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36 protocols using probe sonicator

1

Preparation and Characterization of PIC-SNEDDS

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A SNEDDS was prepared by combining PIC with tween 80, PEG 200 and oleic acid (4:4:2) according to previous solubility studies. Components were mixed in their respective percentages totaling 1 g, were mixed with 50 mg PIC and placed in a vortex (5 min). This was followed by sonication using a Sonics probe sonicator (20 kHz, 1500 W, Sonics, Newtown, CT, United States) for 50 s to allow for the complete dissolution of PIC. PIC- SNEDDS globule size was determined by a dynamic light scattering technique utilizing a Nano-ZS particle size analyzer (Malvern Instrument, Worcestershire, United Kingdom), using 100 μL of PIC-SNEDDS, diluted with 10 ml of 0.1 N HCl, vortexed (1 min), then measured. Average globule size was 75 ± 2.1 nm.
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2

Solvent-Based SNEDDS Formulation

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Based on the preliminary solubility studies, Tween 80 and PEG 200 were chosen together with PSO for the formation of SNEDDS [34 (link)]. The percentage of each formula component (total weight 1 g), according to the experimental design, and 5 mg TDL, were mixed and then vortexed for five minutes. The formulation was then sonicated for 50 s in a Sonics probe sonicator (20 kHz, 1500 W, Sonics, Newtown, CT, USA).
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Preparation and Characterization of PIC-SNEDDS

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A SNEDDS formulation was prepared by combining polyethylene glycol 200 (surfactant) and Tween 80 (cosurfactant) with oleic acid at a ratio of 4:4:2. After that, 50 mg PIC was mixed with the components using a vortex mixer for 5 min at room temperature totaling 1 g of PIC-SNEDDS. The PIC-SNEDDS formulation was further sonicated in water for 50 s using a sonics probe sonicator (20 kHz, 1500 W, Sonics, Newtown, CT, USA) to allow for complete dissolution. The particle size of the resultant nanoformulation was determined using the dynamic light scattering (DLS) technique integrated into the Zetasizer analyzer (Malvern Instrument, Worcestershire, UK). For that, 100 μL of the PIC-SNEDDS formulation was diluted with 10 mL of 0.1 N HCL in a screw-capped glass vial and measured at 25 °C. The average particle size was 75 ± 2.1 nm.
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ChIP Assay Verification via DNA Pull Down

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To verify the results of ChIP assay, the DNA pull down assay was performed basically according to the manufacturer’s protocol51 (link) with some modifications. Briefly, HSV-1-infected HeLa cells were fixed with 1% formaldehyde and sonicated on ice for 10 cycles at 30% power for 10 s with 20 s pauses between each cycle using a probe sonicator (Sonics & Materials, Inc.). Then, cell lysates were incubated with biotin-labeled HSV-1 ICP0 TSSs or scrambled sequence of ICP0 TSS4 and after washing, bound proteins were detected by western blotting with anti-H3K4Me3 antibodies (Abcam, ab8580), anti-H3K27Me3 antibodies (Abcam, ab6002), anti-H3K27Ac antibodies (Abcam, ab4729), or anti-histone H3 antibodies (Abcam, ab1791). Protein ratios of the indicated proteins/histone H3 were analyzed with ImageJ software.
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5

Paclitaxel-Loaded IR780 PLGA Nanoparticles

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50 mg PLGA-COOH, 2 mg IR780, and 1 mg paclitaxel were dissolved in 2 ml dichloromethane. 200 μl PFP was added to the above-mixed solution. The probe sonicator (Sonics and Materials Inc., USA) was used to conduct the first emulsification (60 W, 3 min, 5 s on and 5 s off). Next, 5 ml of 4% PVA aqueous solution was added to the above solution for the second emulsification (45 W, 3 min, 5 s on and 5 s off). 10 ml of isopropanol solution (2%) was added and magnetically stirred for 6 h to remove dichloromethane. Finally, the nanoparticles (PIP NPs) were purified and washed by centrifugation.
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6

SRSF2 Regulation of Histone Marks

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To investigate the roles of SRSF2 in the status of histone modification near the TSS of genes, ChIP assay was conducted according to Dahl’s protocol [56 (link)]. In brief, 1 × 106 Jurkate E6 cells transfected with SRSF2 siRNA or control siRNAs were fixed with 1% formaldehyde and sonicated on ice for 10x10 s, with 20 s pauses between each 10 s session and 30% power using a probe sonicator (Sonics & Materials, Inc.). After centrifugation, the supernatants were incubated with anti-H3K4Me3 antibody (Abcam, ab8580), anti-H3K27Me3 antibody (Abcam, ab6002), anti-H3K27Ac antibody (Abcam, ab4729), or anti-STAT3 Y705 antibody (Abcam, ab76315). Chromatin DNA was purified by Dynabeads protein G (Invitrogen, 10004D) and subjected to real-time PCR. The region-specific primers used are listed in Table S1.
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7

