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3 protocols using anti cdkn1a p21

1

Comprehensive Autophagy Assay Protocol

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The chemicals used in our experiments were: CA-4 (Selleckchem, Houston, TX, USA, S7204), CQ diphosphate (Selleckchem, S4430), and puromycin (Selleckchem, S7417), CHX (Medchem Express, NJ, USA, HY-12320), LysoTracker Red DND-99 (Invitrogen, Carlsbad, CA, USA, L-7258), LysoSensor Yellow/Blue DND-160 (Invitrogen, L-7545). The antibodies used in our experiments were: anti-MAP1LC3B/LC3B (Cell Signaling Technology, Beverly, MA, USA, 2775), anti-SQSTM1 (Cell Signaling Technology, 8025), anti-LAMP1 (Cell Signaling Technology, 9091), anti-NDRG1 (Cell Signaling Technology, 9485), anti-EGFR (Cell Signaling Technology, 4267), anti-p-AKT (Cell Signaling Technology, 13038), anti-p-ERK (Cell Signaling Technology, 9101), anti-cleaved PARP (Cell Signaling Technology, 5625), anti-CDKN1A/p21(Cell Signaling Technology, 2947), anti-CDKN1B/p27 (Cell Signaling Technology, 3686), anti-caspase 3 (Epitomics, Burlingame, CA, USA, 1087-1), anti-caspase 8 (Epitomics, 1007-1), anti-caspase 9 (Epitomics, 3392-1), anti-HIF-1α (Novus, Littleton, CO, USA, NB100-105), anti-CTSB (Proteintech, Rosemont, IL, USA, 12216-1-AP) and anti-CTSD (Proteintech, 21327-1-AP). Alexa Fluor 488- and 568-conjugated secondary antibodies were purchased from Invitrogen (A21429 and A11029).
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2

Antibody Characterization for Immunoblotting and ChIP

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The following commercial antibodies were used for immune blotting with the indicated dilutions: anti-BRD2 (Cell Signalling, 5848, AB_10835146), anti-BRD3 (Bethyl, A302-368, AB_1907251), anti-BRD4 (Bethyl, A301-985, AB_2620184), anti-GAPDH (Santa Cruz, sc-47724, AB_627678), anti-CDKN1A/p21 (Cell Signalling, 2947, AB_823586), anti-cleaved PARP (Cell Signalling, 9541, AB_331426) and anti-γH2A.X (Cell Signalling, 2577, AB_2118010). anti-γH2A.X (1:50, 2577) and Alexa Fluor 594 anti-rabbit secondary antibody (1:100, Thermo Scientific, A-11012) were used for spheroid confocal microscopy. anti-BRD2 (5848), anti-BRD3 (A302-368) and anti-BRD4 (A301-985) were used for chromatin immuno-precipitation (ChIP).
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3

Western Blot Analysis of Protein Samples

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Adjusted protein lysates were supplemented with loading buffer (12% glycerol, 60 mM Na2EDTA pH 8, 0.6% SDS, 0.003% bromphenol blue) and denatured for 10 minutes at 95 °C before SDS-PAGE. Proteins were wet-transferred to a nitrocellulose membrane at 80 V for 2 hours in transfer buffer (25 mM Tris-HCl pH 7.6, 192 mM glycine, 20% methanol, 0.03% SDS). Membranes were blocked in 5% milk powder diluted in TBST (50 mM Tris-HCl pH 7.6, 150 mM NaCl, 0.05% Tween 20), before an overnight incubation at 4 °C with the primary antibodies. After three times washing with TBST, membranes were incubated with HRP-coupled secondary antibodies for 1 hour at room temperature, followed by another three washes with TBST. Blots were developed with Pierce ECL Substrate Kit following the manufacturer’s instructions. The following antibodies were used: anti-FLAG M2 (mouse, F1804, Sigma-Aldrich), anti-GAPDH (mouse, ACR001P, Acris), anti-TRIM71 (rabbit, kind gift from the Yamanaka lab), anti-TRIM71 (rabbit, PAB19293, Abnova), anti-SHCBP1 (rabbit, 12672–1-AP, Proteintech), anti-Cdkn1a/p21 (rabbit, 2947, Cell Signaling Technology), anti-EGR1 (rabbit, 4154, Cell Signaling Technology), anti-UPF1 (rabbit, 9435, Cell Signaling Technology), anti-VINCULIN (mouse, V9131, Sigma-Aldrich), anti-ubiquitin (rabbit, 3933, Cell Signaling Technology) and anti-tubulin (mouse, T9026, Sigma-Aldrich).
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