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10 protocols using ab88388

1

Western Blotting of Cell Lysates for Protein Detection

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Western blotting of whole cell lysates was performed as previously described (74 (link)). Briefly, normalized amounts of eluates were resolved by SDS-PAGE in 4-to-20% mini-Protean gels (Bio-Rad) at 110 V for 15 min, followed by 200 V for 25 min. Following transfer onto nitrocellulose membranes, blots were blocked and probed with 5% (vol/vol) nonfat dry milk in Tris-buffered saline plus 0.05% Tween 20 (TBS-T). Primary antibodies used were rabbit anti-ALIX (Abcam [ab88388]; 1:1000), rabbit anti-Hgs (Abcam [ab155539]; 1:1000), rabbit anti-Rab11a (Abcam [ab88388]; 1:1000), rabbit anti-Rab27a (Abcam [ab55667]; 1:1000), rabbit anti-Rab27b (Cell Signaling Technology [ab44813]; 1:1000), mouse anti-GAPDH (Santa Cruz [sc365062]; 1:1000), mouse anti-β-actin (Santa Cruz [sc47778]; 1:1000), or antisera targeting A. phagocytophilum P44 or APH1235. Rabbit P44 antiserum was generated by New England Peptide. Rabbit anti-APH1235 (45 (link)) was a gift from Dr. Erol Fikrig of Yale University, New Haven, CT. Secondary antibodies were horseradish peroxidase-conjugated horse anti-mouse IgG or anti-rabbit IgG (Cell Signaling Technology; 1:10,000). All blots were incubated with chemiluminescent substrates, imaged, and processed as described (74 (link)).
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2

Exosome Marker Protein and GFP Detection

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For the detection of EV (exosome) marker proteins and GFP, isolated EVs or lysate of CD63‐GFP‐HeLa cells was added to the SDS sample buffer. The boiled samples were separated via 10% SDS/PAGE, transferred onto polyvinylidene fluoride membranes (GE Healthcare, Pittsburgh, PA, USA), and treated with anti‐CD63 antibody (TS63; Abcam, Cambridge, UK), anti‐ALIX antibody (ab88388; Abcam), anti‐calnexin antibody (ab22595; Abcam), and anti‐GFP antibody‐ChIP grade (ab290; Abcam). A secondary antibody labeled with horseradish peroxidase [anti‐mouse IgG HRP NA931V (GE Healthcare) and goat anti‐rabbit IgG (ab6721, Abcam)] was used, and the immunoreactive species were detected using the Enhanced Chemiluminescence (ECL) Plus Western Blotting Detection System (GE Healthcare) with the Amersham Imager 600 (GE Healthcare) and iBright western blot imaging system (Thermo Fisher Scientific Inc.).
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3

Exosome protein analysis by Western blot

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Exosome samples were subjected to SDS-PAGE on 12% gels, followed by Western blotting. Proteins were blotted to PVDF membranes, and membranes were blocked in 5% milk in PBS/0.1% Tween 20 (PBS/Tween). The following primary antibodies were used: rabbit anti-ALIX (1:1000, Abcam, ab88388), rabbit anti-Tsg101 (1:2000, Abcam, ab125011), rabbit anti-GM130 (1:1000, ABclonal, A5344). Blots were visualized using HRP-conjugated secondary antibodies and the ECL Detection Reagent (Thermo Fisher Scientific) and were imaged on a LAS3000 image reader (Raytest, Germany).
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4

Extracellular Vesicle Protein Profiling

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After RIPA cleavage, we extracted total protein and measured with BCA method. After quantitative denaturation, 60 μg proteins were loaded via SDS-PAGE (with a constant voltage of 110 V) and transferred onto nitrocellulose membranes (with a constant current of 300 mA), then the membrane containing proteins was blocked with 5% BSA. The first incubation and second incubation were carried out according to the operation steps. The expression of the protein was expressed by the gray value. Primary antibodies list: CD63 (ab134045, Abcam), Tsg101 (ab125011, Abcam), Alix (ab88388, Abcam).
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5

Exosome Protein Characterization Protocol

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Cells or exosomes were harvested and lysed in RIPA buffer (50 mM Tris-HCl, pH 7.4, 150 mM NaCl, 1% Triton X-100, 1% Na deoxycholate, 0.1% SDS, 1 mMEDTA) supplemented with complete protease inhibitor cocktail (Sigma-Aldrich). Lysates were centrifuged at 12,000 g for 30 min at 4°C to remove insoluble material, after which protein concentrations were determined using a Bradford assay kit using bovine serum albumin (BSA) as a standard according to the manufacturer's instructions. Proteins were resolved on SDS-polyacrylamide gels, and then transferred to a polyvinylidene difluoride (PVDF) membrane. After blocking with 5% (w/v) fat free milk, the membrane was stained with the corresponding primary antibodies followed by incubation with the appropriate secondary HRP-conjugated antibodies. The membrane was incubated with the following primary antibodies: anti-CD63 antibody (Abcam, ab134045), anti-TSG101 antibody (Abcam, ab125011), anti-ALIX antibody (Abcam, ab88388) and anti-CAV1 antibody (Abcam, ab2910), anti-ARF6 antibody (Abcam, ab131261), anti-Rac1 antibody (Abcam, ab155938), anti-CLTC antibody (Abcam, ab21679), anti-GAPDH (Cell signaling).
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6

Isolation and Characterization of Extracellular Vesicles from Adipose-Derived Stem Cells

