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134 protocols using ubiquitin

1

Western Blot Analysis of Protein Targets

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Antibodies to CK2α, SIRT1, ubiquitin, and β-actin were obtained from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Antibodies against FoxO3a and acetylated Lys were obtained from Cell Signaling Technology (Beverly, MA, USA). Western blotting was performed as described previously (6 (link)).
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2

Mitochondrial Protein Expression Analysis

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The antibodies against following proteins were used in the study: actin (Sigma, A1978, 1:500), ALR (Santa Cruz Biotechnology, Sc‐134869, 1:500), ATP5A (Abcam, ab14748, 1:500), COA7 (Sigma, HPA029926, 1:500), COX4 (Abcam, ab14744, 1:500, and Cell Signaling Technology, 4850, 1:2,000), COX5B (Santa Cruz Biotechnology, Sc‐374417, 1:500), COX6A (Rabbit Serum, 3282.7, 1:1,000), COX6B (Abcam, ab110266, 1:500), COX17 (Proteintech, 11464‐1‐AP, 1:100), GAPDH (Santa Cruz Biotechnology, Sc‐47724, 1:1,000), HSP60 (Sigma, H4149, 1:500), MIA40 (Rabbit Serum, WA136‐5, 1:500), MIC60 (Novus Biologicals, NB100‐1919, 1:1,000), NDUFS1 (Santa Cruz Biotechnology, Sc‐50132 1:1,000), SDHB (Santa Cruz Biotechnology, Sc‐25851, 1:500), TIMM9 (Abcam, ab57089, 1:200), TIMM22 (Proteintech, 14927‐1‐AP, 1:500), TOMM20 (Santa Cruz Biotechnology, Sc‐11415, 1:500), SDHA (Santa Cruz Biotechnology, Sc‐166947, 1:1,000), YME1L (Proteintech, 11510‐1‐AP, 1:100), ubiquitin (Santa Cruz Biotechnology, Sc‐8017, 1:500), UQCR1 (Sigma, HPA002815, 1:500).
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3

Cell Culture and Antibody Usage

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The human U2OS cell line was grown in McCoy's 5A with L-glutamine medium (Cellgro, Corning) supplemented with 10% FBS (GenDEPOT) and 1% penicillin/streptomycin (Gibco). The 293T cell line was grown in DMEM (Cellgro, Corning) with 4.5 g/L glucose, L-glutamine, and sodium pyruvate medium supplemented with 10% FBS and 1% penicillin/streptomycin. Antibodies used are: Cezanne (Santa Cruz, sc-514402), RAP80 (Bethyl Laboratories, A300-763A), Abraxas (homemade), HA (Cell Signaling Technology, 3724s, 2367s), GFP (Invitrogen, A11122, A11120), K63 (EMD Millipore, 05-1308), ubiquitin (Santa Cruz, sc-8017), Ubc13 (Zymed, 37-1100), Ube2S (Cell Signaling Technology, 11878s), Lamin A (Sigma, L1293), GAPDH (Invitrogen, MA5-15738), BRCA1 (Santa Cruz, sc-6954), 53BP1 (Upstate, 05-726), γH2AX (Upstate, 05-636 JBW103), Rad18 (Abcam, ab188235), and pRPA32 (Bethyl, A300-245).
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4

Whole-Cell Lysate Preparation and Immunoblotting

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Whole-cell lysates were prepared from fracture callus tissues or C2C12 cells, an osteoblast/myoblast precursor cell line that was purchased from ATCC (Manassas, Virginia). Homogenised fracture callus tissues with liquid nitrogen or cells were lysed with mammalian protein extraction reagent (Pierce Chemical, Dallas, Texas) containing a protease inhibitor mixture (Roche Applied Science, Indianapolis, Indiana). Whole cell lysates (10 μg protein/lane) were loaded in 10% Sodium Dodecyl Sulfate (SDS)-PAGE gels, transferred to a nitrocellulose membrane, and immunoblotted with antibodies to β-actin, ubiquitin (Santa Cruz Biotechnology) and Itch (BD Biosciences, San Jose, California). Bands were visualized using ECL chemiluminescence (Amersham Biosciences, Piscataway, New Jersey).
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5

