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13 protocols using doxycycline hyclate

1

Glutamatergic Neuron Differentiation from ESCs

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Neuronal differentiation of ESCs into cortical glutamatergic neurons was carried out as previously described92 (link). In brief, the differentiation was carried out by adding doxycycline hyclate (2 μg/mL) to N2 supplemented media (Thermo Fisher, 17502048) with patterning factors SB431542 (Tocris, 1614, 10 μM), XAV939 (Stemgent, 04–00046, 2 μM) and LDN-193189 (Stemgent, 04–0074, 100 nM), as described previously92 (link)–94 (link). Puromycin selection was used (5μg/μL), from days 2 to 6 to remove non-transduced cells. At 4 days post induction, neuronal cells were resuspended into Neurobasal media (Gibco, 21103049) that was supplemented with B27 (Gibco, 17504044, 50X), doxycycline (2 μg/mL), brain-derived neurotrophic factor (BDNF), ciliary neurotrophic factor (CTNF), and glial cell-derived neurotrophic factor (GDNF) (R&D Systems 248-BD/CF, 257–33 NT/CF, and 212-GD/CF at 10 ng/mL each). From this point onwards the neurons were either co-cultured with murine glial cells that were derived from early postnatal (P1-P3) mouse brains as described previously95 (link) or were left to grow as monocultures (mouse strain https://www.jax.org/strain/100012; animal ethical committee approval by Harvard University: Animal Experimentation Protocol (AEP) # 93–15).
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2

Xenograft Tumor Growth and Inhibition

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Eight-week-old female athymic nu/nu mice (Charles River laboratories, Wilmington, MA, USA) were used for xenograft studies. Mice were housed four/cage in sterile cages, kept under light/dark cycles (12 h:12 h), and were acclimated for 7–10 days before the experiments.
Vector transfected (control) and doxycycline-inducible MDA-MB-468 cells (clone 2) were suspended 1:1 in PBS/Matrigel (BD biosciences, San Jose, CA, USA) and inoculated into the inguinal mammary fat pad (2 × 106 cells/100 μL). After surgery, mice were provided water containing 4% sucrose with or without 1 mg/mL doxycycline-hyclate (Thermo Fisher, Pittburgh, PA, USA). Tumor dimensions were measured twice/week and tumor volume was calculated as length × width2 × 0.52. In half of the mice, when tumors were about 150 mm3 in volume (controls) or 250 mm3 in volume (mice inoculated with clone 2), Alzet osmotic mini-pumps (model 1004, Durect Corporation, Cupertinoo, CA, USA), were implanted sc in the dorsal neck. These pumps with a 100-μL reservoir are rated for a continuous delivery at 0.11 μL/h for 4 weeks. The pumps delivered a 37% solution of hydroxypropyl-β-cyclodextrin (HPCD) (CTD, Gainesville, FL, USA) in PBS (control), or 50 mM SMI-6-HPCD complex in PBS. After 3 weeks, animals were euthanized and the tumors were weighed.
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3

Conditional Ccnd1 Overexpression in Pax7+ Muscle Stem Cells

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TRE-Ccnd1WT and TRE-Ccnd1K112E mice transgenic for human Ccnd1 with or without the K112E mutation under TRE regulation have been published previously31 (link),32 (link). Pax7rtTA mice contain rtTA-M2 followed by an IRES, mouse Pax7, and polyadenylation tail knocked in to the first exon of the Pax7 locus. Both lines were maintained by breeding heterozygous animals to wild-type animals. Experimental animals (Pax7rtTA/+, Pax7rtTA/+; TRE-Ccnd1WT, and Pax7rtTA/+; TRE-Ccnd1K112E) were generated by intercrossing the two lines and aging the appropriate genotypes until use. All transgenic animals were treated for seven days with doxycycline by providing doxycycline hyclate chow (Envigo, TD.120769), delivering a daily dose of 2-3 mg doxycycline based on consumption of 4-5 grams each day. On the sixth and seventh days, doxycycline hyclate (Thermo Fisher ICN19895510) was injected intraperitoneally at 50 mg/kg in 0.9% NaCl. MuSCs were isolated on the eighth day based on immunophenotype via FACS as described above.
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4

