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20 protocols using flotillin 2

1

Antibody panel for protein analysis

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Flotillin-1 and flotillin-2: mouse monoclonal (BD Biosciences, Heidelberg, Germany) and rabbit polyclonal (Sigma-Aldrich) antibodies; vinculin: mouse monoclonal antibody (Sigma-Aldrich); FAK and pY397-FAK: mouse monoclonal (BD Biosciences); ERK1/2: rabbit polyclonal (C-14, Santa Cruz Biotechnology, Heidelberg, Germany) antibodies; pERK2: mouse monoclonal antibody (E-4, Santa Cruz); GAPDH: mouse monoclonal antibody (Abcam, Cambridge, UK); α-actinin: rabbit polyclonal H-300 antibody (Santa Cruz) for IP, mouse monoclonal antibody (BD Biosciences) for Western blot and mouse monoclonal antibody (BM-75-1, Sigma-Aldrich) for immunofluorescence; His-tag: mouse monoclonal antibody (Novagen, Darmstadt, Germany), myc-tag: mouse monoclonal antibody (Santa Cruz Biotechnology).
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2

Antibody Sourcing for Western Blotting

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Antibodies were purchased as follows: UCH-L1 (381000) from Thermo Fisher Scientific (Rockford, IL, USA); myc (sc-40) and HSC-70 (sc-7298) from Santa Cruz Biotechnology (Santa Cruz, CA, USA); Flotillin-2 (610383) from BD Biosciences (San Jose, CA); Flag (F3165) and β-actin (A1978) from Sigma-Aldrich (St. Louis, MO, USA); and GAPDH (glyceraldehyde-3-phosphate dehydrogenase; H00002597-M3) from Abnova (Taipei, Taiwan). Anti-mouse (NA931V) and anti-rabbit (NA934V) secondary antibodies for Western blotting were purchased from GE Healthcare (Little Chalfont, United Kingdom).
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3

Western Blotting and Zymography of Cellular Proteins

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Cells or vesicles were homogenized in RIPA lysis buffer (150 mM NaCl, 0.1% SDS, 0.5% Na-deoxycholate, 1% Triton X-100, 50 mM Tris, pH 7.2). Up to 50 µg of protein were separated by SDS–PAGE (8% gels) and transferred onto a nitrocellulose membrane (75 min at 10 V). The blocked membrane was incubated with primary antibodies specific to EMMPRIN (#sc-13976), MUC-1 (#sc-7313), TSG101 (#sc-7964, all three from Santa Cruz), Flotillin-2 (#610383, BD), Tubulin (#05-829, Millipore), p38 MAPK total protein (#9212), phospho-p38 MAPK (#9211), c-jun total protein (#9165), and phospho-c-jun (#9261, all four from cell signaling). Signals were detected after incubation with anti-rabbit (#sc-2004) or anti-mouse (#sc-2005, both from Santa Cruz) HRP-labeled secondary antibodies using ECL Prime (Amersham Biosciences). Ponceau S staining was routinely used as loading control. Zymography was performed as previously described (Hagemann et al., 2004 (link)). Briefly, cell lysates (35 µg), supernatants (12 µl), or MV (35 µg) were loaded onto SDS–PAGE gels (8%) supplemented with 1 mg/ml gelatine. After electrophoresis, gels were incubated overnight in renaturation buffer (200 mM NaCl, 5 mM CaCl2, 0.02% Brij-35, pH 7.5) and stained with Coomassie brilliant blue.
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4

Exosome Characterization by Western Blot

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Western blot was carried out for exosomes and cells lysates as previously described [12 (link)]. Briefly, exosomes were lysed in RIPA lysis and extraction buffer (Thermo Scientific). Protein concentration was determined using the BCA (bicinchoninic acid) Protein Assay Kit (Pierce). Blots were incubated with primary antibodies for Flotillin-1 (1:1000; BD biosciences), Flotillin-2 (1:5000; BD biosciences) and TSG101 (1:1000; Abcam) overnight at 4 °C. Corresponding HRP-conjugated anti-rabbit or anti-mouse (1:10,000, Pierce) secondary antibodies were incubated for 1 h at room temperature (RT). Bands were visualized with an ECL kit (Pierce). The density of the immunoblots was determined by image lab software and analyzed using Image J program.
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5

Western Blot Analysis of Membrane Proteins

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Standard western blotting was carried out using 6%–20% gradient gels. The primary antibodies used were as follows: zDHHC5 (1:1,000, Sigma, HPA014670), NCX1 (1:1,000, Swant, R3F1), PLM (FXYD1, 1:1,000, Abcam, ab76597), Flotillin-2 (1:1,000, BD Biosciences, 610383), Caveolin-3 (1:4,000, BD Biosciences, 610420), HA-tag (1:5,000, Roche, 11867423001). The secondary antibodies used were as follows: Rabbit anti-mouse HRP (1:2,000, Jackson ImmunoResearch 111-035-144), Goat anti-rabbit HRP (1:2,000, Jackson ImmunoResearch 315-035-003), Goat anti-rat HRP (1:2,000, Jackson ImmunoResearch, 313-035-003), Donkey anti-guinea pig (1:2,000, Jackson ImmunoResearch, 106-035-003).
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6

