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10 protocols using nucblue fixed readyprobes reagent

1

Immunocytochemical Staining of CE-OOCs

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Immunocytochemical staining for vimentin (3.7 μL/mL; ab92547; Abcam, Cambridge, MA, USA) and cytokeratin-18 (CK-18; 1 μL/mL; ab668; Abcam) was performed after 96 hours, as previously described.26 ,29 Manufacturer’s instructions were used to calculate the staining dilutions to ensure uniform staining. After 96 hours, cells were fixed with 4% paraformaldehyde, permeabilized with 0.5% Triton X, and blocked with 3% bovine serum albumin in 1× PBS, prior to incubation with primary antibodies overnight at 4°C. After washing with 1× PBS, the CE-OOCs were incubated with Alexa Fluor 488– and 594–conjugated secondary antibodies (Thermo Fisher Scientific) diluted 1:400 in 1× PBS for 2 hours in the dark. The CE-OOCs were washed with 1× PBS, and then also treated with NucBlue Fixed ReadyProbes Reagent (R37606; Thermo Fisher Scientific, Waltham, MA) to stain the nucleus.
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2

Immunocytochemical Staining of VCD-OOCs

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Immunocytochemical staining for α-smooth muscle actin (14-9760-82, Thermo Fisher Scientific, Waltham, MA) for hFM-DEC, cytokeratin(CK)-14 (ab51054: Abcam for ECTO, Cambridge, MA, USA), CK-18 (ab668; Abcam) and MUC5A (ab3649; Abcam) for ENDO, pan-cytokeratin (#4545, Cell Signaling Technology, Danvers, MA) for VEC, type I collagen (ab34710; Abcam) and vimentin (ab92547; Abcam) STROMA were performed after 48 h, as previously described.49 (link),57 Manufacturer’s instructions were used to calculate the staining dilutions to ensure uniform staining. After 48 h, cells were fixed with 4% paraformaldehyde, permeabilized with 0.5% Triton X, and blocked with 3% bovine serum albumin in 1× PBS before incubation with primary antibodies overnight at 4 °C. After washing with 1× PBS, the VCD-OOCs were incubated with Alexa Fluor 488–, 594, and 647–conjugated secondary antibodies (Thermo Fisher Scientific) diluted 1:400 in 1× PBS for 2 h in the dark. The VCD-OOCs were washed with 1× PBS and treated with NucBlue® Fixed ReadyProbes Reagent (R37606; Thermo Fisher Scientific) to stain the nucleus.
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3

Immunocytochemical Staining of Glial and Immune Cells

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Immunocytochemical staining for Glial fibrillary acidic protein (GFAP) (1:500; ab68428; Abcam, Cambridge, MA, USA) ionized calcium-binding adaptor molecule 1 (Iba1) (1:100; ab221003; Abcam, Cambridge, MA, USA), and CD11b (1:100; ab197701; Abcam, Cambridge, MA, USA) was performed after 48 h, as previously described.46,47 Manufacturers’ instructions were followed for determining appropriate dilutions of antibodies to ensure specific and uniform staining. After 48 h, cells were fixed with 4% paraformaldehyde, permeabilized with0.5% Triton X, and blocked with 3% bovine serum albumin in 1× PBS, before incubation with conjugated antibodies for 2 hours at room temperature in the dark. Secondary rabbit (1:1000) was added for 1 h for GFAP. The OOCs were washed with 1× PBS, and then also treated with NucBlue® Fixed ReadyProbes Reagent (R37606; Thermo Fisher Scientific, Waltham, MA) to stain the nucleus.
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4