Preparation and Use of Small Molecules

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Small molecules were purchased from Sigma (St. Louis, MS, USA) or Thermo Fisher (USA), and 5 mM stocks in water (doxycycline hyclate, EGCG, methylene blue) or ethanol (coumarin 1, diflunisal, rifamycin SV, rifampicin) were prepared and stored at −20 °C until needed. “Oxidized” EGCG was prepared by incubating aliquots of EGCG overnight at 37 °C in water, which were then stored at −20 °C. All experiments were carried out in phosphate-buffered saline (PBS; 1.5 mM KH2PO4, 8.1 mM Na2HPO4, 2.7 mM KCl, 138 mM NaCl, pH 7.4) at 37 °C.
Data were analyzed and figures prepared using the “Tidyverse” [59 (link)] suite of tools for R [60 ], within the RStudio environment [61 ]. Final figures were prepared using Adobe Acrobat.
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5

Directed Differentiation of iPSCs into Neurons

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iPSCs were dissociated into single cells using Accutase (STEMCELL Technologies), and 300,000 iPSCs were seeded into 1 well of a Matrigel-coated 6-well plate in mTeSR 1 medium with Y-27632 Dihydrochloride. The next day, lentiviruses encoding NGN2-GFP (Addgene 79823) and rTTA (Addgene 66810) were added to the medium with 4 μg/mL hexadimethrine bromide (MilliporeSigma). The medium was changed every 24 hours for 2–3 days. When transduced iPSCs reached 70% confluence, 1 μg/mL of doxycycline hyclate (MilliporeSigma) was added to induce NGN2-GFP expression. Transduction efficiency was determined by expression of NGN2-GFP. At day 1 of induction, mTeSR 1 medium was changed to BrainPhys Neuronal Medium (STEMCELL Technologies) containing 1× N2 (Thermo Fisher Scientific), 1× B27 (Thermo Fisher Scientific), 20 ng/mL BDNF (PeproTech), 20 ng/mL GDNF (PeproTech), 500 μg/mL Dibutyryl c-AMP (MilliporeSigma), 200 nM l-ascorbic acid (MilliporeSigma), 1 μg/mL natural mouse laminin (Thermo Fisher Scientific), 1 μg/mL doxycycline hyclate, 1 μg/mL puromycin (Thermo Fisher Scientific), and 1 μM cytosine arabinoside (MilliporeSigma). Transduced iPSCs were maintained in supplemented BrainPhys Neuronal Medium, with doxycycline hyclate removed at day 3 after induction, and half of the medium was changed every 3 days till the assay was performed.
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6

Cellular Trafficking Inhibitor Protocol

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Doxycycline hyclate (2 μg/ml, Acros Organics). EIPA (25–75 μM, MilliporeSigma). Tunicamycin (10 μg/ml, MP Biomedicals). Brefeldin A (10 μg/ml, Cayman Chemical). Monensin (25 nM, Alfa Aesar). P-3FAX-Neu5Ac (Tocris) was used at 100 μM unless stated otherwise. SR-7826 (BioVision) and (–)-Blebbistatin (Biogems) were used at 3.33 μM, unless stated otherwise.
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7

Doxycycline Administration in Cell and Embryo Cultures

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Stock solutions of doxycycline hyclate (Acros Organics, Fair Lawn, NJ, USA, 446060250) were made to a final concentration of 1 mg/ml in water, filter sterilized, and stored at −20°C as single use aliquots. DF-1 cells and mandibles were treated in culture with the stock solution diluted in DMEM, with minocycline microspheres (Arrestin) added directly to each well, or by suspending microspheres in PBS and injecting them into the lower jaw with a 30-gauge needle. Pluronic F-127 (MilliporeSigma, Burlington, MA, USA, P2443-250G) was dissolved at a final concentration of 35% (w/v) in DMEM growth medium rocking at 4°C for 48 h. Dox was added to Pluronic F-127 for a final concentration of 500 ng/ml and injected into the lower jaw with an 18-gauge needle. For in ovo treatments, 2.5 µl (for chick) and 3.75 µl (for duck) of the 1 mg/ml dox stock solution was diluted with 750 µl of HBSS. This solution was then gently pipetted into the egg adjacent to the embryo and allowed to diffuse.
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8

