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8 protocols using non immune igg

1

Immunoprecipitation of Mitochondrial Proteins

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For immunoprecipitation, purified mitochondria from HUVECs were lysed in NP-40 buffer on ice for 20 min followed by centrifugation at 12,000 × g for 25 min. The mitochondrial lysate was then incubated with 2 μg anti-MSI2 antibody (#10770-1-AP, Proteintech, Wuhan, China) or anti-AGO2 antibody (#10686-1-AP, Proteintech) and 40 μL Protein A/G PLUS-Agarose beads (#sc-2003, Santa Cruz Biotechnology, Dallas, Texas, USA) overnight at 4°C with gentle rotation. The beads were washed and boiled in 2X SDS polyacrylamide gel electrophoresis (SDS-PAGE) loading buffer. Non-immune IgG (#12-370, Millipore, Burlington, MA, USA) was used as a negative control. For western blotting, total and mitochondrial proteins were extracted and loaded on a 10% gel followed by gel electrophoresis. Subsequently, the separated proteins were transferred to a 0.2 μm polyvinylidene difluoride membrane (#1620177, Bio-Rad, Berkeley, CA, USA). Next, the membrane was blocked with 5% non-fat milk and incubated with primary antibodies overnight at 4°C with gentle rotation. After washing, the membrane was incubated with the corresponding secondary antibodies at room temperature for 1 h followed by visualization using a ChemiDoc XRS+ imaging system (Bio-Rad). All antibodies used in this study were listed in Supplementary Table 1.
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2

Boyden and Spheroid Invasion Assays

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Boyden and spheroid invasion assays were performed as described in Supplementary materials and methods. For HER2 inhibition experiments, irbinitinib (10 nM) or trastuzumab (2 µg/ml) were added in the upper compartment of the inserts and on the top of gels, respectively. DMSO or non-immune IgG (Millipore, Temecula, CA) served respectively as negative controls.
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3

Histology and Immunohistochemistry of Aggregates

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For histology, aggregates were fixed in 4% paraformaldehyde for 1 h, followed by dehydration in graded alcohols, paraffin embedding, sectioning to 4 μm, and staining with haematoxylin/eosin (H&E) or alcian blue (Sigma) as described previously [7 (link), 8 (link)]. For visualisation of ALP activity, a histochemical assay was performed according to the instructions of the supplier (Sigma).
Immunohistochemistry on alternate sections was performed as described previously [7 (link)]. Briefly, following the respective pre-treatments with pepsin (1 mg/mL), or chondroitinase ABC (Sigma; 5 U/mL), or trypsin (0.25%) sections were incubated overnight with the following primary antibodies: monoclonal anti-COL type II (Acris Antibodies GmbH, Hiddenhausen, Germany), anti-chondroitin-4-sulphate (CS4) (Millipore GmbH, Schwalbach, Germany) or anti-collagen type X (COL type X) (Calbiochem, Bad Soden, Germany). Immunohistodetection was performed by treatment with Advance™ HRP link and Advance™ HRP enzyme (Dako, Hamburg, Germany) followed by diaminobenzidine staining (DAB kit; Sigma), and slides were finally counterstained with hemalaun (Merck, Darmstadt, Germany). In addition, controls with non-immune Ig G (Sigma) instead of the primary antibodies were also performed.
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4

Blocking Cellular Interactions in VSMC Mechanics

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To perform blocking studies, 5 different media conditions were used: (i) regular VSMC media, (ii) VSMC media with 50
μg/ml anti-integrin β1 antibody (Fisher), (iii) VSMC media with 50 μg/ml anti-N-cadherin antibody
(Sigma-Aldrich), (iv) VSMC media with 50 μg/ml of anti-integrin β1 antibody and 50 μg/ml of anti-N-cadherin
antibody (both antibodies), and (v) VSMC media with 50 μg/ml of non-immune IgG (Sigma-Aldrich). non-immune IgG was used as
a negative control as it was not expected to affect cellular interactions and mechanical properties. The antibody concentration of
50 μg/ml was chosen as it has been shown to be effective blocking concentration in other studies (Mendrick and Kelly, 1993 (link); Sun et al., 2005 (link); Yiin et al., 2009 (link)). Cells were exposed to different media conditions as soon as they were seeded on the
substrate and were maintained in culture for a period of 5 days after which AFM nanoindentation studies were performed to study
mechanical properties. This culture period was selected as VSMCs have been shown previously to stiffen in the first 3–5
days of culture (Hemmer et al., 2008 , Hemmer et al.,
2009
). After this initial stiffening period, cell mechanical properties remain stable for 7–10 days (Hemmer et al. 2009 , Deitch et al. 2012 (link)).
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5