Preparation of Eucalyptus and Nutmeg Nanoemulsions

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The preparation of eucalyptus nanoemulsion (E-NE) and nutmeg nanoemulsion (N-NE) from eucalyptus essential oil (E-EO) and nutmeg essential oil (N-EO), respectively, was performed according to the method of Rodríguez-Burneo et al. (2017) (link), with short modifications. In a nutshell, the oil-water nanoemulsions were prepared using essential oils (14%, v/v), ethanol, (3%, v/v) and Tween 80 (3%, v/v). These components of the oily phase were vigorously mixed for 5 min at 15000 rpm with a magnetic stirrer (RCT digital hotplate stirrer). The 20% of prepared oily phase was combined with distilled water (aqueous phase), while continuously stirring magnetically for 15 minutes to obtain the final volume of 100%. To develop the coarse emulsions, further homogenize to be done for 3 min at 16,000 rpm using a high-speed homogenizer. To avoid evaporation and successfully create nanoemulsions, the previously prepared coarse emulsions were placed in an ice bath during ultrasonication process. The coarse emulsions were sonicated using a probe sonicator (Sonics & Materials Inc., U.S.A.) with a diameter of 6 mm at 75% of full power amplitude (75 W) for 20 min. For further work, the nanoemulsion was kept in opaque bottles at room temperature.
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8

Purification of Anti-EGFR-iRGD Protein

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Escherichia coli BL21 (DE3), which express recombinant proteins anti-EGFR-iRGD, was preserved by our laboratory.48 (link),49 (link) The E. coli massively proliferated when cultured in Lysogeny broth (LB) after resuscitation. Proteins anti-EGFR-iRGD were then expressed in E. coli BL21 (DE3) after induction by isopropyl β-d-1-thiogalactopyranoside (IPTG) at 37°C for 4 h. The cells were collected and suspended in 5 mM imidazole buffer solution and subsequently disrupted using probe sonicator (Sonics, Newtown, CT, USA). The supernatant of cell lysate was purified using the protein liquid chromatography system (ÄKTA™ Pure; GE Healthcare UK Ltd, Little Chalfont, UK), and the purified proteins were obtained after dialysis to remove midazole.
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9

Liposomal Protein Encapsulation Protocol

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Liposomes formed after overnight hydration were sonicated at 60% amplitude control (probe sonicator, Sonics and materials Inc., USA) for total duration of 30 sec consisting of three cycles. Duration of each cycle was 10 sec with 10 sec interval. The formulation was maintained on ice bath during sonication. The liposomes were then transferred into polypropylene tubes and centrifuged at 450 g for 3 min to remove the coarse particles. The supernatant was then centrifuged at 34,600 g for 60 min (Sigma Laborzentrifugen 3k30, Germany) to collect the nanoparticles. The pellet obtained was used for calculating the particle size and percentage drug encapsulation. For size measurement pellet was dispersed in ultrapure water (Milli-Q, Millipore) and analyzed using photon correlation spectroscopy (Malvern Zetasizer). Nanoliposomes were made to release entrapped protein by treating them with 1% triton X-100 [15 ] and the amount of protein was estimated using Lowry method [16 (link)]. The amount of protein was calculated by comparing the absorbance (Biospec-1601, Shimadzu, Japan) with the standard curve plotted using bovine serum albumin.
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10

Polydopamine-Coated PLGA Nanoparticles

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PTX-loaded PLGA NPs (PTX@NP) were prepared with three different PLGA polymers by the single-emulsion method. Briefly, 50 mg of PLGA (4, 30 or 150 kDa) was dissolved in 4 mL of CH2Cl2 and mixed with 50 μL of 5 wt% PTX (i.e., 2.5 mg) in CHCl3. The PTX/PLGA mixture was added to 10 mL of 4 wt% polyvinyl alcohol (PVA) in water, and emulsified by a probe sonicator (Sonics Vibracell, Newtown, CT, USA) for 2 min in ice, pulsing at a power level of 7W and a 2:1 duty cycle every 6 sec. The emulsion was added to 20 mL of deionized (DI) water and stirred for 1 h, and the organic solvent was removed by rotary evaporation for 1 h. The resulting PTX@NP was collected by centrifugation at 16,000 rcf for 20 min at 4 °C and washed twice with DI water. For preparation of DiR-loaded PLGA NPs (DiR@NP), DiR were dissolved in the organic phase with PLGA at a target DiR content of 0.25 wt%.
An aqueous suspension of 0.1 wt% PTX@NP (1 mL) was mixed with an equal volume of 0.1 wt% dopamine HCl in Tris buffer (10 mM, pH 8.5). The mixture was incubated on an orbital shaker for 3 h at room temperature to coat the NP surface with a layer of polydopamine (pD). The pD-coated NP (NP-pD) was collected by centrifugation at 16,000 rcf for 20 min at 4 °C and re-dispersed as a 2 wt% suspension.
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