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12 protocols using ultra low attachment 6 well dishes

1

Sphere Formation Assay for A2780 Cells

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A2780 cells were trypsinized, dispersed into single cells and approximately 10,000 cells were seeded per well in ultra-low attachment 6 well dishes (Cat No: 3471, Corning) and cultured in stem cell-specific serum free media (2 mL) [Serum free DMEM/F-12 media (1:1) supplemented with growth factors [recombinant human epidermal growth factor (EGF) (Cat No: PHG0313, Invitrogen) and fibroblast growth factor (FGF) (Cat No: RFGFB50, Invitrogen)] to form spheres. Cells were continuously monitored for the sphere formation and fresh media with supplements and DMSO or 20µM GANT61 were added every 72 hours. Images were captured using the Nikon TE2000 microscope.
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2

Bladder Cancer Spheroid Culture

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The human bladder cancer T24 cells and normal uroepithelial SV-HUC-1 cells were obtained from Cell Bank of the Type Culture Collection of Chinese Academy of Sciences (Shanghai, China) and incubated in McCoy's 5A or F-12K medium supplemented with 10 or 20% heat-inactivated fetal bovine serum, respectively, at 37 °C in a humidified atmosphere with 5% CO2.
T24 cells were incubated with serum-free DMEM/F12 (Hyclone, Waltham, MA, USA) medium in ultra-low attachment 6-well dishes (Corning, Tewksbury, MA, USA). Growth factors including EGF, b-FGF and IGF-1 were supplied at a concentration of 20 ng/ml (PeproTech, Rocky Hill, NJ, USA) each day (T24 sphere cells). Three days after seeding, the propagated spheroid bodies were collected and digested by StemPro Accutase (Thermo Fisher, Waltham, MA, USA) to single cell suspension for subsequent experiments except for 3D infection test, in which they were directly used. The same medium and growth factors were utilized for T24 cells in ordinary 6-well dishes (Conditioned T24 cells).
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3

Tumor Spheroid Formation and Characterization

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Cells were seeded into ultra-low attachment 6-well dishes (Corning Life Sciences, NY, USA) and cultured in serum-free DMEM-F12 containing 20 ng/ml epidermal growth factor (EGF), 10 ng/ml basic fibroblast growth factor (bFGF), 2% B-27 (Life Technologies, Gaithersburg, MD, USA), and 2 mM L-glutamine (Life Technologies, Gaithersburg, MD, USA) as previously described. Spheroids were incubated in a 5% CO2 chamber at 37 °C for seven days. The culture medium was changed every three days. The diameter and number of tumor spheres in three random magnification fields were calculated under All-in-one Fluorescence Microscope (BZ-X700, Keyence Corp, Atlanta, GA, USA) in the bright light model. Spheroids were collected after 7 days except when noted otherwise. Protein was extracted for analysis, or cells were dissociated with Accutase (Innovative Cell Technologies, San Diego, CA, USA) and used for other experiments.
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Establishing Lung Cancer Spheroid Model

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The human lung cancer A549 cells were obtained from Cell Bank of Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (Shanghai, China) and maintained in RPMI 1640 medium supplemented with 10% heat-inactivated foetal bovine serum. All the cells were incubated in a humidified atmosphere with 5% CO2 at 37°C.
A549 cells were seeded in ultra-low attachment 6-well dishes (Corning) and maintained in serum-free DMEM/F12 (Hyclone Beijing, China) medium supplemented with 20 ng/mL EGF, bFGF and IGF1 (PeproTech, Rocky Hill, NJ, USA). After adding growth factors (20 ng/ml) for two other days, the propagated spheroid bodies were collected for subsequent experiments. At the same time, A549 cells were cultured in ordinary 6-well dishes with the above medium and growth factor as control.
Adenoviruses ZD55-EGFP and ZD55-TRAIL were previously constructed 31 . Embelin and Resveratrol were obtained from Sigma-Aldrich. LY294002 was purchased from Cell Signaling Technology (Beverly, MA, USA).
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5

Culturing Tumor Spheres from MKN28 Cells

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MKN28 control and CDK1 stable knockdown cells were seeded into ultra-low attachment 6-well dishes (Corning, Corning, NY) and cultured in serum-free DMEM/F12 supplemented with 20 ng/mL epidermal growth factor (EGF), 10 ng/mL basic fibroblast growth factor (bFGF), 2% B-27 (Life Technologies, Carlsbad, CA). The culture medium was changed every three days. The diameter and number of tumor spheres in three random 100x magnifications fields were calculated under All-in-one Fluorescence Microscope (BZ-X700, Keyence Corp, Atlanta, GA) using the bright field mode.
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6