Western Blot Analysis of Extracellular Vesicles

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Brain homogenates (10 μg protein), fibroblast lysates (10 μg protein), and EVs proteins (15 μl of the lysate corresponding to 25% of the EVs lysate total volume), were separated by 4–20% tris-glycine gel electrophoresis (Criterion precast gel, Bio-Rad, Hercules, CA) and transferred onto PVDF membranes (Immobilon, EMD Millipore, Billerica, MA). Membranes were incubated with antibodies to CD63 (1:250, Cat# sc-15363, Santa Cruz Biotechnology, Dallas, TX), Alix (1:1000, Cat# ABC40, EMD Millipore), TSG101 (1:1000, Cat# 4A10, GeneTex, Irvine, CA), Flotillin-1 (1:1000, Cat# 610821, BD Biosciences, San Jose, CA), Flotillin-2 (1:1000, Cat# 610384, BD Biosciences), rab35 (1:1000, Cat# 9690, Cell Signaling Technology, Danvers, MA), and β-actin (1:2500, Cat# ab8226, Abcam, Cambridge, MA). The secondary antibodies used were HRP conjugated anti-rabbit, and anti-mouse antibodies (Jackson ImmunoResearch, West Grove, PA). Protein bands were quantified using ImageJ software (NIH, Bethesda, MD). All data are shown as the trisomic to diploid ratio for Ts2 and 2N mice, or for DS patients and 2N control subjects.
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7

Antibody Sourcing and Validation Protocol

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Antibodies were purchased as indicated: UCH-L1 (381000) from Thermo Fisher Scientific, Rockford, IL USA; HIF-1α (sc-10790), N-cadherin (sc-271386), and Vimentin (sc-66002) from Santa Cruz Biotechnology, Santa Cruz, CA, USA; Flotillin-2 (610383) from BD Biosciences, San Jose, CA, USA; Flag (F3165), CD44 (SAB4300691), and CD63 (SAB4301607) from Sigma-Aldrich, St. Louis, MO, USA; GAPDH (H00002597-M3) from Abnova, Taipei, Taiwan; anti-mouse (NA931V) and anti-rabbit (NA934V) secondary antibody for western blotting was purchased from GE Healthcare, Little Chalfont, UK; secondary antibody for immunoflorescence microscopy, donkey anti-mouse Alexa Flour 488 (A-21202) and 594 (A-21203) and donkey anti-rabbit Alexa Flour 488 (A-21206) and 594 (A-21207), was purchased from Thermo Fisher Scientific, Rockford, IL USA.
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8

Extracellular Vesicle Protein Analysis

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Western blotting was performed according to standard protocols. Primary antibodies: mouse monoclonal antibodies against Flotillin-2 (BD Biosciences), Alix (BD Biosciences), TSG101 (GeneTex Inc., Irvine, CA, USA), CD-63 (BD Biosciences), and rabbit anti-Calnexin (StressGene). Secondary antibodies were obtained from Dianova and Invitrogen.
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9

Antibody Profiling of Cellular Organelles

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Primary antibodies were: mouse monoclonal antibodies against Myc clone 9E10 (Sigma), Flotillin-2 (BD Biosciences), α-Synuclein (Invitrogen), Alix (BD Biosciences), TSG101 (GeneTex Inc., Irvine, CA, USA), CD63 (BD Biosciences), 6E10 anti-APP (Signet), GAPDH clone 6C5 (Abcam), rabbit anti-Glutamate Receptor GluR2/3 (Chemicon), rabbit anti-Glutamate Receptor GluR1 (Chemicon), rabbit anti-Calnexin (StressGene), rabbit anti-GFP (Invitrogen), rabbit anti-Integrin β5 (Millipore), rabbit anti-UBC9 (Santa Cruz), and rat anti-LAMP1 (1D4B) (Santa Cruz). SUMO-2 antibody was kindly provided by F. Melchior (Heidelberg, ZMBH, Germany) [5 (link)]. Secondary antibodies were obtained from Dianova and Invitrogen.
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10

HEK Cell Transfection and Western Blot Protocol

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All chemicals were of the highest grade available and were purchased from Sigma–Aldrich unless indicated otherwise. All HEK cell transfections utilized Lipofectamine 2000 (ThermoFisher Scientific). Primary antibodies were from the following sources: PLM phospho-S68—custom made38 (link), zDHHC5—Sigma–Aldrich HPA014670 (diluted 1:2000 for western blots), Flotillin 2—BD Biosciences 610383 clone 29 (1:2000), PLM—Abcam ab76597 (1:2000), HA tag—Roche, clone 3F10 (1:2000), FLAG—Sigma F1804 clone M2 (1:2000), Caveolin 3—BD Biosciences 610421 clone 26 (1:5000), sodium pump α1 subunit, Development Studies Hybridoma Bank, clone α6F (1:100), Ras—Merck 05-516, clone RAS10 (1:2000). HRP-linked secondary antibodies were from ThermoFisher Scientific (antirat, diluted 1:2000 for western blots) and Jackson ImmunoResearch (antirabbit and antimouse, both diluted 1:2000 for western blots). Western Blots utilized Immobilon Western Chemiluminescent HRP Substrate (Merck Millipore, Watford, UK) and were visualized and analyzed using a ChemiDoc XRS acquisition system running QuantityOne software (BioRad).
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