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21 protocols using t4049

1

Investigating Phosphorylation Signaling Pathways

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[4-(5-amino-4-carbamoylimidazol-1-yl)-2,3-dihydroxycyclopentyl] methyl dihydrogen phosphate (ICA-1 T) (Therachem, Jaipur, India) and 8-hydroxy-1,3,6-naphthalenetrisulfonic acid (ζ-Stat) (NSC 37044) was provided by National Institute of Health (NIH, Bethesda, MD, USA). Sterile distilled water was used as the solvent. Materials were acquired as follows; primary antibodies of PKC-ζ (sc-17781, Santa Cruz Biotech), PKC-ι (610175, BD Biosciences), p-PKC-ι (T555, 44–968 G), p-PKC-ζ (T410, PA5-17837) and E-Cadherin (701134, Thermo Fisher Scientific), Vimentin (5741S), p-Vimentin (S39, 13614S), p-Vimentin (S56, 7391S), p-Smad2 (S465/467)/Smad3 (S423/425) (8828S) and SNAIL1 (3879S, Cell Signaling Biotechnology). PRRX1 (ab211292) and p-Vimentin (S71, ab115189, Abcam). p-Vimentin (S6, ADI-KAM-CC245-E) and p-Vimentin (S33, ADI-KAM-CC246-E, Enzo Life Sciences). β-actin-peroxidase (A3854, Sigma). Enhanced chemiluminescence solution (34,080, Pierce Inc.). siRNA (human small interfering RNA) for PKC-ζ (SR321432), PKC-ι (SR321426), SNAIL1 (SR304489, OriGene Inc.) and PRRX1 (AM16708, Thermo Fisher Scientific). DPBS without Mg2+ and Ca2+ ions (Dulbecco’s phosphate-buffered saline, D8537) and Trypsin–EDTA (Ethylenediaminetetraacetic acid, T4049, Sigma Aldrich).
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2

RPE1 Cell Seeding on Hydrogels

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Prior to seeding on hydrogels, RPE1 cells
were grown under normal cell culture conditions at 37 °C and
5% CO2 in DMEM supplemented with 10% fetal bovine serum
(Sigma-Aldrich Inc.), 1% penicillin/streptomycin (Sigma-Aldrich Inc),
and 1% GlutaMAX (35050061, ThermoFisher Scientific) until they reached
80% density. Afterward, cells were trypsinized (T4049, Sigma-Aldrich
Inc.), counted, and diluted to a concentration of 20 000 cells/mL.
The excess liquid left after swelling was aspirated from the hydrogel
surface and 1 mL of normal RPE1 growth media containing 20 000
RPE1 cells were dispensed into each well. Cells seeded on hydrogels
were cultured for 72 h at 37 °C and 5% CO2 in DMEM
normal culture media described in the preceding section.
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3

Bioink Preparation for 3D Bioprinting of Breast Cancer Cells

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The human breast cancer cell line, MDA-MB-468, was purchased from ATCC (LCG standards, Teddington, UK) and cultured in Dulbecco’s modified Eagle’s medium (DMEM, high glucose, SH30243.01, Cytiva, Marlborough, USA), supplemented with 10% fetal bovine serum (FBS, FBS12A, Capricorn Scientific, Ebsdorfergrund, Germany), and 1% penicillin/streptomycin (15140-122, Gibco, Thermo Fisher Scientific, Waltham, MA, USA), in a humidified atmosphere of 5% CO2 at 37 °C. The MDA-MB-468 routinely passaged every 2 or 3 days and tested for mycoplasma.
To prepare the bioinks for printing, exponentially growing MDA-MB-468 were trypsinized (T4049, Sigma-Aldrich, St. Louis, MO, USA), and the viable ones were counted on a hemocytometer via trypan blue (15250-061, Gibco) exclusion. The cells were then centrifuged at 1500 rpm for 5 min, and resuspended at 2.5, 7.5, and 20 × 104 cells/μL, in medium with or without 10% glycerol (autoclaved sterile, 40058-ATO, Lach-Ners.r.o.). The resuspended cells were kept on ice until direct printing, normally within one hour.
After printing, the cells (coverslips) were transferred into 24-well plates, and 0.5 mL of complete medium was added to each well.
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4

HeLa Cell Culture Conditions

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HeLa, HeLa S3 and Phoenix A cell lines (originally from ATCC) were grown in Dulbecco’s modified eagle medium (D5796, Sigma Aldrich) supplemented with 10% Fetal Bovine Serum (F7524, Sigma Aldrich). Cells were incubated at 37°C and 5% CO2 and passaged using Trypsin-EDTA (0.25%, T4049, Sigma Aldrich).
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5

Profiling Chromatin Modifications in Podocytes

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Fixed WT podocytes were FACS-sorted as described earlier, snap-frozen, and stored at −80°C until all samples were ready. MEFs infected with lentiviral overexpression constructs were trypsinized (trypsin-EDTA, Sigma T4049) and fixed in 1% PFA for 10 min at room temperature. Fixed cell pellets were washed with PBS, snap-frozen, and stored at −80°C until all samples were ready. Nuclei extraction, quantification, barcoding, multiplexing, and ChIP were performed using the RELACS protocol as previously described (69 (link)). Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645) and sequenced on the NovaSeq 6000 instrument (Illumina). The antibodies used are listed in table S7. Each ChIP was performed with two biological replicates. Data processing, quality control, trimming, mapping, and H3-normalized coverage file were performed using snakePipes DNA-mapping and ChIP-seq pipeline (95 (link)). Further analysis and plotting were performed using deepTools (98 (link)). The output from “deepTools - ComputeMatrix” was used for boxplots. For H4K16ac, which is known for genebody enrichment, individual genes were fit into 1000 bins using the “ComputeMatrix-scale region” function of deepTools. For all other marks, TSS ± 500 bp were used.
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6

