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33 protocols using knockout sr

1

Chondrogenic Differentiation of Embryoid Bodies

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EBs (n=20) were transferred onto 6-well plates coated with Matrigel™ (Corning Incorporated). After 24 h, the medium was replaced with a chondrogenic medium (ChM) (day 0) composed of DMEM/F12 (Sigma-Aldrich; Merck KGaA), 2% KnockOut™ SR (Thermo Fisher Scientific, Inc., Waltham, MA, USA), 1 mM sodium pyruvate (Biowest, Nuaillé, France), 10−7 M dexamethasone, 50 µM ascorbic acid, 50 µM L-proline, 1% penicillin-streptomycin (all provided by Sigma-Aldrich; Merck KGaA), 1% ITS+ premix (Corning Incorporated), and 10 ng/ml TGF-β3 (ImmunoTools, Friesoythe, Germany). The EBs were cultured for 21 days and the medium was changed every second day.
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2

Isolation and Culture of hiSMCs and hiNSCs

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Primary human intestinal smooth muscle cells (hiSMCs) were obtained from
ScienCell and cultured in smooth muscle cell medium (SMCM, ScienCell). Cells
were cultured in T-75 cm2 tissue culture flasks (Corning), maintained
at 37°C, 5% CO2 humified atmosphere and harvested with 0.25%
trypsin-EDTA (Gibco) prior to seeding. Cells at passage number 4–5 were
used for the experiments. Human induced neural stem cells (hiNSCs) were
generated and expanded as previously described [17 (link)]. Briefly, expanded hiNSCs were lifted
off mouse embryonic fibroblasts (MEFs) using TrypLE Select and pelleted. The
cell pellet was resuspended in hiNSC expansion media consisting of KnockOut
Serum Replacement DMEM (Thermo Fisher), GlutaMax (Thermo Fisher), KnockOut SR
(Thermo Fisher), Antibiotic-Antimycotic (Thermo Fisher) and 2-mercapto (Thermo
Fisher), bFGF Basic (Thermo Fisher). The resuspended cell solution was vortexed
and passed through a 40μm filter to achieve single cell suspension. The
resulting single cells obtained from hiNSC colonies were then used for scaffold
seeding. The media were changed every other day.
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3

Differentiation of iPSCs into Embryoid Bodies

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The EBs were derived from iPSCs by in vitro differentiation, as previously described.26 (link) Briefly, gently scraped human iPSCs were transferred to an ultra-low attachment plate. Cells were maintained in suspension to generate EBs in EB medium consisting of 20% KnockOut SR (10828010, Thermo Fisher Scientific), 2 mM GlutaMAX Supplement (35050061, Thermo Fisher Scientific), 0.1 mM MEM Non-Essential Amino Acids Solution (11140076, Thermo Fisher Scientific), and 0.1 mM 2-Mercaptoethanol (31350010, Thermo Fisher Scientific) in KnockOut DMEM/F-12 (12660012, Thermo Fisher Scientific). EB medium was changed every day. After 5 days of growth suspension, EBs were transferred onto Matrigel- (354277, Corning) coated plates (353047, Corning) to allow for attachment. The entire EB plate was harvested on day 8 for qRT-PCR) to confirm germlayer markers.
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4

Culturing HEK 293 and ES Cells

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HEK 293 cells (ATCC) were cultured using standard conditions in media containing: DMEM (Life Technologies), 10% FBS (Applied StemCell), and Penicillin-Streptomycin (Life Technologies).
ES cells were cultured using standard conditions in media containing: DMEM (Life Technologies), 7.5% ES-sure FBS (Applied StemCell), 7.5% KnockOut SR (Life Technologies) Penicillin-Streptomycin (Life Technologies), Glutamax (Life Technologies), HEPES buffer (Life Technologies), 2-mercaptoethanol (Life Technologies), and MEM-NEA (Life Technologies). LIF was replaced daily and ES cells were passaged every 48 h.
For long recruitment experiments (>1 h), cells were treated with 3 nM RAP (Selleckchem) and/or 3 nM FK506 (Abcam) added directly to culture dish and changed daily. For short recruitment experiments (≤1 h), cells were treated with 30 nM RAP and/or FK506 in suspension.
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5

Macrophage Cytokine Response to Milk Exosomes

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Immortalized murine macrophages (MH-S, ATCC, Manassas, VA) were grown to 80% confluency on 12-well plates in growth medium (ATCC, 30–2001 supplemented with 10% FCS and pen/strep). Immediately before initiating experiments, complete medium was replaced with extracellular vesicle-free medium (30–2001 containing 10% serum replacement (KnockOut SR, Life Technologies, Grand Island, NY)) for 2 h. MH-S cells were treated with medium alone (con) 1% DE alone, con + milk EVs, or 1% DE + milk EVs, and incubated 24 h. Culture supernates were harvested for cytokine measurements, cells were counted and lysates were prepared for arginase assays. The quantity of EVs used was adjusted to approximate the nanovesicle content in a 10% fat-free milk solution, thus, 24.8 × 106 exosomes were added to each of the exosome-treated wells. Three independent experiments were performed with triplicate wells for each condition, and inflammatory markers were measured in duplicate on immunoassays (N=18 technical replicates).
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6