Multimodal Cell Characterization via ICC

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Immunocytochemical staining for Vimentin (Abcam; ab92547; 1:300) in DECs, and Vimentin + Cytokeratin (CK)-18 (Abcam; ab668; 1:800) in AMCs and AECs, Histocompatibility Antigen (HLA)-G (Abcam; ab52455; 1:200) in CTCs, CK-7 (Abcam; ab9021; 1:600) in STBs and CTBs, and MUC18 (Abcam; ab233923; 1:200) in HUVECs were used as cell-specific markers. Antibodies were titrated to determine appropriate dilutions to ensure specific and uniform staining. After 24 h in culture, cells were fixed and permeabilized with 70% ethanol at 4C for 24 h. Before blocking, cells were washed 2x with 1× PBS and then blocked with 3% bovine serum albumin in 1× PBS for 1 h before incubation with primary antibodies overnight. Cells were washed three times in 1× PBS and then incubated with species-specific secondary antibodies (Abcam; Alexa Fluor 488-rabbit; ab150073) (Invitrogen; Alexa Fluor 594-mouse; A11005) (1:1000) for 1 h. Devices were washed with 1× PBS and then treated with NucBlue® Fixed ReadyProbes Reagent (R37606; ThermoFisher Scientific, Waltham, MA) (2 drops per ml) to stain the nucleus and imaged as described below.
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5

Comprehensive Immunocytochemical Profiling of FMi-OOCs

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Immunocytochemical staining for Vimentin (Abcam; ab92547; 1:300), Cytokeratin (CK)-18 (Abcam; ab668; 1:800), Histocompatibility Antigen (HLA)-G (Abcam; ab52455; 1:200), and HLA-DR (Abcam; ab929511; 1:50) were used to monitor cell types and document their immune regulatory status. Antibodies were titrated to determine appropriate dilutions to ensure specific and uniform staining. After 72 h, cells were fixed with 4% paraformaldehyde, permeabilized with 0.5% Triton-X, and blocked with 3% bovine serum albumin in 1× PBS, before incubation with primary antibodies overnight. Cells were washed three times in 1× PBS and then incubated with species-specific secondary antibodies (Abcam; Alexa Fluor 488-rabbit; ab150073) (Invitrogen; Alexa Fluor 594-mouse; A11005) (1:1000) for 1 h. The FMi-OOCs were washed with 1× PBS and then treated with NucBlue ® Fixed ReadyProbes Reagent (R37606; ThermoFisher Scientific, Waltham, MA) (2 drops per ml) to stain the nucleus. Primary and secondary concentrations were validated based on previous FMi-OOC-based studies.
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6

Immunophenotyping of Cultured Cells

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Immunocytochemical staining for CD45 (Abcam; ab30470; 1:200), Vimentin (Abcam; ab92547; 1:500), Cytokeratin (CK)-18 (Abcam; ab668; 1:800), HLA-G (Abcam; ab52455; 1:200), and HLA-DR (Abcam; ab929511; 1:50) were used to monitor cell types and document their immune regulatory status. Antibodies were titrated to determine appropriate dilutions to ensure specific and uniform staining. After 24 hours, cells were fixed with 4% paraformaldehyde, permeabilized with 0.5% Triton-X, and blocked with 3% bovine serum albumin in 1× PBS, before incubation with primary antibodies overnight. Cells were washed three times in 1× PBS and then incubated with species-specific secondary antibodies (1:1000) for 1 hour. The MPSs were washed with 1× PBS, and then treated with NucBlue® Fixed ReadyProbes Reagent (R37606; ThermoFisher Scientific, Waltham, MA) to stain the nucleus. Primary and secondary concentrations were validated based on previous chip-based studies.
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7