Investigating PSMC5 Protein Interactions

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Neuro 2A cells were transfected with wildtype or mutant forms of PSMC5. Two days after transfection, cells were washed in PBS, lysed in RIPA buffer (50 mM Tris pH 7.4, 150 mM NaCl, 1 mM EDTA, 1% NP-40, 0.25% sodium deoxycholate, 10 mM sodium butyrate, protease inhibitor cocktail). Lysates were split and incubated with either nonimmune IgG (Sigma) or anti-FLAG antibodies (Sigma) for 3 hr at 4°C. Immunoprecipitation was performed with Protein G beads (Invitrogen) as described [19 (link)]. Briefly, immunoprecipitated proteins were subjected to SDS-PAGE and analyzed by Western blotting using anti-FosB/ΔFosB antibody (Cell Signaling Technology) based on published protocols [7 (link)]. For in vivo protein binding assays, we used purified nuclear fractions from punch-dissected NAc of mice after chronic cocaine treatment (20 mg/kg IP daily for 7 days, with mice used 24 hr after the last injection). Co-immunoprecipitation from nuclear fractions was performed using the Nuclear Complex Co-IP kit (Active Motif) following the manufacturer’s instructions. The following antibodies were used: MYC or ß-actin, Cell Signaling Technology (Danvers, MA), PSMC5 and histone H3, Abcam (Cambridge, MA), CBP, p300 and BRG1, Santa Cruz Biotechnology (Santa Cruz, CA), and FLAG M2, Sigma.
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6

HMGB1 Modulation in Ischemia Pretreatment

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Mice received single intraperitoneal injections of recombinant human HMGB1 (10 μg per mouse; Sigma-Aldrich)14 (link) or anti-HMGB1 neutralizing polyclonal antibody (600 μg per mouse; Shino-Test Corporation)37 (link) at 1 h before ischemia induction, concurrent with the start of electroacupuncture pretreatment. Negative control mice were injected with saline instead of rhHMGB1 or with non-immune IgG (Sigma Aldrich) instead of anti-HMGB1 antibody.
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7

Histological Analysis of Collagen Hydrogels

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Type I collagen hydrogel aggregates were fixed at day 21 in 4% paraformaldehyde, followed by dehydration, paraffin embedding, sectioning and staining with hematoxylin/eosin (H&E), alcian blue and ALP (all Sigma) according to previously published protocols [33 (link)]. Alternate sections were used for immunohistochemistry. The following antibody treatments were used: type II collagen (COL II) (pepsin (1 mg/ml; Sigma)/monoclonal anti-COL II antibodies (Acris Antibodies GmbH, Hiddenhausen, Germany)); chondroitin-4-sulfate (CS4) (chondroitinase ABC (5 U/mL; Sigma)/monoclonal anti-CS4 antibodies (Millipore GmbH, Schwalbach, Germany)); type X collagen (COL X) (0.25% trypsin; Sigma)/polyclonal anti-COL X antibodies (Calbiochem, Bad Soden, Germany)). Visualization of the immunostainings was performed by treatment with Advance™ HRP link and Advance™ HRP enzyme (Dako, Hamburg, Germany) followed by diaminobenzidine staining (DAB kit; Sigma). Thereafter, the slides were counterstained with hemalaun (Merck, Darmstadt, Germany). Controls with non-immune IgG (Sigma) were performed for all immunohistochemical analyzes.
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8

Histopathological Evaluation of Fibrous Capsule

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Sample sections were deparaffinized using CitriSolv (Fisher
Scientific) followed by rehydration in a graded series of ethanol. Following
hydration, the sections were then stained with Hematoxylin and Eosin (Sigma)
to visualize cell and tissue morphology and distribution. Three measurements
of fibrous capsule thickness were obtained by a histopathologist for each
sample using a calibrated eyepiece reticle in order to calculate an average
value per sample. Macrophage presence was examined using immunohistochemical
staining with a mouse anti-CD68 antibody (Abcam, Cambridge, United Kingdom)
in conjunction with a peroxidase-based detection system using
3,3’-diaminobenzidine chromogen (Vector Labs, Burlingame, CA).
Toluidine Blue (Sigma) staining was used to detect the gel. Sample sections
incubated with non-immune IgG (Sigma) instead of CD68 antibody served as
negative controls, sections of skin sample served as naïve controls,
and sections of spleen served as positive controls. Severity of macrophage
presence was graded by a histopathologist using the guideline of
“+” indicating mild, “++” moderate, and
“+++” severe response, with blind assessment. Slides were
viewed with a Zeiss Axio Imager Z1 (Carl Zeiss, Oberkochen, Germany) optical
microscope and images were captured using AxioVision software (Carl
Zeiss).
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