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38 protocols using ab140601

1

Detecting Cellular Signaling Pathways

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Antibodies against p38 (#8690), p-P38 (#4511), ERK1/2 (#4695), p-ERK1/2 (#4376), JNK (#9212), p-JNK (#9255), HNF1α (#89670), HNF4α (#3113) were obtained from Cell Signaling Technology (Cell Signaling Technology, Inc., Danvers, MA, USA). Antibodies against OTUD5 (ab254742), HBc (ab8638), HBx (ab2741), GAPDH (ab181602), Ubiquitin linkage-specific K48 (ab140601), Ubiquitin linkage-specific K63 (ab179434) were obtained from Abcam (Abcam, Cambridge, UK).
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2

Immunoblotting analysis of signaling proteins

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The experiments were performed according to the previous report [9 (link)]. Proteins were quantified using a BCA protein assay kit (Thermo Scientific, Waltham, MA), and 25 μg proteins were separated using 10% SDS-PAGE and transferred to a PVDF membrane (Millipore). The antibodies for USP5 (1 : 500, #ab155993), TRAF6 (1 : 500, #ab33915), p65 (1 : 500, #ab16502), phos-p65 (1 : 500, #ab76302), IκBα (1 : 500, #ab32518), phos-IκBα (1 : 500, #ab133462), β-actin (1 : 1000, #ab179467), Myc (1: 1000, #ab32), Flag (1 : 1000, #ab49763), and K48-ub (1 : 500, #ab140601) were all bought from Abcam (Abcam, Cambridge, USA).
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3

Western Blot Analysis of Protein Interactions

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As formerly described, the Co-IP, western blotting, GST pull-down as well as in vitro ubiquitination assays were implemented [18 (link), 25 (link)]. For the Western blot analysis, cells or tissues were dissolved in Tris (20 mM, with a pH of 7.8), NaCl (150 mM), 0.1% Triton X-100 with protease inhibitors (phenylmethylsulphonyl fluoride (PMSF) 100 mM, 1 μM pepstatin and 5 μg/ml aprotinin). Subsequently, SDS/PAGE was applied to separate the equal amounts of cell lysates, which were electrotransferred to the membranes of polyvinylidene fluoride (Millipore, USA) and blocked in skim milk (5%). Through using the specific primary antibodies, and then the proper secondary antibodies conjugated with HRP, the membranes were immunoblotted. The immunoreactive bands were observed using a chemiluminescence kit with high sensitivity. The following antibodies were used: antibodies against FAT10 (1:1000, Santa cruz, sc-393630), USP7 (1:1000, Abcam, ab108931), CHK1 (1:1000, CST, #2360), CDKN1A (1:1000, Abcam, ab102013), TGF-β (1:1000, Abcam, ab215715), and CTGF (1:1000, Abcam, ab209780), Flag (1:1000, Sigma, F1804), His (1:1000, Abmart, M30111), ubiquitin (1:1000, Abcam, ab140601) and Tubulin (1:1000, Abcam, ab7291).
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4

Ubiquitin Immunoprecipitation Assay

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This assay was conducted following previous description (21 (link)). Above all, IP lysis buffer (20-188, Millipore) was utilized for gathering MG132-treated/-untreated M0 cells in advance. To collect the supernatants, the cell lysates were subjected to 20-minute centrifugation at 16,000 × g. Subsequently, the collected supernatants were pre-cleared with protein A/G beads, followed by 2-hour incubation with primary antibody of Ubiquitin (ab140601, Abcam). Then, the immunoprecipitated protein complexes were collected and eluted, followed by transferring to SDS-PAGE gel. Eventually, the eluted samples and input fractions were subjected to western blot analysis.
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5

TRIM26 Ubiquitination and GPX4 Regulation in Oxidative Stress

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Antibodies and reagents were acquired from designated suppliers:
TRIM26 (ab188017, Abcam), TRIM26 (27013-1-AP, Proteintech), TRIM26 (sc-393832, Santa Cruz Biotechnology), GPX4 (ab125066, Abcam), GPX4 (sc-166570, Santa Cruz Biotechnology), PLK1 (ab189139, Abcam), p-PLK1 (ab155095, Abcam), β-actin (ab8226, Abcam), K48-ubiquitin (ab140601, Abcam), K63-ubiquitin (12930, Cell Signaling Technology), anti-Flag (66008, Proteintech), anti-Myc (16286, Proteintech), p-S/T (61 G, abmart), p-S/T (612549, BD Biosciences), Anti-His (66005, Proteintech), anti-Flag (14793, Cell Signaling Technology), anti-Myc (2276, Cell Signaling Technology), Anti-His (12689, Cell Signaling Technology), anti-HA (3724, Cell Signaling Technology),
MDA (ab27642, Abcam), 4-HNE (ab48506, Abcam), MG132 (S1748, Beyotime), cycloheximide (HY12320, MedChemExpress), Chloroquine (HY-17589A, MedChemExpress), Onvansertib (HY-15828, MedChemExpress), MLN0905 (HY-15155, MedChemExpress), Recombinant Human PLK1 (ab271716, Abcam).
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6

