAPI for 1 h. This was followed by transfer of the screens containing the cells into microscopic glass slides and mounting the cells with Vectashield medium (Vector laboratories, Inc.). The specimens were examined using a confocal microscope (Leica DMI 4000B). To label Kupffer cells in human 3D co-culture, they were incubated with 4 μl fluorescence-labeled latex beads (cat #: 17154, Polysciences, Inc.) in 1 ml Cell press serum containing media for 1 h at 37 °C and subsequently washed extensively with PBS. To quantify the number of hepatocytes and Kupffer cells, flow cytometry analysis was performed from human 3D liver co-cultures. First, cells were washed three times with PBS and then detached from the scaffolds by 20 min incubation with Accutase (PAA Laboratories, GmbH) at 37 °C. Dissociated cells were centrifuged for 5 min at 1200 rpm, fixed with 2% PAF for 15 min at RT, and then permeabilized and blocked in 10% normal goat serum (NGS)/0.1% saponin in PBS for 1 h at RT.