Doxycycline Delivery Methods for In Vitro and In Ovo Studies

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Stock solutions of doxycycline hyclate (Acros Organics, 446060250) were made to a final concentration of 1 mg/ml in water, filter sterilized, and stored at -20 °C as single use aliquots. DF-1 cells and mandibles were treated in culture with the stock solution diluted in DMEM, with minocycline microspheres (Arrestin) added directly to each well, or by suspending microspheres in PBS and injecting them into the lower jaw with a 30gauge needle. Pluronic F-127 (Sigma, P2443-250G) was dissolved at a final concentration of 35% (w/v) in DMEM growth medium rocking at 4°C for 48 h. Dox was added to Pluronic F-127 for a final concentration of 500 ng/ml and injected into the lower jaw with an 18-gauge needle. For in ovo treatments, 2.5 µl (for chick) and 3.75 ul (for duck) of the 1mg/ml dox stock solution was diluted with 750 µl of HBSS. This solution was then gently pipetted into the egg adjacent to the embryo and allowed to diffuse.
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9

Stem Cell Differentiation Protocol

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Laminin (23017-95), CyQUANT NF (C35006), bovine pituitary extract (13038-14), HBSS, RPMI, DMEM, DMEM:F12, penicillin-streptomycin, pyruvate solution, fetal bovine serum (FBS), BODIPY 493/503 (D3922), B-27™ Supplement (50X), serum free (17504044) were from Life Technologies; Recombinant Human FGF-basic (100-18B) from Peprotech; doxycycline hyclate (D9891), nicotinamide (N3376), dexamethasone (D4902), 2-deoxyglucose (D6134), Sodium oxamate (O2751), collagenase (C7657), glucose (G7528), tamoxifen (T5648), Sodium oleate (O7501), Bovine Serum Albumin (A7030), Alcian Blue (B8438), Roche cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail (11836170001), ROCK inhibitor: Y-27632 (SCM075) were from Sigma;, Forskolin (1099), IBMX (2845), KT5720 (1288), WWL113 (5259) were from Tocris; mouse EGF (354001), NuSerum IV (355104), ITS+ Premix (354352) and Matrigel (354234) were from Corning; dispase (165–859; Roche); Sp-8-Br-cAMPS (B002 ) and 8-pCPT-2′-O-Me-cAMP (C041) were from Biology Life Science Institute; Oleic acid-[1-14C] was from Perkin-Elmer (NEC315070UC); 4-Bromocrotonic Acid (BrCA) (B2298) was from TCI America; iTaq universal SyBR Green Supermix (BIO-RAD), Protein Block (X0909; DAKO); MACH2 HRP-Polymer (HRP520H) and Betazoid DAB Chromogen Kit (BDB2004H) from Biocare Medical; HG-9-91-01 and KIN112 were kindly provided by Dr. Nathanael Gray.
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10

SARS-CoV-2 Spike Protein Analysis

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For primary antibodies, anti-spike S1 (MM42) antibody was obtained from Sino Biological (Cat#40591-MM42), anti-spike S2 (1A9) antibody was obtained from Abcam (Cat# ab273433), anti-CD9 (HI9a) antibody was obtained from BioLegend (Cat#312102), anti-Hsp90 (F-8) antibody was obtained from Santa Cruz Biotechnology (Cat#sc-13119), and anti-alpha galactosidase A antibody was obtained from Proteintech (Cat# 66121–1-Ig). For secondary antibodies, anti-human IgG (H+L) HRP conjugated antibody was obtained from Invitrogen (Cat#31410), and anti-mouse IgG HRP conjugated antibody was obtained from Cell Signaling (Cat#7076S). Doxycycline hyclate was obtained from PeproTech (Cat#2431450), zeocin was obtained from ThermoFisher (Cat#R25001), and puromycin was obtained from MilliporeSigma (Cat#P8833–25MG). To make A647-labeled anti-S2 antibody, 100 ug of anti-SARS-CoV-2/S2 (1A9) antibody was conjugated to A647 using the Lightning-Link Conjugation Kit (Abcam, Cat# ab269823) according to the manufacturer’s protocol.
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