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205 protocols using collagen type 1

1

Binding Kinetics of SIRPα-CD47 Interaction

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Binding between SIRPαFc/CBD–SIRPαFc and CD47 was detected with Biacore. Sensor S Sensor Chip CM5 (GE Healthcare, Chicago, IL, USA) was activated by EDC-NHS and then caught SIRPαFc/CBD–SIRPαFc proteins on its surface. Human CD47 solution was attenuated into six gradients and flew through the chip in order. A signal–time curve was recorded and analyzed with Biacore T200 (GE Healthcare).
ELISA was performed to measure the affinity between CBD–SIRPαFc and collagen type I. A 96-well ELISA plate was coated with 100 μg/ml collagen type I (Corning, Tewksbury, MA, USA) or 2% BSA at 4°C overnight, then blocked by 2% BSA in PBS-T for 2 h at 37°C. Wells were washed with PBS-T for 5 times and incubated with SIRPαFc or CBD–SIRPαFc in five concentration gradients at 37°C for 2 h. After being washed, wells were incubated with HRP-conjugated anti-human IgG1 Fc fragment antibody at 37°C for 2 h. After a final wash, wells were incubated with TMB substrate at 37°C for 30 min. Absorbance at 450 nm was measured, and an absorbance–concentration curve was drawn in GraphPad Prism 8 software. The KD value was calculated through non-linear regression (assuming one-site specific binding).
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2

Hormone-responsive Vascular Tissue Engineering

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HUVEC and HLF were expanded using the same techniques used in 2D culture. PDA treated PDMS microarrays were loaded with 2 ×106 cells/ml HLF and 2 ×106 cells/ml HUVEC in a hydrogel comprised of blended collagen type I (2.25 mg/ml collagen type I, Corning) and fibrin (5mg/mL fibrinogen activated with 1 U/ml thrombin, Sigma Aldrich). Hydrogels were allowed to solidify at 37°C for 30 minutes. Stromal vascular tissues were cultured in vascular cell growth media supplemented with VEGF (ATCC), 25 μg/mL aprotinin (Sigma Aldrich), and charcoal stripped serum (Gibco) for 48 hours. Media was changed to phenol red free media containing 2% charcoal stripped serum for complete hormone starvation for 24 hours before exposing the gels to 0nm, 1nm, or 10nm E2 in ethanol or 0nM, 1nM, or 10nM DHT for 72 hours.
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3

3D Invasion Assay for HCC Cells

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The HCC cells were centrifuged and fully mixed with DMEM medium, and the pH value of type I collagen (Corning) was adjusted to 7–7.5. Then, the HCC cell suspension was mixed with type I collagen solution in equal proportion and added to the 96-well culture plate (Corning, USA). The mixture was incubated in a 37 °C incubator for 40 minutes and 160 μL DMEM medium was added to each well. Three days later, the invasion of HCC cell spheres was observed by inverted microscope (ZEISS). Finally, the proportion of tumor sphere invasion area was calculated by ImageJ software.
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4

T Cell Migration in 3D Collagen Gels

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T cells in complete X-Vivo media supplemented with 100 IU/ml IL2 were suspended in a 2 mg/ml type I collagen (Corning) solution. For density-dependent migration studies, T cells in Immunocult media were activated with Immunocult CD2/CD3/CD28 expansion solution (STEMCELL) supplemented with 100 IU/ml IL2. T cells were then suspended in 2 mg/ml type I collagen (Corning) and a 0.22 μm-filtered reconstitution buffer that consisted of HEPES, HBSS, and sodium bicarbonate in milliQ-purified water. The T cell-collagen solution was solidified in a 37 °C and 5% CO2 incubator for 1 hr. Immunocult media supplemented with 100 IU/ml IL2 was then added on top of the T cell-collagen gels. The gels were then incubated for 48 hrs and imaged for 1 hr on a Nikon Ti2 microscope equipped with a live-cell system maintained at 37 °C and 5% CO2. Time-lapse images were constructed into time-lapse movies using Nikon Elements, and cell positions were tracked frame-by-frame to generate cell trajectories using Metamorph. Analysis of cell trajectories to pull out multiple parameters to characterize cellular motility was performed in Matlab (MathWorks) following the principles and equations previously reported13 (link),66 (link).
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5

Aortic Ring Sprouting Assay for Angiogenesis

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The aortic ring sprouting assay was performed as previously (20 (link)). Briefly, aortas were harvested from 8 to 10 weeks old mice and washed with DMEM/F14 medium (Gibco, Carlsbad, USA) supplemented with 100 U/mL penicillin, and 100 μg/mL streptomycin. The dissected aortas were subsequently cleaned, sectioned in 12–16 rings of 1 mm length, and embedded in collagen type 1 (Corning, New York, USA). After polymerization of the collagen gel, microvascular endothelial cell growth medium (PeloBiotech, Planegg, Germany) supplemented with 100 U/mL penicillin, 100 μg/mL streptomycin, and 2% murine serum (BD) was added into the well. Tube-like structures were allowed to develop over 7 days. Thereafter, samples were fixed in 4% PFA and endothelial cells were visualized using antibodies against CD31 (Dianova, Hamburg, Germany) and VE-Cadherin (R&D), while NG2 (Merck, Darmstadt, USA) staining was employed to detect pericytes. The total volume of vascular and perivascular sprouting in each explant was calculated trough the IMARIS-BITPLANE 9.3 software. Additionally, total sprout length was measured with ImageJ.
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6

