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11 protocols using synthemax 2 sc substrate

1

Establishment of human skeletal myogenesis model

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The model of human-skeletal myogenesis was established as described previously52 (link). Briefly, human iPS cells [clone: 201B7, provided by CiRA (Kyoto University, Japan)] were stably transfected with a PB-TAC-ERN vector encoding myogenic differentiation 1 gene (Tet/ON-MYOD1)-IRES-mCherry cDNA. Then, the appropriate cell clones (MyoD-hiPSCs) were chosen via G418 selection. For myogenic differentiation, MyoD-hiPSCs were seeded onto Matrigel (BD Biosciences, San Jose, CA, USA) or Synthemax II-SC Substrate (Corning, Corning, NY, USA)-coated dishes without feeder cells. Twenty-four hours after seeding (day 0), doxycycline (1 mg/mL) was added to the ES cell medium. Twenty-four hours after induction via doxycycline (day 1), culture medium was replaced with differentiation medium composed of alpha Minimal Essential Medium (aMEM; Nacalai Tesque, Kyoto, Japan) supplemented with 5% Knockout Serum Replacement (KSR; Thermo Fisher Scientific, Waltham, MA, USA) and doxycycline (1 mg/mL), as described previously52 (link). Two MyoD-hiPSCs clones (#2 and #11) were used to confirm reproducibility in most experiments performed in this study.
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2

Efficient Induction of Intestinal Organoid Cells

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To induce IM cells, hiPSC/ESC colonies grown on feeder layers of mitomycin C-treated mouse SNL feeder cells [37] (link) were first dissociated by an enzymatic method with CTK dissociation solution, and incubated on gelatin-coated plates for 30 min to remove SNLs. Then, the cells were dissociated into single cells by gentle pipetting after the treatment with Accutase (Innovative Cell Technologies, Inc.) for 20 min. The cells were then seeded on Matrigel (Matrigel Matrix Growth Factor Reduced, BD)-coated plates at a density of 1.5×105 cells/cm2.
For the original small molecule methods, the dissociated hiPSCs/ESCs were treated with 3 µM CHIR99021 and 1 µM AM580 (Santa Cruz Biotechnology) or 1 µM TTNPB (Santa Cruz Biotechnology) in Stage 1 medium for two days. Next, the culture medium was replaced with Stage 2 medium containing 1 µM AM580 or 1 µM TTNPB. The Stage 2 cultures were maintained for an additional three to 12 days. The growth factor method was previously described as a “single-cell method” [19] (link).
For the serum-free small molecule methods, the cells were cultured with a serum-free medium containing DMEM/F12 + Glutamax supplemented with 1×B27 supplement (Invitrogen) and 500 U/ml penicillin/streptomycin on Synthemax (Synthemax II-SC Substrate, Corning)-coated plates throughout the differentiation culture.
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3

Dox-induced Senescent Cardiomyocyte Generation

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Optimal conditions to obtain a Dox-induced senescent phenotype were empirically determined by dose response experiments, exposing iCMs to Dox at concentration ranging from 0.2 µM to 5 µM. Briefly, spontaneously beating iCMs were enzymatically dissociated (Multi Tissue Dissociation Kit 3, Miltenyi Biotec) and then plated in Synthemax II-SC Substrate (Corning)-coated wells (5×104 cells/cm2). After 24-48 hours, part of the wells had medium replaced with Dox-containing maintenance medium to obtain senescent-like cardiomyocytes (SenCMs). After 3 hours from Dox administration, all cells were washed twice with PBS and placed back in fresh maintenance medium.
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4

Quantifying GSC Migration with Synthemax

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Cell migration analysis was performed on GSCs plated as an adherent monolayer in the presence of 1 μg/mL Synthemax II-SC substrate (Corning). GSCs were pretreated with SM for 6 h prior to performing scratches. Cells migrating from the leading edge were photographed using phase-contrast microscopy. Distance was measured in a 10 × field using ImageJ (National Institutes of Health).
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5

Monoclonal cell line generation

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After 10 days of blasticidin selection, polyclonal cell populations were collected with accutase and 1,000 cells seeded into 6-cm dishes precoated with Synthemax II-SC Substrate (Corning, 3535) at a concentration of 5 μg/cm2 in mTeSR-E8 medium supplemented with 10× CloneR (Stem Cells, 05888). The medium was changed every day with blasticidin-supplemented mTeSR+Plus medium (10 μg/m). After 10 days, visible colonies were manually transferred into 12-well plates precoated with Vitronectin XF. Surviving monoclonal cell lines were expanded and used in later analyses.
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6

