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6 protocols using ab4812

1

Antibody-Based Protein Detection Assay

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Antibodies against human KDM1A (ab17721 and ab90966), CK1δ (ab48031), GATA6 (ab22600), and USP22 (ab4812) were from Abcam. Antibodies against GST (sc-138), Tuj-1(sc-58888), CK1α (sc-6477), CK1ε (sc-6471), BMP2 (sc-6895), CDKN1A (sc-397), and α-Tubulin (sc-5286) were from Santa Cruz Biotechnology. Antibodies against human GSK3β (9315), GSK3α (9338), CD133 (3663), phospho-GSK3β-S9 (9336), Oct4 (2750), H3K4me2/3 (9725 and 9751) and Myc-tag (2276) were from Cell Signaling Technology. Antibodies against phospho-serine/threonine (612548) and nestin (611658) were from BD Transduction Laboratories. Antibodies against hemagglutinin (HA)-Tag and Flag-tag were from Sigma. Hoechst 33342, Alexa Fluor 488 goat anti-rabbit antibody, and Alexa Fluor 594 goat anti-mouse antibody were from Molecular Probes. The specific antibody against phospho-KDM1A S683 was produced by Signalway Antibody. Supplementary Table 1 contains detailed information about the used antibodies.
Temozolomide (TMZ), tideglusib, lithium chloride, glutathione S-transferase (GST) beads, cycloheximide (CHX), and MG132 were from Sigma. Puromycin, hygromycin, and D4476 (4-[4-(2,3-dihydro-benzo[1,4]dioxin-6-yl)-5-pyridin-2-yl-1H-imidazol-2-yl] benzamide) were from EMD Biosciences. Protein G agarose was from Life Technologies. The recombinant active GSK3β (G09-10G) and CK1α (C64-10G) proteins were from SignalChem Lifesciences Corp.
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2

Immunofluorescence Staining of Transfected Cells

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At 48 h after transfection with siRNAs, adherent cells were fixed by incubation for 10 min in 4% paraformaldehyde and were then permeabilized by incubation with 0.1% Triton X-100 in phosphate-buffered saline (PBS) for 10 min at room temperature. For blocking, cells were incubated for 1 h at room temperature in PBS containing 7.5% goat serum and 7.5% foetal bovine serum and then incubated overnight at 4°C with the indicated primary antibody. The following antibodies were used for IF: GFP (1/200, ab6673, abcam), PML (1:100, sc966, Santa Cruz), PCAF (1:50, ab12188, Abcam), GCN5 (1:100, 3305, Cell signaling), TRF2 (1:100, IMG-124A, Imgenex), and USP22 (ab4812, Abcam). Secondary labelling was performed using an Alexa Fluor 488- or 594-conjugated antibody (Molecular Probes) at room temperature for 1 h.
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3

Antibody-Based Protein Detection Assay

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Antibodies against human KDM1A (ab17721 and ab90966), CK1δ (ab48031), GATA6 (ab22600), and USP22 (ab4812) were from Abcam. Antibodies against GST (sc-138), Tuj-1(sc-58888), CK1α (sc-6477), CK1ε (sc-6471), BMP2 (sc-6895), CDKN1A (sc-397), and α-Tubulin (sc-5286) were from Santa Cruz Biotechnology. Antibodies against human GSK3β (9315), GSK3α (9338), CD133 (3663), phospho-GSK3β-S9 (9336), Oct4 (2750), H3K4me2/3 (9725 and 9751) and Myc-tag (2276) were from Cell Signaling Technology. Antibodies against phospho-serine/threonine (612548) and nestin (611658) were from BD Transduction Laboratories. Antibodies against hemagglutinin (HA)-Tag and Flag-tag were from Sigma. Hoechst 33342, Alexa Fluor 488 goat anti-rabbit antibody, and Alexa Fluor 594 goat anti-mouse antibody were from Molecular Probes. The specific antibody against phospho-KDM1A S683 was produced by Signalway Antibody. Supplementary Table 1 contains detailed information about the used antibodies.
Temozolomide (TMZ), tideglusib, lithium chloride, glutathione S-transferase (GST) beads, cycloheximide (CHX), and MG132 were from Sigma. Puromycin, hygromycin, and D4476 (4-[4-(2,3-dihydro-benzo[1,4]dioxin-6-yl)-5-pyridin-2-yl-1H-imidazol-2-yl] benzamide) were from EMD Biosciences. Protein G agarose was from Life Technologies. The recombinant active GSK3β (G09-10G) and CK1α (C64-10G) proteins were from SignalChem Lifesciences Corp.
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4

