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6 protocols using syringe filter

1

Synthesis and Characterization of Fluorescent Conjugates

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Citric acid monohydrate, sucrose, ethylenediamine, protoporphyrin IX, sodium chloride, (N-(3-Dimethylaminopropyl)-N′-ethylcarbodiimide), N-Hydroxysuccinimide, 2-hydroxyethylagarose, formaldehyde, perinaphthenone, 2-(N-Morpholino) ethanesulfonic acid, acetone, dimethyl sulfoxide, 2-mercaptoethanol and N,N-dimethylformamide were acquired from Sigma Aldrich (United Kingdom). Dulbecco’s modified Eagle’s medium (DMEM, high glucose), Dulbecco’s modified Eagle’s medium (DMEM, high glucose, without phenol red), foetal bovine serum (FBS), Quant-iT Picogreen dsDNA quantification kit, Pierce LDH cytotoxicity assay kit, and trypsin-EDTA were obtained from Thermo Fisher (United Kingdom). Syringe filters with a 0.2 μm pore size were acquired from Sarstedt (United Kingdom). 1 KDa MWCO, 6.4 ml/cm dialysis tubing was acquired from Spectrum Labs (United States of America). All chemicals were used as received unless stated otherwise. Deionized water was used for all buffers and samples in experiments. Septa steel ring caps and 35 ml glass reaction vessels were obtained from CEM Corporation (United Kingdom).
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2

Synthesis and Characterization of Fluorescent Probes

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Citric acid monohydrate, sucrose, ethylenediamine, protoporphyrin IX, sodium chloride, resazurin sodium salt, (N-(3-Dimethylaminopropyl)-N’-ethylcarbodiimide), N-Hydroxysuccinimide, formaldehyde, phenalenone, 2-(N-Morpholino) ethanesulfonic acid, acetone, dimethyl sulfoxide, 2-mercaptoethanol and N,N-dimethylformamide were acquired from Sigma Aldrich (United Kingdom). Dulbecco’s Modified Eagle’s Medium (DMEM, high glucose), Dulbecco’s Modified Eagle’s Medium (DMEM, high glucose, without phenol red), fetal bovine serum (FBS), phosphate buffer saline (PBS), and trypsin–ethylenediaminetetraacetic acid solution were obtained from Thermo Fisher (United Kingdom). Syringe filters with a 0.2 μm pore size were acquired from Sarstedt (United Kingdom). 1 KDa MWCO, 6.4 ml/cm dialysis tubing was acquired from Spectrum Labs (United States of America). All chemicals were used as received unless stated otherwise. Deionized water was used for all buffers and samples in experiments. Septa steel ring caps and 35 ml glass reaction vessels were obtained from CEM Corporation (United Kingdom).
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3

Phage Cocktail Titer Optimization

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Three commercially available cocktails with phages against E. coli were used, Ses and Intesti of ELIAVA Biopreparations Ltd. (Tbilisi, Georgia) and Pyobacteriophag of Microgen Ltd. (Perm, Perm Territory, Russia) [32 (link),33 (link)]. The plaque assay was performed using the E. coli ATCC 29522 reference strain to determine the phage stock titer. Briefly, phage cocktail tenfold dilutions in 0.9% NaCl were made. Then, 50 μL of diluted phage stock were mixed with 100 μL of freshly grown bacterial suspension in 0.7% molten LB agar, previously incubated in LB broth for 16–18 h at 37 °C, and were poured onto a TSA plate. After overnight incubation at 37 °C, phage plaques on each plate were counted, and the phage titer (PFU/mL) was calculated. To achieve a higher phage cocktail titer, webbed plates of phage titration were used, and 12 mL of LB broth medium was poured on the plate and left at room temperature for 2 h. The supernatant with LB broth and overlay agar was removed and collected in 15 mL plastic tubes. Chloroform (CHCL3) was added with the final concentration of 2–3%, and the tubes were mixed and left at 4 °C for 2 h. Subsequently, the tubes were centrifuged at 6000× g for 15 min at 4 °C, and the supernatant was filtered using a 0.2 μm filter (Syringe filter, Filtropur S, Sarstedt, Nümbrecht, Germany).
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4