Feeder-free H9 hESC Culture

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H9 (WA-09) human embryonic stem cells were obtained from WiCell (Madison, WI) and, after initial feeder-based expansion on a layer of mitotically inactive human fibroblasts (D551), routinely cultured under feeder-free conditions on Synthemax II-SC substrate (Corning)-coated cell culture plates (as described previously [46 (link)]).
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7

Scratch Assay for EV-Treated Cell Migration

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A scratch assay was performed to assess the migratory potential of EV treated cells as previously described.[22 (link),45 (link)] In brief, EV treated GSCs cultured in the presence of 0.025 mg/mL Synthemax II-SC substrate (Corning) to induce a monolayer were scratched using a pipette tip to create a wound. Medium was immediately refreshed and 2×1010/mL EVs were added. Cells migrating from the leading edge were photographed at different time points using phase-contrast microscopy. Distance was measured in 10× field using ImageJ (National Institutes of Health).
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8

Isolation and Culture of Adult Human Retinal Pigment Epithelial Cells

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Adult human retinal pigment epithelial (ahRPE) cells were obtained from The Eye Bank for Sight Restoration (New York, NY, USA). Primary RPE cells were isolated from one donor with written informed consent for research purpose signed by the next of kin. A cryovial of 5.0 x 105 cells was shipped to the Veneto Eye Bank Foundation in dry ice. After arrival, the cryovial was thawed in a 37°C water bath for 3 minutes. Thawed cell suspension was centrifuged at 259 x g for 5 minutes. The cell pellet was re-suspended in base medium for ahRPE cells containing DMEM/F12 and αMEM solution with 2% FBS plus additional supplements [18 (link)]. For initial cell thawing and plating, base medium was supplemented with FBS to achieve a final concentration of 10% (v/v) FBS. The cells where then plated in Synthemax II-SC Substrate (Corning)-coated 24-well culture plate (Corning) at a density of ~ 1.0 x 105/1.9 cm2 and maintained in a humidified incubator kept at 37°C in 5% CO2. The media was changed every 4th day. Cells were cultured for a minimum of 4 weeks. For gene expression analysis, ahRPE cells were plated either on dDM unfolded over PET TC inserts with 1.0 μm pore size, 12-well format (6.0 x 105 cells/dDM) or Synthemax II-coated Sarstedt transwell inserts 1.0 μm pore size, 24-well format (2.0 x 104 cells/insert).
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9

Generation and Maintenance of KOLF2-C1 hiPSCs

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The human iPS cell line KOLF2 was generated by the Human Induced Pluripotent Stem Cells Initiative consortium at the Sanger Institute using fibroblasts from a healthy adult male with the CytoTune 1 Sendai method68 (link). Specifically, the subline KOLF2-C1 isolated by single-cell cloning was used for the generation of the CHD1L-KO clones. KOLF2-C1 cells were kept under feeder-free conditions in TeSR-E8 medium (StemCell Technologies), on tissue culture plates coated with Synthemax II-SC substrate (Corning). Cells were dissociated from the plates using gentle cell dissociation buffer (StemCell Technologies) and passaged every 3–5 days.
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10

Cell Culture and Differentiation Protocols

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The human embryonal carcinoma NTERA-2 (NT2) cell line was obtained from ATCC. NT2, 293T, and HeLa cells were cultured in DMEM high glucose with GlutaMAX (Invitrogen) supplemented with 10% fetal bovine serum (FBS; HyClone, Piscataway, NJ). Large scale culture of NT2 cells were described (Fong et al., 2011 (link)). Mouse ES cell line D3 was purchased from ATCC (Manassas, VA) and adapted to feeder-free condition as described (Fong et al., 2011 (link)). Differentiation of D3 cells was induced by maintaining cells in LIF-free ES cell medium containing 2–5 mM all-trans retinoic acid (Sigma Aldrich) for up to 7 days. Human ES cell line H9 (WiCell, Madison, WI) was maintained in feeder-independent conditions, using Synthemax SC-II Substrate (Corning) and grown in TeSR-E8 (Stemcell Technologies, Canada). Media was changed daily and cell cultures were passaged using Dispase (Stemcell Technologies), according to the manufacturer's protocol.
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