Collagen-Methylcellulose Organoids for Cancer Research

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The basis of the collagen gels used was collagen type 1 (3 mg/mL, Corning) containing 10% 10× M199 medium (Sigma-Aldrich) and 0.22 M NaOH mixed with methylcellulose (Sigma-Aldrich) (MC) media (70% methylcellulose (1.5% w/v in DMEM and 2 mM I-glutamine), 20% DMEM and 10% FCS). 5*105 fibroblasts were suspended in 500 µL consisting of equal amounts of collagen suspension and MC media and poured into 24-well plates. Depending on the experimental setup, rSPARC was added to the gels as well. Empty collagen gels were casted as controls. Collagen gels were allowed to solidify in a humidified chamber at 37 °C for 30 min and then supplied with 1 mL DMEM containing 10% FCS. After 4 days, 5 × 105 cancer cells were added on top of both fibroblast containing as well as empty gels and allowed to attach for 24 h. Afterwards, gels were washed, supplied with DMEM containing 10% FCS and incubated at 37 °C in a humidified atmosphere with 7.5% CO2, renewing the media every 48 h. After additional 6 days, gels were washed with phosphate buffered saline (PBS), fixed with 1mL 4% formaldehyde (Histofix, PanReac AppliChem, Darmstadt, Germany) for 24 h and then processed for IHC.
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7

Spheroid Angiogenesis Assay Optimization

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Four thousands of HUVECs in 100 μl culture medium containing 1.2% methylcellulose (Sigma Aldrich; Merck KGaA, Darmstadt, Germany) were generated to form spheroids in 200 μl round-bottom non-adherent tubes. The spheroids were then harvested and embedded in collagen type 1 (2 mg/ml, pH 7.4) (Corning, Bedford, USA) for 30 min to obtain matrix polymerization. Then, 200 μl of the supernatants of LPS-treated (collected in Section 2.7), plasmid transfected (collected in Section 2.8), or rhFN-treated (collected in Section 2.9) HCEps, HCSCs, or HCECs were added onto the gel and cultured for another 30 h. Finally, the spheroids were photographed.
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8

Immortalized Stria Vascularis Cell Culture

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The micro dissected stria vascularis from an H-2Kb-tsA58 transgenic (immorto) mouse cochlea was cut into several pieces and placed onto BD Cell Tak™ (BD Biosciences, Bedford, MA.) coated- tissue culture dishes. Outgrowths were propagated at 33°C in DMEM/F-12 Media (Gibco, Grand Island, NY.) supplemented with 15% heat-inactivated fetal bovine serum (Atlanta Biologicals, Atlanta, GA.), 50 units/ml mouse recombinant γ-interferon (Calbiochem, La Jolla, CA.) and penicillin, streptomycin, glutamine (Gibco). Outgrowths were dissociated with 0.05% trypsin, 0.02% EDTA (Gibco) and cloned by limiting dilution. Fifty clones were subsequently frozen back, twenty of which were expanded for further characterization by RT-PCR and immunofluorescence. To expand, sub confluent (≤80%) clonal cultures were dissociated and replated 1:5 in 10% FBS, 10 U/ml γ-interferon containing medium on dishes coated with rat tail Collagen Type 1 (Corning, Bedford, MA.) at 33°C. To induce differentiation, dissociated cells were plated in 5% FBS- containing medium without γ- interferon, placed at 37°C for at least seven days.
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9

Primary Human Brain Microvascular Endothelial Cells Culture

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Primary human brain microvascular endothelial cells (HBMECs) from CSC systems were purchased from ScienCell Research Laboratories, Inc. They were maintained in EGM-2 Endothelial Cell Growth Medium-2 Bullel kit (Lonza Group, Ltd.) on a Collagen type 1 (Corning, Inc.)-coated 10 cm diameter plate in a 37°C humidified atmosphere of 95% air and 5% CO2 in incubator and used for experiments at 80% confluency.
THP-1 was purchased from ZQ Cell Research and cultured in RPMI1640 (GE Healthcare) medium supplemented with 0.05 mM β-Mercaptoethanol (Sigma-Aldrich; Merck KGaA), 10% FBS (Gibco; Thermo Fisher Scientific, Inc.) and 1% penicillin streptomycin (Thermo Fisher Scientific, Inc.). Cells were grown in a humidified atmosphere of 5% CO2 at 37°C and used for experiments at >80% confluency.
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10

Tracking WNT5B-Mediated Cell Migration

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143B control and WNT5B KO spheres were grown for 3 days in 96‐well low attachment plates, and then, using wide‐based pipet tips, spheres were diluted and plated onto grid plates to select for droplets with single spheres. These single spheres were subsequently plated onto collagen type 1 (Corning)‐coated 96‐well plates and treated with 10 ng/mL recombinant WNT5B or 20 µM LGK‐974. Spheres were allowed to settle to the collagen and were imaged at intervals of 0, 6, 12, and 24 h. The sphere migration area was measured using ImageJ.
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