Phenotypic Characterization of Organ-on-Chip Cells

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Each chamber of the OOC devices were staining with individual cell-specific antibodies in order to document that cells on-chip maintained in utero characteristics. Immunocytochemical staining for cytokeratin (CK)-7 (ab9021; Abcam, Cambridge, MA, USA), E-cadherin (ab15148 Abcam, Cambridge, MA, USA), and MUC18 (ab75769; Abcam, Cambridge, MA, USA) was performed after 24 h, as previously described.46,47 (link) Manufacturers' instructions were followed for determining appropriate dilutions of antibodies to ensure specific and uniform staining. After 24 h, cells were fixed with 4% paraformaldehyde, permeabilized with 0.5% Triton X, and blocked with 3% bovine serum albumin in 1× PBS, before incubation with primary antibodies overnight at 4 °C. After washing with 1× PBS, the PLA-OOCs were incubated with Alexa Fluor 488-, 594-, and 647-conjugated secondary antibodies (Thermo Fisher Scientific) diluted 1 : 400 in 1× PBS for 2 h in the dark. The PLA-OOCs were washed with 1× PBS, and then also treated with NucBlue® Fixed ReadyProbes Reagent (R37606; Thermo Fisher Scientific, Waltham, MA) to stain the nucleus. OOCs were fixed in 4% paraformaldehyde for 15 min and stained using the Masson Trichrome method to identify collagen within the microchannels. Three microscopic fields for each condition were captured at 10×.
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8

Immunocytochemical Characterization of OOC Cells

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Each chamber of the OOC devices were staining with individual cell-specific antibodies in order to document that cells on-chip maintained in utero characteristics. Immunocytochemical staining for cytokeratin (CK)-7 (ab9021; Abcam, Cambridge, MA, USA), E-cadherin (ab15148 Abcam, Cambridge, MA, USA), and MUC18 (ab75769; Abcam, Cambridge, MA, USA) was performed after 24 h, as previously described.46 (link),47 (link) Manufacturers’ instructions were followed for determining appropriate dilutions of antibodies to ensure specific and uniform staining. After 24 h, cells were fixed with 4% paraformaldehyde, permeabilized with 0.5% Triton X, and blocked with 3% bovine serum albumin in 1× PBS, before incubation with primary antibodies overnight at 4°C. After washing with 1× PBS, the PLA-OOCs were incubated with Alexa Fluor 488–, 594–, and 647–conjugated secondary antibodies (Thermo Fisher Scientific) diluted 1:400 in 1× PBS for 2 h in the dark. The PLA-OOCs were washed with 1× PBS, and then also treated with NucBlue® Fixed ReadyProbes Reagent (R37606; Thermo Fisher Scientific, Waltham, MA) to stain the nucleus. OOCs were fixed in 4% paraformaldehyde for 15 min and stained using the Masson Trichrome method to identify collagen within the microchannels. Three microscopic fields for each condition were captured at 10x.
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9

Actin and Nucleus Fluorescence Imaging

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A549/LivePAR cells were seeded into each well of an 8-chamber glass bottom vessel (Thermo Fisher Scientific; Waltham, MA, USA; Cat# 155409) at a density of 5 × 104 cells per well. After 24 h, cells were washed twice with 1XPBS, then fixed with 4% formaldehyde while simultaneously staining with Alexa Fluor 647 phalloidin (Invitrogen; Waltham, MA, USA; Cat# A22287) and NucBlue Fixed ReadyProbes reagent (Invitrogen; Waltham, MA, USA; Cat# R37606) for 30 min at 4 °C according to the manufacturer protocols. Cells were washed three times with 1XPBS, and cells were imaged using a Nikon A1rsi laser scanning confocal microscope.
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10

Microscopic Analysis of EGFP-Tagged Protein Complexes

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U2OS or ES-2 cells expressing either the EGFP-fused WWE domains or EGFP-fused Af1521 macrodomain variants were cultured in wells of an 8-chamber glass bottom vessel (Thermo Fisher Scientific) at a density of 7×104 cells per well. After 24 hours, cells were washed twice with 1X PBS. Next, cells were fixed with 4% formaldehyde supplemented with Triton 100-X (Thermo Fisher Scientific) for permeabilization of the cells, and Alexa Fluor 647 phalloidin (Invitrogen) to stain filamentous actin (F-actin). Cells were incubated at 4°C for 20 minutes according to the manufacturer’s protocol. Subsequently, cells were washed once with PBS and then NucBlue Fixed Ready Probes reagent (Invitrogen) was added for 20 minutes at room temperature according to the manufacturer’s protocol to stain the nuclear compartment. Cells were washed three times with 1X PBS, and then were imaged using a Nikon A1rsi laser scanning confocal microscope.
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