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24 protocols using ab37355

1

Adiponectin and AMPK Modulation in Endurance

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For the neutralizing antibody experiment, mice that had undergone the ET programme were injected subcutaneously with either control IgG (Cont group, ab37355, Abcam) or rabbit polyclonal antibody (pAb) against adiponectin (pAb‐Adip group; 450 µg/kg/d, ab3455, Cambridge, UK) 1×/week for 8 weeks, and they underwent endurance and drop‐up tests (1×/month); For the AdipoR1 inhibition experiment, mice that had undergone the ET programme were injected subcutaneously with either control mouse IgG (Cont group, ab37355) or rabbit pAb against adipoR1 (pAb‐AdipoR1 group; 450 µg/kg/day, ab70362, Abcam) 1×/week for 8 weeks, and they underwent endurance and drop‐up tests (1×/month); For a specific AMPK inhibition experiment, mice that had undergone the ET programme were injected subcutaneously with either dimethyl sulfoxide (DMSO group, Sigma‐Aldrich) or AMPK inhibitor compound C (Com‐C group; 10 mg/kg, 2 times/week, EMD Chemicals Inc, Gibbstown, NJ) 1×/week for 8 weeks, and they underwent endurance and drop‐up tests (1×/month). They were eventually sacrificed for biochemical and morphological analyses.
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2

Protein-Mediated Functionalization of Gold Surfaces

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To enable the biorecognition assays, the gold surface is modified with detection proteins using noncovalent physicochemical adsorption. First, protein A/G (recombinant fusion protein with protein A- and protein G-binding sites) solution (500 μg ml−1) in 10 mM acetate buffer (pH 4) with 0.5% glycerol is deposited on the clean Au sensor in a microarray format. A non-contact, low-volume liquid dispenser (sciFLEXARRAYER S3, Scienion, Dortmund, Germany) is used to create microarrays of protein A/G droplets (150 pl) with 100 μm diameter and 250-μm period. After 1 h incubation, the chips are washed in phosphate-buffered saline (PBS, pH 7.4) for 5 min under constant agitation to remove excess proteins. The remaining area on the bare Au surface is blocked by incubating the whole chip in 1 % v/v bovine serum albumin (BSA) in PBS. Then, the chip is sequentially incubated in mouse IgG solution (Abcam-ab37355, Cambridge, UK, concentration 200 μg ml−1) and its matching goat anti-mouse IgG solution (Sigma-Aldrich-M2650, St Louis, MO, USA), each step followed by PBS washing. Wet media measurements are performed in PBS buffer, whereas for dry measurements, chips are rinsed in deionized water to remove the salt residuals and dried with N2 after each incubation step.
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3

Immune Cell Profiling in BALF

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Cells collected from BALF were incubated in 100 μl 1×RBC lysis buffer (BioLegend) on ice for 10 min, and then quenched by adding 1 ml PBS. Cells from each sample were resuspended in 100 μl Stain Buffer (554656, BD Pharmingen) and incubated for 15 min on ice with 1 μg mouse IgG (ab37355, Abcam, 1:500) for Fc blocking. Then cells were incubated with primary monoclonal antibodies including rat anti-mouse Gr1/Ly-6G-Alexa Fluor 594 (Novus, 1:200), rat anti-mouse CD11b-FITC (R&D System,1:200) and rat anti-F4/80-APC (R&D System,1:200). Flow cytometry was performed using FACS LSR Fortessa X20 (BD Biosciences) and data were analyzed by BD FACSDiva 8.0.1 and FlowJo v10.8.1.
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4

Flow Cytometry for Extracellular Vesicle Identification

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Flow cytometry was used to identify fractions containing EVs according to their tetraspanin content and performed as reported before[16 (link)]. Antibodies anti-CD9 (1:10, Clone VJ1/20), anti-CD63 (1:10, Clone TEA 3/18), or polyclonal isotype (1:5000, Abcam (ab37355), Cambridge, UK) were added to samples an incubated at 4°C for 30 min. After two washes, beads were incubated with FITC-conjugated secondary antibody (SouthernBiotech, Birmingham, AL) and analysed in a FacsVerse flow cytometer (BD Biosciences, San Jose, CA). Approximately 10,000 beads/sample were acquired and analysed using the Flow Jo software (Tree Star, Ashland, OR). In all samples, the top three tetraspanin-containing chromatographic fractions (those containing EVs) were pooled and used in experiments thereafter.
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5

Investigating circCOL1A2 and miR-424-5p Interactions

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This assay was performed by the Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (#17–700, Millipore, WI, USA) following the supplier’s protocol. First of all, cell lysates were collected from 1 × 106 HK-2 cells using RIPA lysis buffer, with 10% lysate saving as the input. The remaining lysate was subjected to overnight incubation using 100 μL magnetic beads conjugated with 10 μg Immunoglobulin G (IgG control) (ab37355, Abcam) or Argonaute-2 antibody (Ago-2, ab186733, Abcam) under 4℃. After the isolation of the co-precipitated RNA, qRT-PCR was performed to measure circCOL1A2 and miR-424-5p levels.
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6