Immunoblotting and Co-immunoprecipitation Analysis

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Immunoblotting and co-immunoprecipitation analyses were performed as previously described21 (link). Briefly, immunoblotting samples were prepared with RIPA lysis buffer (50 mM Tris-HCl, 150 mM NaCl, 1% Nonidet P-40, 0.1% SDS, 0.5% sodium deoxycholate and protease and phosphatase inhibitors at pH 7.5). Co-immunoprecipitation samples were prepared with IP lysis buffer (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1% Nonidet P-40, 5% glycerol, 1 mM EDTA with protease and phosphatase inhibitors). Then, 500 μg of protein was incubated with each antibody for 24 h at 4°C, followed by incubation with protein A-sepharose or protein G-agarose beads (Roche Applied Science) for 2 h. Samples were subjected to SDS-PAGE and transferred to nitrocellulose membranes. Antibodies against phospho-IRS-1(S302), phospho-IRS-1(S612), Akt, ERK, phospho-Akt, and phospho-ERK were purchased from Cell Signaling Technology, and antibodies against Flag, HA, ubiquitin, GAPDH, and phospho-IRS-1(Y628) were purchased from Santa Cruz Biotechnology (CA, USA). The IRS-1 antibody was purchased from BD Transduction Laboratories (CA, USA), and the phospho-IRS-1(Y608) antibody was purchased from Merck Millipore (MA, USA).
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6

Protein Expression Analysis in Cell Lysates

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The cells were lysed with PRO-PREP Protein Extraction Solution (iNtRON Biotechnology Inc., Korea) and the following antibodies were used for western blot analysis: DBC1 (Bethyl Laboratories, Mongomery, TX), AR (Santa Cruz Biotechnology, Santa Cruz, CA), P53 (Novocastra, Newcastle, UK), acetylated-P53 (Cell Signaling Technology, Beverly, MA), P21 (Santa Cruz Biotechnology, Santa Cruz, CA), P27 (Santa Cruz Biotechnology, Santa Cruz, CA), BAX (Santa Cruz Biotechnology, Santa Cruz, CA), BCL-2 (Santa Cruz Biotechnology, Santa Cruz, CA), TGFβ (Cell Signaling Technology, Beverly, MA), NFκB (Santa Cruz Biotechnology, Santa Cruz, CA), PCNA (Santa Cruz Biotechnology, Santa Cruz, CA), Rho A (Santa Cruz Biotechnology, Santa Cruz, CA), Ubiquitin (Santa Cruz Biotechnology, Santa Cruz, CA), PARP1 (Santa Cruz Biotechnology, Santa Cruz, CA), and actin (Sigma, St. Louis, MO). Western blot images quantified with ImageJ software. For IP, polyclonal anti-DBC1 or anti-AR antibodies were cross-linked to Dynabeads-protein A (Invitrogen, Carlsbad, CA). DBC1 or AR antibodies were immobilized with Dynabeads-protein A for 20 min and then incubated with cell lysates for 1 h at 4 °C. DBC1- or AR-IP complexes were washed three times and the proteins were eluted. Thereafter, we performed western blotting.
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7

Immunoblotting of Cellular Stress Markers

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Immunoblotting was performed as previously described [13 (link)]. Briefly, whole cell lysates were collected in RIPA buffer, and 10–30 μg total protein was fractionated by SDS-PAGE and transferred to PVDF membranes (Millipore). Primary antibodies to BIP, ATF4, CHOP, RAD51, α-actin (all from Cell Signaling) and ubiquitin (Santa Cruz) were applied followed by horseradish peroxidase-conjugated goat antirabbit IgG (H + L) and goat anti-mouse (H + L) (Jackson ImmunoResearch) as secondary antibodies. Pierce™ ECL (Thermal Scientific) or ECL™ prime (GE Healthcare) were used as substrate.
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8

