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6 protocols using sym10

1

Isolation and Culture of Human Umbilical Cord Endothelial Cells

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Primary human EC were isolated from human umbilical cords [39 (link)]. Cells from multiple individuals were pooled and used at early passages (P2-4). Cells were cultured in MCDB 107 medium (Sigma Life Sciences) supplemented with 15% FBS (Atlas Biologicals), 150 μg/ml endothelial cell growth supplement (ECGS), and 90 μg/ml heparin (Sigma-Aldrich). Recombinant TNF-α (R&D Systems) was used at 2 ng/ml. Recombinant IFN-γ (R&D Systems) was used at 450 U/ml. Cells were serum starved in MCDB media for 3 hours prior to the addition of agonists. Antibodies used in immunoblotting were anti-PRMT5 (Millipore 07–405), anti-p65 (Millipore 06–418), anti-dimethyl-arginine symmetric (SYM10, Millipore, 07–412), anti-CXCL11 (R&D Systems MAB672), anti-MCP1 (Cell Signaling Technology #2027), and anti-GAPDH (Cell Signaling Technology #2118). ChIP antibodies included anti-FLAG M2 (Sigma F1804) and anti-SDMA (SYM10). Additional details of the antibodies used are provided in S1 Table.
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2

Immunoprecipitation of hnRNPA1 and MEP50

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Granulosa cells isolated from mice at 16–18 days old were cultured in 10 cm dishes and lysed with lysis buffer (50 mM Tris–HCl [pH 7.5], 150 mM NaCl, 1 mM EDTA, 1% Nonidet P-40) supplemented with protease inhibitors cocktail (Roche) and 1 mM PMSF. 1 mg of protein were first pre-cleared with protein A/G agarose beads (GE, 17-0618-01, 17-5280-01) for 1 hr at 4°C, then incubated with HnRNPA1 antibody (Abcam, ab5832), or MEP50 antibody (Abcam, ab154190) for 4 hr at 4°C. Then protein A and G agarose beads were added and incubated overnight. The immunoprecipitates were washed four times in lysis buffer supplemented with cocktail and PMSF, resolved in loading buffer, incubated for 5 min at 95°C, and then analyzed by western blotting. The antibodies used in western blotting include PRMT5 (Millipore, 07-405), SYM10 (Millipore, 07-412), HnRNPA1 (Abcam, ab5832), and MEP50 (Abcam, ab154190).
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3

Protein Immunoprecipitation and Western Blot

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The following antibodies were used for immuno-precipitation and Western Blot experiments, according to the manufacturer's instruction: DGCR8 (Abcam ab90579), EWSR1 (Abcam ab54708), FUS (Bethyl A300–293A), DDX5 (Abcam ab126730), Drosha (Santa Cruz sc-33778), Vinculin (VCL) (Millipore 06–866), PRMT1 (Abcam ab73246), ASYM24 (Millipore), SYM10 (Millipore), Mono-Methyl Arginine (R*GG) (D5A12) (Cell Signaling Technology 8711), LAMIN A/C (sc-6215), Lamin B1 (Abcam ab16048), GAPDH (Abcam ab9484), H3 (Abcam ab1791), H4 (Abcam ab7311), H4R3me2a (Active Motif 39705), TAF15 (Bethyl Laboratories A300–308A), ILF3 (Bethyl A303–615A), ILF2 (sc-271718), DDX17 (sc-130650), HDAC1 (Abcam ab7028) and HA.11 (Biolegend 901513).
MS023 and MS094 compounds were kindly provided by the SGC Toronto—Structural Genomic Consortium (http://www.thesgc.org/scientists/groups/toronto). Compounds were dissolved in DMSO and used at a final concentration of 10 μM for the indicated time intervals.
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4

Protein Expression Analysis in Lung Tissue

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Right lung lobes were homogenized and lysed in RIPA buffer (10 mM Tris pH 8.0, 5 M NaCl, 0.5 M EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) containing protease and phosphatase inhibitors (ThermoFisher Scientific). Primary antibodies: PRMT5 (Abcam ab31751, 1:1000), H4R3 (MilliporeSigma SAB4300870, 1:500), SYM10 (MilliporeSigma 07–412, 1:300), ROR-γt (Life Technologies 14–6981-82, 1µg/ml) and β-actin (Sigma-Aldrich A1978, 1:50,000). Secondary antibodies (1:20,000): donkey anti-rabbit or anti-rat 800CW and donkey-anti-mouse 680RD (Li-cor). Blots were imaged on an Odyssey-CLx and quantified with Image Studio software (Li-Cor).
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5

Co-immunoprecipitation of PRMT5, KLF5, and SYM10

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To perform the co‐immunoprecipitation experiment, we seeded A549 and ASTC‐a‐1 cells in 15 cm culture dishes and lysed the cells using lysis buffer (20 mM Tris pH 7.4, 150 mM NaCl, 2 mM EDTA, 2 mM EGTA, 1 mM sodium orthovanadate, 50 mM sodium fluoride, 1% Triton X‐100, 0.1% SDS and 100 mM phenylmethylsulfonyl fluoride). Afterward, we centrifuged the lysates at maximum speed for 10 min at 4°C, and the cleared cell extracts were pre‐cleared with protein A and protein G beads (Santa Cruz Biotechnology, cat# sc‐2001 and cat# sc‐2002) at 4°C for 1 h. We then added 5°μg of primary antibodies, including PRMT5 (Santa Cruz Biotechnology, cat# sc‐376937), KLF5 (Cell Signaling Technology, cat# 51586), SYM10 (Millipore& Sigma, cat# 07‐412), HA (BioLegend, cat# 901502) or isotype IgG to the cleared cell extracts and incubated them overnight at 4°C. Next, we incubated the cell extracts with protein A or protein G beads at 4°C for 3 h, followed by three washes with wash buffer (100 mM NaCl, 50 mM Tris pH 7.5, 0.1% NP‐40, 3% glycerol and 100 mM phenylmethylsulfonyl fluoride). Finally, we eluted the beads‐bound proteins by adding 1× Laemmli sample buffer and heating at 95°C for 10 min. We analysed the protein–protein interactions using western blotting.
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6

Lung Tissue Myeloperoxidase and Protein Analysis

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The tissue isolation and the myeloperoxidase assay were performed as described (20) . Briefly, diluted sample MPO was bound to anti-MPO coated plates (Hycult Biotech HK210-01) followed by washes. Fluorescence (ex 535nm, em 590nm) after addition of H2O2 and ADHP was acquired in kinetic mode (10min, every 30 sec) on a Biotek Cytation 1. Results reported as RFU/second. Western blotting. Right lung lobes were homogenized and lysed in RIPA buffer (10 mM Tris pH 8.0, 5 M NaCl, 0.5 M EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) containing protease and phosphatase inhibitors (ThermoFisher Scientific). Primary antibodies: PRMT5 (Abcam ab31751, 1:1000), H4R3 (MilliporeSigma SAB4300870, 1:500), SYM10 (MilliporeSigma 07-412, 1:300), ROR-gt (Life Technologies 14-6981-82, 1µg/ml) and β-actin (Sigma-Aldrich A1978, 1:50,000). Secondary antibodies (1:20,000): donkey anti-rabbit or anti-rat 800CW and donkey-anti-mouse 680RD (Li-cor). Blots were imaged on an Odyssey-CLx and quantified with Image Studio software (Li-Cor).
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