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14 protocols using anti tsg101

1

Western Blot Antibody Validation

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The nitrocellulose membranes were blocked and antibodies were applied in 5% milk in TRIS-buffered saline/Tween-20 (TBST, 0.1M TRIS-HCl, 0.9% [w/v] NaCl, 0.1% [v/v] Tween-20, pH 7.5). The antibodies used were anti-NF45/ILF2 (Bethyl, A303-147A-M), anti-DHX9 (Bethyl, A300-855A-M), anti-Matrin-3 (Bethyl, A300-591A-M), anti-hnRNPA1 (Novus, NB100-672), anti-Caprin-1 (Proteintech, 15112-1-AP), anti-GST (Santa Cruz, sc-459), anti-DDX3X (Sigma, HPA001648), anti-actin (Santa Cruz, sc-1616), anti-FLAG (Sigma, A8592), anti-Alix (Santa Cruz, sc-49268), anti-TSG101 (GeneTex, GTX70255), anti-CD63 (Santa Cruz, sc-15363), and anti-Histone H3 (Cell Signaling Technology, 9715). The immunoblotting images were acquired with the Chemidoc MP Imaging System (Bio-Rad) and quantified with the Image Lab software (Bio-Rad).
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2

Western Blot Analysis of Extracellular Vesicles

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Western blot analysis was carried out using standard methods. Briefly, cells and EV pellets were lysed on ice with lysis buffer (150 mmol/L NaCl, 50 mmol/L TRIS pH 7.4, 0.25% NP40, 1mM EDTA, 0.1% Triton X100, 0.1% SDS, 0.1 mg/mL phenylmethylsulfonyl fluoride, protease cocktail inhibitor (Merck Life Science, Milan, Italy; cat. no.04693159001), 50 mmol/L NaF, and 10 mmol/L Na3O4V. For Western blots, equal protein concentrations (quantified with the Bicinchoninic Acid (BCA) method, Merck Life Science, Milan, Italy; cat. no. B9643) were resolved via 12% SDS–PAGE and transferred to PVDF membranes (Biorad Laboratories S.r.L. Rome, Italy). Antibodies used were: anti-ALIX (Covalab, Bron, France; cat. no. PAB 0204, 1:1000); anti-TSG101 (Gene Tex, Irvine, CA, USA; cat. no. GTX70255); anti-calnexin (Enzo, Farmingdale, NY, USA; cat. no. ADI-SPA-860-F 1:1000); anti-GFP (Merck Millipore, Milan, Italy; cat. no. 3580, 1:1000); goat anti-rabbit IgG, HRP (Abcam, Cambridge, UK; cat. no. 6721) or goat anti-mouse IgG, HRP (Abcam, Cambridge, UK; cat. no. 6728), 1:5000. ECL Western blotting substrate (GeneTex, Irvine, CA, USA; Trident fento Western HRP substrate, cat. no. GTX14698) was added before detection with a BioRad Chemidoc XRF+ (Biorad Laboratories S.r.L. Rome, Italy). Full blots are shown in Figure S6.
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3

Depletion of Endocytic Regulators in HeLa Cells

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Cells were transfected with small interfering RNA (siRNA) using Oligofectamine (Invitrogen) on days 1 and 2 and harvested on day 4. siRNA duplexes were synthesized by Dharmacon, the target sequences were: 5′-CCA GUC UUC UCU CGU CCU A-3′ (Tsg101), 5′-AGA GAC AAG UGG AGG UAA A-3′ (Hrs), both as previously described 18 (link), 5′-GTT CTT GCT CTA CGT CCT C-3′ (CD63), as previously described 16 (link). Negative control siRNA was used for control cells (Mammalian AllStar negative siRNA, Qiagen). Efficiency of knockdown was assessed by western blotting using anti-Hrs (Enzo Lifesciences), anti-Tsg101 (Genetex) and anti-CD63 (1B5, a generous gift from Mark Marsh, University College, London) antibodies.
For concurrent depletion and expression studies, HeLa cells were transfected with siRNA on days 1 and 2 and transfected with PMEL (a generous gift from Michael Marks, University of Pennsylvania) on day 3 using Lipofectamine 2000 reagent (Invitrogen), following manufacturer's guidelines.
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4