Antibodies and Inhibitors for Peroxisomal Proteome

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The antibodies used were as follows: TRIM37 (sc-515044; Santa Cruz Biotechnologies), ECH1 (sc-515270; Santa Cruz Biotechnologies), ACOT1/2 (sc-373917; Santa Cruz Biotechnologies), GSTK1 (sc-515580; Santa Cruz Biotechnologies), ubiquitin (sc-8017; Santa Cruz Biotechnologies), PMP70 (sc-514728; Santa Cruz Biotechnologies), LAMP1 (sc-20011; Santa Cruz Biotechnologies), VDAC1 (sc-390996; Santa Cruz Biotechnologies), Sec61-β (sc-393633; Santa Cruz Biotechnologies), PSMA2 (2455; Cell Signaling Technology), cleaved Caspase 3 (9664; Cell Signaling Technology), cleaved poly-ADP ribose polymerase (5625; Cell Signaling Technology), GAPDH (2118; Cell Signaling Technology), actin (A1978; Sigma-Aldrich), myc (C3956; Sigma-Aldrich), PEX14 (ab109999; Abcam), HA (11867423001; Roche), GFP (632593; Clontech), and histidine (34660; QIAGEN). Antibodies against PEX5 and PTS1 were previously described by Wiemer et al. (1995) (link). The inhibitors used were as follows: CHX (C104450; Sigma-Aldrich) and MG132 (C2211; Sigma-Aldrich). Components for in vitro ubiquitylation were purchased from Boston Biochem: UBE1 (E-305), E2 enzyme set (K-980B), and ubiquitin (U-100H). USP2 was provided by E. Bennett (University of California, San Diego).
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9

Mouse Ovary Isolation and Irradiation

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Animal care and handling were performed according to the guidelines set by the World
Health Organization (Geneva, Switzerland). Eight-day-old (P8) female CD-1 mice were
purchased from Charles River Laboratories. Ovaries were harvested, transferred in
sterile flat-bottom 96-well plates with 100 µl MEM (+ L-Glu, Gibco) supplemented with
5% FBS, 0,4% BSA (w/v), Pen/Strep and 70 µM Br-cAMP and cultured in an incubator at
37°C with 5% CO2.
Ovaries were treated overnight with either DMSO or CHX (50 µg/mL) prior following
experiments. IRR ovaries were exposed to 1.5 Gy of γ-irradiation on a rotating
turntable in a 137Cs irradiator, at a dose rate of 2.387 Gy/min. For
inhibition of Chk2 in ovary culture the inhibitor BLM-277 (Merck Millipore, 220486)
was used 2 hr prior γ-irradiation in indicated concentrations.
The following antibodies were used for detection of endogenous protein of ovary
samples by Western Blotting: Msy2 (Santa Cruz, N-13), Ubiquitin (Santa Cruz, P4D1),
p63 (Santa Cruz, H-129) and β-Actin (Santa Cruz, C4).
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10

Comprehensive Protein Analysis in Stem Cells

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The primary antibodies used were: OXPHOS (ab110413, Abcam), TOM20 (sc-11415, Santa Cruz), LC3 (B7931, Sigma for WB), LC3 (M152–3, MBL for immunostaining), pULK1 S757 (6888, Cell Signaling), p62 (610832, BD Bioscience), Ubiquitin (sc-8017, Santa Cruz), LAMP1 (sc-5570, Santa Cruz), TFEB (mbs120432, MyBiosource), Histone H3 (9715, Cell Signalling), GAPDH (ab8245, Abcam), Parkin (sc-32282, Santa Cruz), PINK1 (BC100–494, Novus), MTF2 (M6444, Sigma), OPA1 (612606, BD Bioscience), DLP1 (611113, BD Bioscience), Oct4 (09–0023, Stemgent), Nanog (4903, Cell Signaling Technologies), Sox2 (09–0024, Stemgent), SSEA4 (ab16287, Abcam), TRA 1–81 (09–0011, Stemgent), TRA 1–60 (09–0010, Stemgent) and Nestin (ab22035, Abcam). The secondary antibodies for immunoblot studies were horseradish peroxidase-conjugated anti-mouse (Jackson ImmunoResearch, West Grove, PA) or anti-rabbit (Thermo Fisher Scientific) and for immunofluorescence were anti-mouse or anti-rabbit Cyanine Cy2 or Cy3 labeled (Jackson ImmunoResearch) and anti-mouse or anti-rabbit Alexa Fluor 488 or 555 (Thermo Fisher Scientific).
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