Alzheimer's Disease Tissue Immunohistochemistry

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Human brain tissue sections from Alzheimer disease patients and 5xFAD mice were post-fixed in 4% formalin for 48 h, dehydrated in ethanol, and embedded in paraffin. A series of sections was stained for either mouse Ab-T1, anti-Iba-1 (Abcam, ab178847), anti-beta amyloid (Abcam, ab2539)/(Biolegend, 800702 (clone 4G8)), or mouse IgG (Abcam, ab37355).
Immunohistochemical staining was performed on 4-μm sections using the Leica Bond III system (Leica Biosystems Newcastle Ltd, UK). Tissues were pretreated with epitope-retrieval solutions (ER, Leica Biosystems Newcastle Ltd, UK) followed by 30-min incubation with primary antibodies mouse Ab-T1 (2.85 μg/ml), anti Iba-1 (1:1500), anti-beta amyloid (1:600), and mouse IgG (1 μg/ml). The Leica Refine-HRP kit (Leica Biosystems Newcastle Ltd, UK) was used for detection followed by counter-stain with Hematoxylin.
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7

Co-Immunoprecipitation of SGK2 and FOXO1

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Cell precipitates were collected by centrifugation. The cells were resuspended in lysis buffer containing a protease inhibitor cocktail. The cells were then lysed on ice for 30 min, centrifuged at 15,000 rpm for 15 min, and supernatants were collected. Antibodies (5 μg) and proteins (500 μg) were used for immunoprecipitation. The BeyoMag™ Protein A + G Magnetic Beads (Beyotime Biotechnology) were used to collect the precipitated proteins overnight at 4 °C. The magnetic beads were washed with Tris-buffered saline three times. Elution of products was performed by boiling the magnetic beads in Laemmli sample buffer. Finally, Co-IP products and their corresponding inputs were subjected to western blotting. The following antibodies were used: SGK2 (5595, Cell Signaling Technology), FOXO1 (66457-1-Ig, Proteintech), anti-Mouse IgG (ab37355, Abcam) and anti-Rabbit IgG (ab171870, Abcam).
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8

Chromatin Immunoprecipitation of SMC Contractile Genes

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Chromatin Immunoprecipitation (ChIP) was performed as previously described (Dahl and Collas, 2008 (link); Gomez et al., 2013 (link)). In brief, passage-matched control, Myocd-LSD1, Myocd-LSD1NF SMC were fixed with 1% PFA for 10 min at room temperature. Cells were sonicated with a Bioruptor Pico (Diagenode) to obtain chromatin fragments of 200-500 base pairs. Chromatin was incubated with Protein G Dynabeads (Invitrogen, 10004D) and one of the following antibodies: H3K4me2 (2μg; #07-030, Millipore), Flag (4;g #F3165, Sigma Aldrich), H3K9me3 (2μg; ab176916, Abcam), H3K27me3 (2μg; 07-449, Sigma Aldrich), SRF (2μg; sc-13029, Santa Cruz), KLF4 (2μg; sc-20691, Santa Cruz), TET2 (5μg; ABE364, Millipore), H3ac (2μg; 06-599, Millipore), rabbit IgG (Abcam, ab171870) or mouse IgG (Abcam, ab37355). Genomic DNA was extracted with phenol-chloroform from immunoprecipitated (IP) and non-immunoprecipitated (INPUT) samples. Histone modification and protein enrichment was measured by qPCR using primer sets targeting CArG regions of the SMC contractile genes. Results were expressed as IP/INPUT. Primers used for ChIP-qPCR are listed in Key Resources Table.
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9

Immunoprecipitation and Western Blot Analysis

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Cells were lysed with NP-40 (GenDEPOT #N1200-050) plus protease inhibitor and phosphatase inhibitor by sonication (Diagenode). Protein levels were measured with a DC protein assay. Each sample with 1000 μg in 500 μl was precleared using 40 μl protein A/G PLUS agarose (Santa Cruz, sc-2003) and incubated for 30 min with gentle agitation. Using a magnetic stand, the samples were cleared from the beads and the supernatant were transferred to a new tube and incubated with 2–5 μg of antibody per sample and incubated overnight at 4°C rotating. The next day, 50 μL of agarose beads were added to each sample and incubated for 2 h at 4°C with gentle agitation. The beads were washed with NP-40 three times for 5 min each. The samples were eluted in a sample buffer for western blot analysis. The following primary antibodies were used for immunoprecipitation (IP): anti-mouse IgG (Abcam #ab37355), anti-rabbit IgG (Abcam #ab172730), RAP1 (Abcam #ab14404), γH2A (Abcam #ab81299), and lamin A/C (Abcam #ab108595).
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10

Investigating CXCR5 Signaling in BV-2 Microglial Cells

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Here, 5 × 105 BV-2 cells were seeded into six-well plates, and 5 × 103 were seeded onto a Millicell EZ slide (Millipore) in LCM and grown to 80% confluency. Cells were treated with CXCR5 antibody low endotoxin, sodium azide-free (ab225575, 1:100, Abcam). Mouse IgG (ab37355, 1:100, Abcam) was used as a control. Following a 6-h incubation, the LCM medium was removed, and the cells were washed with PBS, and fresh FBS free DMEM media was supplied. Cell cultures were then stimulated with 10 ng/ml of recombinant mouse interleukin-4 rmIL-4 (PMC0045 Thermo Fisher Scientific), and the other wells were treated with 20 ng/ml of recombinant mouse TNF-α (rmTNF-α, PHC3016, Thermo Fisher Scientific) and supplemented with 10 ng/ml of recombinant mouse interferon gamma (rmIFNγ, PMC4034, PHC3016, Thermo Fisher Scientific). Following 12 h of incubation, the cells were washed with PBS, and the total RNA was extracted and purified (RNeasy Purification Kits; Qiagen) using RT-PCR analysis.
BV-2 cells that were seeded into Millicell EZ slides were washed with PBS and fixed with 2% formaldehyde (Sigma-Aldrich) for 10 min for immunocytochemistry analysis.
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