Exosomal Protein Isolation and Analysis

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Proteins were isolated form exosomal fraction by adding SDS sample buffer and heating samples to 70°C for 10 min. Total of 7.5 μg of proteins was loaded in a single well and separated by SDS-PAGE and transferred onto a nitrocellulose membrane. After membranes were blocked for one hour at room temperature in Odyssey Blocking Buffer (LI-COR Biosciences), followed by incubation in primary antibodies diluted in Blocking Buffer with 0.1% Tween-20 overnight at 4°C. Membranes were rinsed with PBS followed by incubation with secondary antibody diluted in Blocking Buffer for one hour at RT. After final rinses, blots were scanned with Odyssey Infrared Imager (LI-COR Biosciences). Primary and secondary antibodies comprised: anti-CD63 (Santa Cruz Biotechnology, sc-15363; 1:1000), anti-Tsg101 (Genetex, gtx70255; 1:1000), goat anti-mouse Alexa Fluor 680 (Thermo Fisher Scientific, A-21058; 1:15,000), goat anti-rabbit Alexa Fluor 790 (Thermo Fisher Scientific, A-11369; 1:15,000).
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5

Antibodies and Reagents for Endocytic and Autophagic Pathways

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The antibodies used were: anti-LAMTOR1 (catalog #8943S;CST), anti-dynamin 2 (DNM2; catalog #ab3457;Abcam), anti-RAB5 (catalog #E6N8S;CST), anti-TSG101 (catalog #GTX70255;GeneTex), anti-RAB35 (catalog #GTX120249;GeneTex), anti-RAB7 (catalog #E9O7A;CST), anti-VPS26A (catalog #ab181352;Abcam), anti-P62 (catalog #D5L7G;CST), anti-LC3B (catalog #E5Q2K;CST), anti-HLA-A (catalog #ab52922;Abcam), anti-HLA-B (catalog #ab193415;Abcam), anti-HLA-C (catalog #ab126722;Abcam) and anti-MHC-II (catalog #ab55152;Abcam).
The reagents used were: 1 μM Dynasore (catalog #HY-15304;MedChemExpress), 5 mM 3-methyl adenine (3-MA;autophagy inhibitor) (catalog #HY-19312; MedChemExpress) and 10 nM mammalian target of rapamycin (RAP;HY-10219; MedChemExpress).
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6

Antibody Detection Techniques in Prion Research

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The following mouse antibodies were used: anti-Rab7 (Sigma), anti-Tsg101 (GeneTex), anti-β-actin (Abcam), anti-GM130 (BD Transduction Laboratories) and anti-prion (SAF32, Cayman chemical; AH6, TSE Resource Center,). The following rabbit antibodies were used: anti-Hrs (Novus Biologicals), anti-TGN38 (AbD Serotec), anti-GFP (Abcam), anti-EEA1 (Cell Signaling), anti-Vps26 (a gift from Juan Bonifacino, Cell Biology Metabolism Program, NICHD, NIH, Bethesda, MD), anti-CI-M6PR (a gift from Linton Traub, Department of Cell Biology, University of Pittsburgh, PA) and anti-Alix (Bethyl Laboratories). Rat anti-LAMP1 antibody (Developmental Studies Hybridoma Bank) was used. PrPc and PrPsc were routinely detected using DyL488, Cy3 and DyL647-conjugated secondary antibodies (Jackson ImmunoResearch Laboratories). Western blots were probed using horseradish peroxidase (HRP)-conjugated secondary antibodies (Jackson ImmunoResearch Laboratories) and InfraRed Dye 680 and 800 secondary antibodies (Li-Cor Bioscience).
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7

