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4 protocols using anti histone h3k36me3

1

Yeast Protein Extraction and Immunoblotting

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Yeast strains of the indicated genotypes (and their wild-type counterparts) were grown in YPD either at permissive or restrictive temperatures. Overnight-saturated cultures were diluted to an OD600 of 0.2 and allowed to grow until they reached an OD600 of 1. Five OD600 equivalents of cells were lysed using a modified TCA extraction method as described (Keogh et al., 2006a (link), 2006b (link)). 10–20 mg of the lysates were separated by SDS-PAGE and variously probed with the following antibodies: anti-FLAG-M2 [for FLAG tagged Spt6] (Sigma-Aldrich, F1804; 1:5000), anti-G6PDH (Sigma-Aldrich, A9521; 1:100,000), anti-histone H3K4me3 (EpiCypher, 13–0004; 1:5000), anti-histone H3K79me3 (Abcam, ab2651, 1:2500) anti-histone H3K36me3 (Abcam, ab9050, ab9050; 1:1000), anti-histone H3 (EpiCypher, 13–0001; 1:50,000), anti-Spt16 (gift from Tim Formosa University of Utah, 1:5000), anti-H3K36me2 (Active Motif, 39255; 1:1000), anti-Set2 (Generated in the Strahl lab, 1:5000), anti-RNAPII-Ser2P (Active Motif, Clone #3E10, 61084; 1:100), anti-H2BK123ub1 (Cell Signaling Technology, 5546; 1:2000), and anti-H2B (Active Motif, 39237; 1:2000). HRP-conjugated anti-rabbit (GE Healthcare, NA934V; 1:10,000) and anti-mouse secondary (GE Healthcare, NA931V; 1:10,000), antibodies were used at 1:1000 and proteins were detected using ECL Prime or enhanced chemiluminescence ECL (Amersham Biosciences).
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2

Western Blot Antibody Panel for Protein Expression

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Western blot was performed as described [58] (link), [59] (link). The primary antibodies used in this study were: anti-Npac (Catalog No. 14833-1-AP, Proteintech), anti-NP60 (Catalog No. sc-390601, Santa Cruz, Dallas, TX), anti-β-actin (Catalog No. sc-81178, Santa Cruz), anti-Oct4 (Catalog No. sc-8628, Santa Cruz), anti-Nanog (Catalog No. sc-33760, Santa Cruz), anti-Sox2 (Catalog No. sc-99000, Santa Cruz), anti-p-ERK (Catalog No. 4370, Cell Signaling Technology, Danvers, MA), anti-ERK (Catalog No. 137F5, Cell Signaling Technology), anti-histone H3K36me3 (Catalog No. ab9050, Abcam), anti-Pol II (Catalog No. sc-899, Santa Cruz), anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) (Catalog No. ab5095, Abcam), anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (Catalog No. ab140509, Abcam), anti-Cyclin T1 (Catalog No. sc-10750, Santa Cruz), anti-Cdk9 (Catalog No. sc-484, Santa Cruz), anti-mouse IgG (Catalog No. sc-2025, Santa Cruz), anti-goat IgG (Catalog No. sc-2028, Santa Cruz), and anti-rabbit IgG (Catalog No. sc-2027, Santa Cruz).
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3

Nuclear Protein Extraction and Western Blot

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The hiNPCs were washed with PBS and resuspended in 100 μl of extraction buffer [10 mM HEPES pH 8, 10 mM MgCl2, 0.1 mM EDTA pH 8, 0.1 mM DTT and halt protease and phosphatase inhibitor cocktail (Life Technologies)]. Samples were centrifuged at 5000 rpm for 10 min at 4°C to remove the cytosolic fraction. Nuclear pellets were resuspended in 0.2 N HCl and put in rotation at 4°C overnight. After centrifugation at 4000 rpm for 10 min at 4°C, supernatants containing nuclear proteins were recovered. Proteins were quantified by Bradford Protein Assay Kit (Sigma-Aldrich). Protein samples were separated by 4–12% Bis–Tris Protein Gels (Thermo Fisher) and transferred on an Amersham™ Protran™ 0.45 μm nitrocellulose (GE-Healthcare) membrane. Membranes were blocked with 5% w/v non-fat dried milk and incubated with the following primary antibodies: anti-CHD8 (NB100-60417, Novus Biologicals) (1:1000), anti-HSP90 (4874S, Cell Signaling Tech.) (1:5000), anti-histone H3 (1:1.000) (4499, Cell Signaling Tech.) and anti-histone H3K36me3 (1:1.000) (Ab9050, Abcam). Proteins were detected using horseradish peroxidase-conjugated secondary antibodies anti-rabbit IgG 1:7500 (GTX213110-01, GeneTex) and visualized by ECL Select WB detection reagent (GE Healthcare) following the manufacturer's instructions. Signal quantification was performed with Imagelab software (BIORAD, version 5.2.1).
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4

Yeast Protein Extraction and Immunoblotting

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Yeast strains of the indicated genotypes (and their wild-type counterparts) were grown in YPD either at permissive or restrictive temperatures. Overnight-saturated cultures were diluted to an OD600 of 0.2 and allowed to grow until they reached an OD600 of 1. Five OD600 equivalents of cells were lysed using a modified TCA extraction method as described (Keogh et al., 2006a (link), 2006b (link)). 10–20 mg of the lysates were separated by SDS-PAGE and variously probed with the following antibodies: anti-FLAG-M2 [for FLAG tagged Spt6] (Sigma-Aldrich, F1804; 1:5000), anti-G6PDH (Sigma-Aldrich, A9521; 1:100,000), anti-histone H3K4me3 (EpiCypher, 13–0004; 1:5000), anti-histone H3K79me3 (Abcam, ab2651, 1:2500) anti-histone H3K36me3 (Abcam, ab9050, ab9050; 1:1000), anti-histone H3 (EpiCypher, 13–0001; 1:50,000), anti-Spt16 (gift from Tim Formosa University of Utah, 1:5000), anti-H3K36me2 (Active Motif, 39255; 1:1000), anti-Set2 (Generated in the Strahl lab, 1:5000), anti-RNAPII-Ser2P (Active Motif, Clone #3E10, 61084; 1:100), anti-H2BK123ub1 (Cell Signaling Technology, 5546; 1:2000), and anti-H2B (Active Motif, 39237; 1:2000). HRP-conjugated anti-rabbit (GE Healthcare, NA934V; 1:10,000) and anti-mouse secondary (GE Healthcare, NA931V; 1:10,000), antibodies were used at 1:1000 and proteins were detected using ECL Prime or enhanced chemiluminescence ECL (Amersham Biosciences).
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