Western Blot Analysis of Protein Expression

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Proteins were separated by SDS-PAGE and transferred to nitrocellulose membrane (Bio-Rad, Hercules, CA, United States). Membranes were blocked in a buffer (TBS: 50 mM Tris-HCl, 150 mM NaCl, pH 7.4) containing 5% bovine serum albumin and 0.1% Tween-20, followed by incubation with the primary antibodys USP22 (ab4812, 1:2000, Abcam, Cambridge, UK), Sirt1 (2496, 1:2000, CST, United States), H2AX (2595, 1:1000, CST, United States), γ-H2AX (Ser 139)(9718, 1:1000, CST, United States), Ubi-H2A (Lys119) (8240, 1:1000, CST, United States), Ku70 (10723-1-AP, 1:1000, Proteintech, United States), Bax (50599-2-lg, 1:1000, Proteintech, United States), cytochrome C (10993-1-AP, 1:1000, Proteintech, United States) or GAPDH (10494-1-AP, 1:3000, Proteintech, United States). The immunoreactive proteins were visualized using the ECL western blotting system (Bio-Rad, Hercules, CA, United States), and densitometric analysis was performed using BioImaging systems (UVP, labworksTM, ver 4.6). Mean values of the data obtained from three separate chambers were presented.
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5

Immunohistochemical Analysis of USP22

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The USP22 immunohistochemical analysis was performed based on previously published methods. 15 Briefly, the tissues were post-fixed with formalin, embedded in paraffin and cut into 4-micrometer sections. Subsequently, the sections were deparaffinized in xylene, rehydrated in ethanol solutions of descending concentration and submerged in ethylenediaminetetraacetic acid (EDTA; pH 8). Antigenicity was retrieved by autoclaving the sections at 121°C for 5 min. After quenching the endogenous peroxidase in 3% H 2 O 2 for 15 min and washing with phosphatebuffered saline (PBS), the sections were incubated with a primary antibody against USP22 (1:200, ab4812; Abcam, Cambridge, UK) overnight at 4°C. A 30-minute peroxidaseconjugated streptavidin incubation and diaminobenzidine incubation were subsequently performed, followed by counterstaining with a commercially available hematoxylin to stain the nuclei (H9627; Sigma-Aldrich, St. Louis, USA).
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6

Exogenous and Endogenous Immunoprecipitation

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For exogenous immunoprecipitation, after 48 hours of expression plasmid transfection into HEK293FT cells, cells were collected and lysed in a chilled nuclear lysis buffer (50 mmol/L Tris‐HCl (pH 8.0), 150 mmol/L NaCl, and 1% Nonidet P40) with 2% (v/v) complete proteinase inhibitor (CPI) and NaVO3. Cells were sonicated, and the supernatants were collected by centrifugation at 14 000 g for 15 minutes at 4°C. Flag‐conjugated protein A + G agarose beads (Sigma) were added to the samples; afterwards, the samples were incubated for 7‐9 hours at 4°C with gentle rotation. For endogenous immunoprecipitation, whole‐cell lysate of abundant U251 cells (about 1 × 107) in the nuclear lysis buffer was divided equally into 2 microcentrifuge tubes and incubated with anti‐USP22 antibody (ab4812; Abcam) and anti‐IgG antibody (ab109489; Abcam) at 4°C respectively. After 6 hours, non‐tagged protein A + G beads (Santa Cruz Biotechnology) were added to each microcentrifuge tube and the mixed samples were incubated at 4°C overnight. After that, the beads were precipitated by centrifugation at 8000 g for 30 seconds at 4°C. Then, the beads were washed 4 times with 1 mL ice‐cold lysis buffer, and the immunoprecipitated proteins were released from the beads by boiling the sample buffer for 2 minutes. The proteins were detected by western blot assay as previously mentioned.
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