Protein Separation and Detection via SDS-PAGE and Western Blotting

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Proteins were separated by SDS-PAGE on Tris gels (Bio-Rad) and were transferred onto PVDF membranes (Bio-Rad), as previously described (Bomberger et al., 2011 (link)). The following antibodies were used for protein detection: anti-ALIX (EMD Milllipore), anti-calnexin (Santa Cruz Biotechnology), anti-CD81 (Thermo Fisher), anti-Flotillin-1 (BD Biosciences), anti-ferritin (Abcam), anti-GM130 (BD Biosciences), anti-Hsp90 (Enzo Life Sciences), anti-lactoferrin (Santa Cruz Biotechnology), anti-MHC-I (LifeSpan Biosciences), anti-RSV (Meridian Life Science, Inc.), anti-transferrin (Santa Cruz Biotechnology), anti-Tsg101 (GeneTex). Secondary antibodies were goat anti-mouse, goat anti-rabbit, and rat anti-goat conjugated to HRP (Bio-Rad).
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8

Protein Separation and Detection via SDS-PAGE and Western Blotting

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Proteins were separated by SDS-PAGE on Tris gels (Bio-Rad) and were transferred onto PVDF membranes (Bio-Rad), as previously described (Bomberger et al., 2011 (link)). The following antibodies were used for protein detection: anti-ALIX (EMD Milllipore), anti-calnexin (Santa Cruz Biotechnology), anti-CD81 (Thermo Fisher), anti-Flotillin-1 (BD Biosciences), anti-ferritin (Abcam), anti-GM130 (BD Biosciences), anti-Hsp90 (Enzo Life Sciences), anti-lactoferrin (Santa Cruz Biotechnology), anti-MHC-I (LifeSpan Biosciences), anti-RSV (Meridian Life Science, Inc.), anti-transferrin (Santa Cruz Biotechnology), anti-Tsg101 (GeneTex). Secondary antibodies were goat anti-mouse, goat anti-rabbit, and rat anti-goat conjugated to HRP (Bio-Rad).
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9

Western Blot Analysis of Extracellular Vesicle Markers

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Protein were prepared with a detergent buffer, and the protein concentration was determined using the bicinchoninic acid (BCA) protein assay (Solarbio, Beijin, China). Equal amounts of protein samples were separated by a 12% gel using sodium dodecyl sulfate-polyacrylamide gel electrophoresis(SDS-PAGE) and transferred onto PVDF membranes (Millipore, Billerica, MA, USA). The membranes were probed with anti-TSG101 (GeneTex, USA), anti-CD63 (Immunoway,USA) antibodies overnight at 4˚C. Immune complexes were detected by enhanced chemiluminescence (Proteintech, Chicago,USA).
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10

Western Blot Analysis of Exosome Markers

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Samples were subjected to PAGE as above, and proteins wet transferred to PVDF membranes using a Mini-PROTEAN Tetra cell (BioRad) at 100 V for 60 min at 4°C. Membranes were blocked with 5% (w/v) skim milk in 1X TBST (150 mM NaCl, 50 mM Tris pH 7.4, 0.1% (v/v) Tween 20) for a minimum of 2 hr at RT, and membranes incubated with primary antibodies: mouse anti-CD63 (Santa Cruz sc-5275), anti-CD81 (Santa Cruz sc-166029), anti-VPS4 (Sigma SAB4200215), anti-TSG101 (GeneTex GTX70255), anti-Alix/PDCD6IP (Cell Signalling Technology #2171), anti-HCMV gB (Abcam ab6499), anti-UL83 (Clone 8F5 Nowak et al., 1984 (link)), anti-UL99 (Clone 10B4 Silva et al., 2003 (link)), anti-β-actin (Sigma, A2228) and rabbit anti-VAMP3 (Abcam ab200657), diluted 1:1000 in 5% skim milk for 1 hr at RT, or overnight at 4°C. Membranes were washed with TBST, and appropriate HRP-conjugated secondary antibodies (Bio-Rad) incubated for 1 hr at RT. After washing in TBST, membranes were incubated in Clarity ECL substrate (Bio-Rad) for 1 min, and imaged using a Gel Doc imaging system (Bio-Rad). Images were viewed and analyzed using ImageJ.
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