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EVs were isolated from ADSCs using the total EV kit (Invitrogen). The ADSCs were incubated in the FBS-free medium for 48 h to collect supernatant. The supernatant was centrifuged at 2000 g at 4°C for 30 min to remove cells and debris. Next, the supernatant was centrifuged at a 100 kDa ultrafiltration device at 4000 g at room temperature for 15 min to partially enrich EVs, which was mixed with 0.5-fold volume of total EV isolation reagent. The mixture was incubated at 4°C overnight and centrifuged at 10000 g at 4°C for 60 min the next day. Precipitates were the isolated EVs, resuspended in PBS, or stored at -80°C.
In addition, the protein levels of such EV-related markers as CD9 (ab236630, 1 : 1000, Abcam), CD63 (ab216130, 1 : 1000, Abcam), ALIX (ab88388, 1 : 1000, Abcam), and calnexin (ab133615, 1 : 5000, Abcam) were measured by Western blot analysis.
The morphological characteristics of EVs were observed under the transmission electron microscope (TEM) (Hitachi H7650, Tokyo, Japan) [34 (link)]. Particle size distribution of EVs was evaluated under a NanoSight nanoparticle tracking analyzer (NTA, Malvern, Marvin, UK) [35 (link)].
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7

Exosome Protein Expression Analysis

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Cells were treated with exosomes for 24 h. After RIPA cleavage, total protein was extracted and measured with BCA method. After quantitative denaturation, protein electrophoresis membrane was transferred, and blockage of membrane used 5% BSA. The first incubation and second incubation were carried out according to the operation steps. The expression of the protein was expressed by the gray value. Primary antibodies list: CD63 (ab134045, Abcam), Tsg101 (ab125011, Abcam), and Alix (ab88388, Abcam).
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8

Isolation and Characterization of Cerebral Endothelial Cell-Derived Small Extracellular Vesicles

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Primary CECs were isolated from cerebral microvessels of healthy male adult rats (2–3 months of age) and aged-DM rats (15 months of age, 2 months of DM) according to published method (Teng et al., 2008 (link)). We have demonstrated that the purity of primary endothelial cells is above 90% (Teng et al., 2008 (link)). The sEVs were isolated from culture medium of passages 1 to 2 CECs using a ultracentrifugation method according to published protocol (Li et al., 2021 (link)). The size and particle number of sEVs were characterized by a nanoparticle tracking analyzer (NTA, NanoSight N300 System, Merkel Technologies, Israel). sEV morphology was examined by means of transmission electron microscopy (TEM, JEM-1500Flash, JEOL). Total proteins extracted from isolated sEVs were used for Western blot analysis for the identification of EV marker proteins. The following primary antibodies were used: CD63 (ab68418, 1:1,000, Abcam), Alix (ab88388, 1:1,000, Abcam), CD31 (ab124432, 1:1,000, Abcam), and Calnexin (ab22595, 1:1,000, Abcam).
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9

Protein Extraction and Western Blot Analysis

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Total cell protein was extracted with RIPA lysate, and the protein concentration was determined using a BCA protein assay kit (Thermo Fisher Scientific, Waltham, MA, USA) in a microplate reader. After denaturation for 10 min with the addition of loading buffer, 50 μg of protein samples were subjected to SDS-PAGE and transferred onto PVDF membranes. The membrane was blocked with blocking solution (5% nonfat dry milk) for 2 h and subsequently washed three times using TBST. Specific primary and secondary antibodies were next added separately, followed by incubation on a shaker. ImageJ software was applied to detect and analyze the gray values of protein bands on the membrane. The following primary antibodies: β-actin (1 : 1000, Abcam, ab8227, Cambridge, UK), NGF (1 : 1000, ab52918, Abcam), TrkA (1 : 1000, ab109010, Abcam), PI3K (1 : 1000, ab32089, Abcam), p-AKT (phospho T308) (1 : 500, ab38449, Abcam), AKT (1 : 1000, ab8805, Abcam), mTOR (1 : 1000, ab109268, Abcam), p-mTOR (phospho S2481) (1 : 1000, ab137133, Abcam), CD63 (1 : 1000, ab134045, Abcam), TSG101 (1 : 1000, ab125011, Abcam), ALIX (1 : 500, ab88388, Abcam), CD9 antibody (1 : 2000, ab92726, Abcam), TRPV1 (1 : 1000, ab6166, Abcam).
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10

Protein Extraction and Western Blot Analysis

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The total protein extracted from the cell lysate using RIPA buffer (Beyotime, Shanghai, China) was quantified by a BCA assay kit (Beyotime). After 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), the separated proteins were electrotransferred onto the polyvinylidene fluoride (PVDF) membrane (Millipore, Boston, MA). Subsequently, the membrane was blocked with 5% skimmed milk and probed with the following primary antibodies from Abcam (Cambridge, UK) rabbit anti-α-SMA (ab32575, 1:2500), rabbit anti-collagen I (ab34710, 1:2500), rabbit anti-SOX4 (ab80261, 1:1500), rabbit anti-DKK1 (ab93017, 1:1500), rabbit anti-β-actin (ab8226, 1:5000), rabbit anti-CD63 (ab134045, 1:1000), rabbit anti-CD81 (ab109201, 1:5000), rabbit anti-CD9 (ab92726, 1:1000), rabbit anti-Alix (ab88388, 1:1000), rabbit anti-TSG101 (ab125011, 1:1000), and rabbit anti-calnexin (ab92573, 1:20000) at 4 °C in the dark. Subsequently, the membrane was re-probed with horseradish peroxidase (HRP)-combined immunoglobulin G (IgG) antibodies (ab6721, 1:5000, Abcam) for 2 h followed by enhanced chemiluminescence (BB-3501, Ameshame, UK) for immunodetection. The protein bands were imaged and analyzed by the BIO-RAD imaging system (California).
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