Anti-B7-H3 CAR-T Cell Production

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CD4+ and CD8+ T cells were isolated from patient apheresis products using the CliniMACS device (Miltenyi Biotec). A 1:1 mixture of CD4-enriched and CD8-enriched cell fractions were then pooled, suspended in X-Vivo 15 (Lonza) media supplemented with 2% KnockOut SR (Life Technologies), 5 ng/mL rhIL-7 (CellGenix), 0.5 ng/mL rhIL-15 (CellGenix) and 10 ng/mL rhIL-21 (Miltenyi Biotec), initiated into culture in a G-Rex 100MCS vessel (Wilson-Wolf), and stimulated using CD3/CD28 CTS® Dynabeads (Life Technologies). Cell products were then transduced with a GMP-grade SIN (self-inactivating) lentivirus encoding the anti-B7-H3CAR, the methotrexate-resistant human DHFR mutein huDHFRdm, and the cell-surface marker EGFRt. On day 3 of culture, 50nM methotrexate (Mylan) was added to the culture vessel to select for cells possessing DHFRdm. On day 7 of culture, CD3/CD28 CTS® beads were removed from the cell suspension using the Dynamag CTS device. Following 10–13 days in culture, patient cells were harvested and washed using the Sepax 2RM device (Cytiva) and resuspended in CryoStor-CS5 (Biolife Solutions) for cryopreservation in CellSeal closed-system vials (Sexton).
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7

Engineered Antigen-Specific T Cell Therapy

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CD4+ and CD8+ T cells were isolated from patient apheresis products using the CliniMACS device (Miltenyi Biotec). A 1:1 mixture of CD4-enriched and CD8-enriched cell fractions were then pooled, suspended in X-Vivo 15 (Lonza) media supplemented with 2% KnockOut SR (Life Technologies), 5 ng/mL rhIL7 (CellGenix), 0.5 ng/mL rhIL15 (CellGenix), and 10 ng/mL rhIL-21 (Miltenyi Biotec), initiated into culture in a G-Rex 100MCS vessel (Wilson-Wolf), and stimulated using CD3/CD28 CTS Dynabeads (Life Technologies). Cell products were then transduced with a GMP-grade SIN (self-inactivating) lentivirus encoding the anti-B7-H3 CAR, the MTX-resistant human DHFR mutein huDHFRdm, and the cell-surface marker EGFRt. On day 3 of culture, 50 nmol/L MTX (Mylan) was added to the culture vessel to select for cells possessing DHFRdm. On day 7 of culture, CD3/CD28 CTS beads were removed from the cell suspension using the Dynamag CTS device. Following 10 to 13 days in culture, patient cells were harvested and washed using the Sepax 2RM device (Cytiva) and resuspended in CryoStor-CS5 (Biolife Solutions) for cryopreservation in CellSeal closed-system vials (Sexton).
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8

Exosome Isolation from iPSCs

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Exosomes were extracted from iPSCs using total exosome isolation reagent (Thermo Fisher Scientific, Waltham, MA, USA) as per the manufacturer’s instructions. Briefly, iPSCs were cultured in 6-well plates, until 80% confluence, in serum-free iPSC growth medium containing Dulbecco’s modified eagle’s medium (DMEM)/Nutrient Mixture F-12 Ham 1:1 (Biological Industries, Beit Haemek, Israel) containing 20% KnockOut SR (Life Technologies, Waltham, MA, USA), 1% nonessential amino acid, 1% L-glutamine (Biological Industries, Beit Haemek, Israel), 0.2% 2-mercaptoethanol (Life Technologies, Waltham, MA, USA), and rhFGF basic (4 ng/mL) (R and D Systems, Minneapolis, MN, USA), at 37 °C, 95% air, and 5% CO2 in an incubator. Culture medium was then collected and centrifuged at 2000× g for 30 min. The supernatant was then transferred to a new tube and mixed well with 5 mL of total exosome isolation reagent. The homogenous solution was incubated at 4 °C overnight and then centrifuged at 4 °C at 10,000× g for 1 h. The supernatant was then aspirated, and the exosomes were suspended in 500 µL PBS and stored at −80 °C until use. Extracted exosomes were analyzed for particle visualization and rapid, automated analysis of size distribution and concentration by nanoparticle tracking system (NanoSight NS300, Weizmann institution, Rehovot, Israel). Exosomes were saved at −80 °C for following experiments.
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9

iPSC Generation, Maintenance, and Characterization

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Generation, maintenance, and characterizations of iPSCs were performed as described elsewhere [17 (link)], with specific modifications described in the Supplementary material. iPSCs and hESC were cultured on MEF feeders in iPSC medium (Knockout DMEM (Life Technologies), containing 20% Knockout SR (Life Technologies), 1% GlutaMAX, 0.1 mM β-mercaptoethanol (Life Technologies), 1% antibiotics, 1% NEAA, and 10 ng/ml basic fibroblast growth factor (bFGF) (Peprotech). For characterization procedures of iPSCs, see Supplementary material.
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10

Culturing Oct4-GFP and Gcnf-null ESCs

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Male and female Oct4-GFP(ΔPE) ESCs and female Gcnf−/− ESCs [8] (link) were grown on gamma-irradiated mouse embryonic fibroblasts (MEFs) in KNOCKOUT DMEM medium containing 4.5 g/l glucose and supplemented with 15% KNOCKOUT SR (Invitrogen), 2 mM L-glutamine (Invitrogen), 100 µM nonessential amino acids (Invitrogen), 1 µM 2-mercaptoethanol (Invitrogen), and 50 µg/ml each penicillin and streptomycin (Invitrogen) in the presence of 1,000 U/ml murine leukemia inhibitory factor (LIF) (ESGRO; Chemicon).
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