Culturing Tumor Spheres from MKN28 Cells

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MKN28 control and CDK1 stable knockdown cells were seeded into ultra-low attachment 6-well dishes (Corning, Corning, NY) and cultured in serum-free DMEM/F12 supplemented with 20 ng/mL epidermal growth factor (EGF), 10 ng/mL basic fibroblast growth factor (bFGF), 2% B-27 (Life Technologies, Carlsbad, CA). The culture medium was changed every three days. The diameter and number of tumor spheres in three random 100x magnifications fields were calculated under All-in-one Fluorescence Microscope (BZ-X700, Keyence Corp, Atlanta, GA) using the bright field mode.
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7

Evaluating Cancer Stem-like Cells via Spheroid Formation

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Spheroid formation assays were performed to evaluate the regulation of cancer stem-like cells (CSCs). OSCC cells were dissociated and suspended in spheroid medium consisting of serum-free DMEM/F12 (Gibco, USA), human bFGF (20 ng/ml, Sino Biological Inc., China), human EGF (20 ng/ml, Sino Biological Inc., China), and B-27 supplement (Life Technologies, USA) in 6-well ultra-low attachment dishes (Corning, USA) under different treatment for 10 days [15 (link)]. The spheroid morphology was observed microscopically, and the number of spheroids was counted and compared.
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8

Culturing Primary Sphere Cells

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Single cells were resuspended in serum-free DMEM/F12 (Welgene) containing 1 × B27 supplement (Invitrogen, Waltham, MA), 20 ng/mL epidermal growth factor, and 10 ng/mL basic fibroblast growth factor (PeproTech, Rocky Hill, NJ). Primary spheres were derived by plating 50,000 to 100,000 single cells per well into 6-well ultra-low attachment dishes (Corning, Corning, NY). Dishes were cultivated for 7 days prior to in vivo cell injection.
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9

Transcriptional Regulation and Self-Renewal Assay

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Total mRNA was reverse‐transcribed into cDNA (AT301 TransGen Biotech, Beijing, China), and real‐time quantitative PCR was performed with CFX96 Real‐Time PCR Detection System (Bio‐Rid, Hercules, CA, USA). For western blot, the protein from cell extracts was separated by 10% SDS‐PAGE electrophoresis and was later transferred onto PVDF membrane. Membranes were incubated with ESR1 (1:3000, EPR4097, ab108398; Santa Cruz, Dallas, TX, USA), TCF4 (1:2000, ab217668; Abcam, Cambridge, MA, USA), CMYC (1:2000, ab32072; Abcam), LEF1 (1:2000, ab137872; Abcam), WNT1 (1:1000, ab15251; Abcam), CTNNB1 (1:1000, C2206; Sigma‐Aldrich, St. Louis, MO, USA), VINCULIN (1:5000, #18799; Cell Signaling Technology, Danvers, MA, USA), and then detected using ECL Blotting Detection Reagents (Merck Millipore, Burlington, MA, USA). Cells of different groups were suspended in DMEM/F12 Medium supplemented with 20 ng/mL EGF (BD Biosciences, San Jose, CA, USA), bFGF and 4 μg/mL insulin (Sigma), and then plated in 6‐well ultra‐low attachment dishes (1000 cells/mL; Corning Incorporated, Tewksbury, MA, USA). To analyse the self‐renewal ability, sphere number of each captured image was counted by using phase contrast microscope (Nikon, Tokyo, Japan).
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10

Macrophage Polarization by EVs and Proteins

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Macrophages were seeded in 6-well ultra-low attachment dishes (Corning) at 5 × 106 cells/well, followed by the addition of sEVs (final concentration 100 ng/ml) or recombinant proteins. Recombinant human annexin A1 (Abcam, Cambridge, UK; final concentration 100 ng/ml), recombinant galectin-3 binding protein (LG3BP) (Aviva Systems Biology, San Diego, CA, USA; final concentration 1 ng/ml), recombinant human lactoferrin (lactotransferrin) (Abcam; final concentration 0.1 ng/ml), recombinant human lactadherin (MFGE8) (R & D Systems, Inc.; final concentration 100 ng/ml), and recombinant human aminopeptidase N/CD13 (R & D Systems; final concentration 100 ng/ml) were used. After 48 h, macrophages were harvested and mRNA expression levels of genes encoding pro- (Il-6, Tnf-a, Mcp-1, Inos) and anti- (Il-10, Ym-1, Fizz-1, Cd206) inflammatory factors were evaluated using real-time PCR.
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