Co-immunoprecipitation of p73 and ubiquitin

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For Co-IP assay, magnetic beads were pre-incubated with the antibody of P73 (1:100, ab202474, Abcam). After that, the cells were lysed in with Co-IP buffer and centrifuged. The supernatant was collected and incubated with the beads overnight at 4 ℃. Finally, the beads were collected and the protein levels in the immunoprecipitates were examined by WB analysis using anti-UB antibody (1:1000, ab140601, Abcam).
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7

Detecting K48 and K63 Polyubiquitination

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The cell lysates were prepared, and 10 µg of TRAF6 (Santa Cruz Biotechnology # sc‐8409) antibodies and 1 mg of each protein sample were used for co‐IP assays (Thermo Scientific, USA) to detect K48‐specific (1:1000, Abcam # ab140601) and K63‐specific (1:1000, Abcam # ab179434) polyubiquitination. The eluted protein samples analysed by Western blot.
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8

Investigating USP2A Interactions with Transcription Factors

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The coding region of human USP2A (accession number NM_004205) without the stop codon was cloned into pcDNA3.2/V5-DEST (Thermo Fisher Scientific) using BP clonase II (Thermo Fisher Scientific). The resultant plasmid encoded C-terminal V5-tagged USP2A. Halo-tagged Oct-1 and Oct-2 expression plasmids were purchased from Promega (Madison, WI). The HA-tagged ubiquitin plasmid was purchased from Addgene (Cambridge, MA). The USP2A, or control pcDNA3.2/V5-DEST plasmid, plasmids encoding Halo-tagged Oct-1 or Oct-2 and HA-tagged ubiquitin were transfected into HEK293FT cells using Lipofectamine 2000 reagent (Thermo Fisher Scientific). The pull-down and elution of Oct proteins were performed using Magne HaloTag beads (Promega) and HaloTEV protease (Promega) as per the manufacturer's instructions. For detection of Western blot bands, corresponding to K48- and K63-linked ubiquitin chains, Oct proteins, HA-tagged ubiquitin, and V5-tagged USP2, 1000-fold-diluted antibodies against polyubiquitin chains formed by K48 residues (ab140601; Abcam) and K63 residues (ab179434; Abcam), Oct-1 (A301-717A; Bethyl Laboratories), Oct-2 (ab179808; Abcam), HA-tag (#3724; CST), and V5-tag (A190-120F; Bethyl Laboratories) were used as the primary antibodies.
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9

TRAF6 Immunoprecipitation and Polyubiquitin Detection

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Immunoprecipitation of TRAF6 was performed using an anti-TRAF6 (ab33915; Abcam) antibody with a Pierce Crosslink IP Kit (Thermo Fisher Scientific) according to the manufacturer's instructions. For detection of Western blot bands, TRAF6 (ab33915; Abcam), polyubiquitin chains formed by K63-linked (ab179434; Abcam) and K48-linked (ab140601; Abcam) primary antibodies were used (1000-fold dilution).
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10

Comprehensive Immunoblotting Assay Protocol

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Immunoblotting assays were carried out as previously described9 with the following primary Abs: DAB2IP (23582‐1‐AP, Proteintech), c‐Myc (ab32072, Abcam), c‐Myc (67447‐1‐Ig, Proteintech), p‐c‐MycS62 (ab185656, Abcam), p‐c‐MycT58 (ab185655, Abcam), glycogen synthase kinase 3β (GSK3β; 10044‐T32, SinoBiological), p‐GSK3βS9 (#5558, CST), Bcl‐2 (12789‐1‐AP, Proteintech), Bax (#5023, CST), B56α (ab89621, Abcam), Ubiquitin (10201‐2‐AP, Proteintech), Ubiquitin (linkage‐specific K48) (ab140601, Abcam), Nanog (#8822S, CST), CD44 (60224‐1‐Ig, Proteintech), CD133 (18470‐1‐AP, Proteintech), and GAPDH (60004‐1‐Ig, Proteintech). Secondary Abs conjugated to HRP (Servicebio) were used, followed by chemiluminescence.
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