Isolation of Equine Small EVs

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Once the cells were 80% confluent, they were first washed to ensure that nanoparticles in FCS did not interfere with the nanoparticles to be gained. For this, the medium in the cell culture flasks was replaced with 20 ml DMEM without FCS and the flasks were gently shaken on a shaker for 5 min. This washing procedure was repeated three times. Subsequently, 12 ml DMEM supplemented with 1% P/S and 1% insulin-transferrin-selenite solution (ITS-H, Capricorn, Germany) to compensate the absence of FCS was added to each cell culture flask. Three days later, the cell culture supernatant containing nanoparticles was harvested and centrifuged at 2700×g for 10 min at room temperature to remove cell debris. The supernatant was then filtered through a 0.2 µm syringe filter (83.1826.001, Sarstedt, Germany). The usual subsequent concentration process, e.g. ultracentrifugation, ultrafiltration or precipitation, was not performed in order to focus on the nanoparticles in the supernatant and the cryoprotectants without additional post-processing. Further purification and identification of nanoparticles containing equine small EVs, for example, has already been performed [29 (link)].
Since special attention was paid to short-term storage until additional concentration and/or experimental or even clinical application, no further processing of the nanoparticles obtained was carried out.
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5

Peptides for Hypoxia-Inducible Factor Regulation

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Reagents, chemicals, and solvents were from Sigma‐Aldrich (Merck), Apollo Scientific, or Thermo Fisher Scientific, except where stated. The HIF1α556–574‐CODD (DLDLEMLAPYIPMDDDFQL), HIF2α523–542‐CODD (ELDLETLAPYIPMDGEDFQL), and HIF3α484–505‐CODD (ALDLEMLAPYISMDDDFQLN) and 3C cyclic (d‐YVWLTDTWVLSRTC)
28 (link),
35 (link) peptides were from GL Biochem (prepared with a C‐terminal amide). Water used for cell culture was purified using a Millipore Elix® 10 system (Merck Life Sciences) and autoclave sterilized (Crystal 300‐RP25, Rodwell Engineering Group). Water used for buffers and molecular experiments was filtered purified by a 0.22‐μm Milli‐Q filtration system (Milli‐Q, Merck Life Sciences). Kanamycin (final concentration 62 mM) was prepared in water sterilized by a benchtop autoclave (LTE TouchClave II, LTE Scientific; program: 121°C and 1 Bar for 15 min) and filtered for impurities with a 0.22‐μm syringe filter (Sarstedt).
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6

Stallion Semen Quality Assessment

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Stallion ejaculates were assessed individually for routine semen quality parameters such as progressive motility and normal morphology. Progressive motility was estimated using computer-aided sperm analysis (CASA; Minitu ¨b). First, the diluted semen was diluted further in the laboratory to a concentration of 25-50 Â 10 6 spermatozoa mL À1 and kept at room temperature for 10-15 min. Samples were analysed in a 10-mm Leja chamber at 378C. The percentage of spermatozoa with normal morphology was determined using eosin-nigrosin staining (Nidacon). Semen smears were prepared by mixing 20 mL semen with the same volume of stain. The mixture was then smeared on a glass slide and air dried. A total of 100 spermatozoa in each ejaculates was examined and classified under phase contrast microscopy oil immersion (Â1000). After assessing sperm quality, 1 mL fresh semen from each ejaculate (containing 100 Â 10 6 spermatozoa) was washed three times at 1200g for 10 min at 48C with phosphate-buffered saline (PBS), which was prepared by dissolving 1 tablet of PBS (Sigma Aldrich) in 200 mL diethylpyrocarbonate (DEPC)-treated water. After 30 min to allow the table to dissolve, the PBS medium was filtered through a Syringe-filter (SARSTEDT) with a pore size of 0.20 mm and stored at 48C until use. Washed sperm pellets were then stored at À808C until RNA extraction.
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