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5 protocols using psma2

1

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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2

Comparative 1DE and 2DE Protein Immunoblots

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1DE and 2DE protein immunoblots (IB) were conducted as previously described [14 (link)]. Total cell lysate samples were separated by 2DE (n = 3 HG, n = 3  NG). For 2DE IB analysis, following IEF of mesangial proteins, the plastic backing of the IPG strips was trimmed off. The acidic most point of the strip was aligned in the IPG well of the Bis-Tris mini gels adjacent to the MW standard lane of the minigel. This procedure insured uniform alignment of IPG strips to the MW standards, in order to compare PHB migration pattern between experimental conditions. Following 1DE or 2DE electrophoresis and transfer, membranes were immunoblotted for PHB (Santa Cruz Biotechnologies, Santa Cruz, CA) at a 1 : 1000 dilution in 5% albumin in Tris-Tween-20 buffered saline (TTBS). PHB spots were imaged on film with luminol images aligned and quantified by densitometry analysis comparing the means of the acidic third and basic third of the PHB charge trains to the total train densitometry. Additional antibodies used for 1DE immunoblots were anti PDI (Stressgen; San Diego, CA) at a concentration of 1 : 10,000 and PSMA2 (Cell Signaling; Danvers, MA) at a concentration of 1 : 1000.
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3

Proteasome Regulation and Autophagy Modulation

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Bortezomib and carfilzomib were purchased from selleck chemicals. Other reagents were purchased from puromycin (Sigma), cycloheximide (Sigma), SUC-LLVY-AMC (Enzo Life Science), Z-Leu-Leu-Glu-AMC (Enzo Life Science), Boc-Leu-Arg-Arg-AMC (Enzo Life Science). Antibodies used were as follows: PA28α (Cell Signaling), PSMA2 (Cell Signaling), S5a (Cell signaling), PA28β (Cell Signaling), Phospho-eIF2α (Ser51) (Cell signaling), eIF2α (Cell signaling), α-tubulin (Genetex), PA28γ (Genetex), PSMB5 (Genetex), PSMB6 (Enzo life science), PSMB7 (Genetex), PSMB8 (Genetex), PSMB9 (R&D systems), PSMB10 (R&D systems), Rpt5 (Enzo life science), Ubiquitin (Cell Signaling), β-actin (Santa Cruz Technology), TCF11/NRF1 (Cell Signaling), LC3B (Cell Signaling), p62/SQSTM1 (MBL International) human Ig lambda light chain (R&D systems), actin (Sigma). pLKO.1 empty vector, shRNA vector targeting human PA28α, NRF1 siRNA (ON-TARGETplus SMARTpool), PA28α siRNA (Accell SMARTpool), and control siRNA were purchased from Dharmacon. Native Mark unstained protein standard was purchased from life technologies.
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4

Immunoblot Analysis of Cellular Proteins

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Immunoblot analysis was performed as described previously61 (link)–63 (link). Primary antibodies included those to PSMA2 (Cell Signaling Technology, 2455), to PSMD1 (Abcam, 140682), to LDHA (Cell Signaling Technology, 3582), to c-Jun (Cell Signaling Technology, 9165), to histone H1 (Merck Millipore, 05–457), to E2F1 (Cell Signaling Technology, 3742), to SV40 LT and ST (Santa Cruz Biotechnology, sc-148), to HSP90 (BD Transduction Laboratories, 610419), and to α-tubulin (Thermo Fisher Scientific, 13–8000), and to calnexin (Medical and Biological Laboratories, M178–3). Horseradish peroxidase–conjugated goat antibodies to mouse or rabbit immunoglobulin G were obtained from Promega62 (link), and ECL reagents were from Thermo Fisher Scientific. Immune complexes were quantified with a ChemiDoc Imaging System (Bio-Rad). Uncropped blot images are provided in Supplementary Figures 4 to 7.
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5

Antibody Sourcing for Protein Analysis

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Antibodies (Abs) anti-P4D1 ubiquitin, -β2, -PSMD2, -p62 were purchased from Santa Cruz Biotechnology (CA). Abs anti-α6 and -PSMD3 were obtained from Invitrogen. Anti-β-actin Ab was from Abgent. Anti-annexin 5 Ab was from BD Science. Abs anti-β1, -RPN10 and -RPT4 were from Enzo Life Science. Anti-β5, -PSMA2, -LC3B, -ADRM1, -AMBRA1 and -HYOU1 were from Cell Signaling Technology (Danvers, MA, USA). Abs anti-mTOR and -S100A9 were from Sigma (St. Louis, MO, USA). Abs anti-UVRAG, -TOLLIP, -VPS33A, and -VTI1A were from Thermo Fisher Scientific (Waltham, MA, USA). Donkey anti-rabbit TexRed and donkey anti-mouse FITC secondary Abs were from Jackson Immunoresearch. Goat anti-mouse Star 635 was from Abberior and Donkey anti-Rabbit Alexa Fluor 594 was from Invitrogen. Fluorescent secondary Abs IRDye® 800CW and IRDye® 680RD were from LICOR. Peroxidase Goat Anti-Rabbit IgG and Peroxidase Rabbit Anti-Mouse IgG were from Jackson Immunoresearch.
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