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8 protocols using rabbit igg control

1

ChIP Assay for NFATC2 Binding

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The EZ-Magna ChIP A/G kit (EMD Millipore, 17-10086) was used to perform chromatin immunoprecipitation (ChIP) as described61 (link). An anti-NFATC2 antibody (Santa Cruz Biotechnology, sc-7296) and control rabbit IgG (Dako, X0936) were used. Q-RT-PCR was used to analyse purified DNA to determine relative fold enrichment compared to input DNA. The sequences of the Ptgs2 (COX2) and Gal (GAL) primers are provided in Supplementary Table 7.
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2

ChIP Assay for NFATC2 Binding

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The EZ-Magna ChIP A/G kit (EMD Millipore, 17-10086) was used to perform chromatin immunoprecipitation (ChIP) as described61 (link). An anti-NFATC2 antibody (Santa Cruz Biotechnology, sc-7296) and control rabbit IgG (Dako, X0936) were used. Q-RT-PCR was used to analyse purified DNA to determine relative fold enrichment compared to input DNA. The sequences of the Ptgs2 (COX2) and Gal (GAL) primers are provided in Supplementary Table 7.
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3

Quantification of β-Adrenergic Receptors

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For the detection of β-adrenergic receptors on cell surfaces, 5 × 105 UM cells were incubated with rabbit anti-human ADRB1, ADRB2, or ADRB3 antibodies (Bioss Antibodies Cat. No. bs-0498R, bs-0947R, bs-1063R), or rabbit IgG control (Dako X 0903) in cell staining buffer (1% calf serum albumin and 0.1% NaN3 sodium azide in PBS for 30 min at 4 °C). After two washing steps with cell staining buffer, the cells were incubated with the secondary antibody goat anti-rabbit Alexa Fluor 488 (Invitrogen Cat. No. A11008, Walthman, MA, USA) for 30 min at 4 °C. After three washing steps with cell staining buffer, the cells were fixed with 4% paraformaldehyde for 15 min at 4 °C, finally resuspended in PBS and stored at 4 °C. Each cell line 104 cells were analyzed by BD FACS Aria III. Histograms of cell populations were visualized and analyzed by usingFlowJo-v10.8.1.
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4

FFPE Spheroid Immunohistochemistry for ABCG1 Expression

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Formalin-fixed paraffin-embedded (FFPE) sections (4 µm) of spheroids were deparaffinised in xylene (2 min) and rehydrated before antigen retrieval in citric acid buffer (10 mM in ddH2O, pH6, [33 (link)]). Endogenous peroxidases were blocked using 3% hydrogen peroxide for 5 min and endogenous biotin, biotin receptors and avidin-binding sites blocked using an avidin/biotin blocking kit (Invitrogen, Waltham, MA, USA). Sections were incubated for 1 h with ABCG1 primary antibody (10 µg/mL, PA5-13462, Thermo-Fisher Scientific) or rabbit IgG control (10 µg/mL, Dako) at room temperature, followed by incubation with the secondary antibody. Sections were then incubated with streptavidin–peroxidase (Abcam Plc.), followed by DAB substrate (Dako) for 10 min and nuclei counterstained with haematoxylin.
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5

Fibrin Immunostaining in Paraffin Lung Sections

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Fibrin staining in the lung was carried out in inflation-fixed and paraffin-embedded lung sections. Immunostaining for fibrin was performed using a polyclonal rabbit anti-human fibrinogen (DAKO; Carpinteria, CA) at a 1:2000 dilution for 60 minutes. Rabbit IgG control (DAKO) was used at the same specifications and served as a negative control. The stains were developed using the peroxidase-based Envision detection system (DAKO). The counterstaining was performed using hematoxylin.
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6

ATRX and Daxx Chromatin Immunoprecipitation

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ATRX and Daxx ChIP were performed as previously described (Law et al., 2010 (link)). In brief, cells were fixed in PBS with 2 mM EGS (Pierce 26103) for 45 min at room temperature followed by 1% formaldehyde for 20 min. Chromatin was sonicated to <500 bp and lysates were immunoprecipitated with 10 μg ATRX H300 (Insight Biotechnology sc-15408), 10 μg Daxx M-112 (Santa Cruz Biotechnology sc-7152), or rabbit IgG control (Dako X0903). Histone ChIPs were performed according to the manufacturer’s instructions (Millipore 17-295) using either 10 μg H3.3 antibody (Millipore 09-838), 5 μg H3K9me3 antibody (Abcam ab8898), or 2 μg H3K4me3 antibody (Abcam ab8580).
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7

Ubiquitin Affinity Enrichment Protocol

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Treated cells were lysed (50mM Tris, 150mM NaCl, 0.2mM Na3VO4, 1% NP40 v/v, 1mM PMSF, Roche cOmplete protease inhibitor tablet, 1mM DTT, 2% SDS) then aliquots were conserved as input. Non-denaturing (No SDS) lysis buffer was used to dilute the remainder of the lysates (<0.1% SDS). 1-2μg of rabbit anti-ubiquitin antibody (#: FL-76, Santa Cruz) or rabbit IgG control (#: X0903, Dako) was added to each appropriate vessel and incubated overnight at 4°C. Sepharose beads (#: 17-0618-01, GE Healthcare) were then added and incubated for a further 4Hrs at 4°C. Beads were washed first with 0.5M KCl then with 0.1M KCl, then treated as lysates in the immunoblotting protocol above.
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8

Histological Analysis of Lung Tissue

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The lung was inflated for 30 minutes at a constant hydrostatic pressure of 20 cm with 4% buffered formalin and immersed in the same solution for 24 h. The fixed lung was trimmed, embedded in paraffin, and cut into 5 μm sections. The sections were stained with hematoxylin and eosin (H&E) for morphological examination.
For immunohistochemistry, lung sections were processed and stained using specific antibodies. Immunostaining for fibrin was performed using a polyclonal rabbit anti-human fibrinogen antibody (Cat# A0080; DAKO corporation, Carpinteria, CA) at a 1:1000 dilution for 60-min. Rabbit IgG control (DAKO) was used at the same specifications. The stains were developed using a peroxidase-based Envision detection system (DAKO corporation; Carpinteria, CA). The counterstaining was performed using hematoxylin.
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