Establishment of a Liver Tumor Cell Line

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Mice were humanely euthanized and rinsed in 70% ethanol. The liver tumor (2–3 g) was dissected, washed in PBS, and minced into ~1 mm fragments using a scalpel blade. All procedures were operated in the hood using autoclaved dissecting tools. The tumor fragments were digested with 0.6 mg/L collagenase (Sigma-Aldrich, C5138) at 37 °C for 15–30 min, then filtered through 100 μm nylon mesh cell strainer (BD, 352360) and spun (700–1000 rpm, 5 min). The cell pellet was resuspended and cultured in 5 ml DMEM with 10% fetal bovine serum (FBS) and 1% Penicillin/Streptomycin at 37 °C and 5 % CO2 for ~4 weeks. The primary liver tumor cells were generated. To obtain a stably passaged cell line, 1 × 107 primary tumor cells were injected into flanks of 6–8 week-old FVB/N mice. When the subcutaneous tumor developed, tumor tissue was dissected into small pieces and digested with trypsin (Sigma-Aldrich, T4049). The new generation of liver tumor cells (P0) were cultured and passaged in vitro for 3 times. Then 1 × 107 “P0” cells were implanted into the flanks of a new recipient FVB/N mouse. These procedures were repeated for three rounds. The stably passaged cell line from c-MET/sgp53 HCC (MP cell) was finally generated.
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7

MTT Assay for Cell Viability

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The MTT (methyl-thiazol-tetrazolium) assay was used to test cellular viability
towards three different types of muscle cells. Briefly, cells in the culture
flasks were harvested using 0.25% trypsin-EDTA solution (Sigma®,
T4049). C2C12 (1.5 × 106 cells/well), A7r5 (5 × 104cells/well) and H9c2 (1.5 × 104 cells/well) were incubated at 37°C in
5% CO2 for 24 hours. The cells were treated with β-CTX-2 fraction
(0.001-0.8 mg/mL; n = 3). Each experiment was carried out in triplicate. Changes
in cell morphology of cells were identified using light microscopy with
magnification 100x following 0 and 24 hours of incubation in the presence of
toxin. Next, following 24 hours of culture, cells were exposed to MTT by the
additions of 12 µL 0.5% MTT solution. After 4 hours, 100 µL dimethyl sulfoxide
(DMSO) was added and Formazan color was detected at 570 nm using a plate reader
(Beckman CoulterTM, AD340). Cells treated with sterile PBS were used
as a negative control.
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8

Measuring Cell Viability and Proliferation

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Cell viability was measured by trypan blue
(9 (link)). Trypsin/Ethylenediaminetetraacetic acid
(EDTA, T4049, Sigma, USA) cell suspensions
of the culture ASCs were used to measure cell
viability. A total of 20 μl of the cell suspension
(500 cells/μl) and 20 μl of trypan blue reagent
(T6146, Sigma, USA) were mixed and incubated
at room temperature for 5 minutes. Viable
cells were counted using a Neubauer hemocytometer
under a light microscope (Olympus
IX71). MTT assays were also used to determine
the effect of ZnO-NPs on cell viability and proliferation.
Briefly, cells were maintained with
culture media for 24, 48 and 72 hours in 24-
well plates. MTT (M2128, Sigma, USA) was
then added to each well (0.5 mg/ml) and cells
were further incubated for 4 hours at 37˚C. We
removed the supernatants and 700 μl of dimethyl
sulfoxide (DMSO, D2650, Sigma, USA)
was added to each well to dissolve the formazan
product. A 680 Microplate reader (BioRad, Hercules,
CA) was used to measure absorbance at
540 nm. MTT assay values were expressed as
the percentage of corresponding average values
in control cultures. Absorbance is in proportion to
the number of living cells in a sample. Thus, the
MTT assay indicates the extent of cell proliferation
(17 (link)).
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9

Chick Forebrain Dissection and Preparation

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White Leghorn chick forebrains (Embryonic Day 8, 9, and 10 (E8-to-E10)) were dissected according to Heidemann et al.11 (link) Forebrain cells were then trypsinized (0.25% Trypsin, T4049, Sigma) for 5–7 min at 37° C before undergoing a few gentle titrations. The trypsin effect was deactivated by the addition of serum-containing medium, and the cell suspension was centrifuged at 1000 rpm for 5 min. Cell pellets were washed one more time using serum-free M199 and were re-suspended in the same medium for plating on MEA chips to record SSA or on glass-bottom culture dishes for immunostaining.
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10

Culturing HeLa Cells for Research

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HELA cell (CCL-2™, ATCC, USA) was chosen as the object for its easy-culture, uniformly growth and fast proliferation. Accordingly the cell culture medium is made of 89 vol% DMEM (Dulbecco’s Modified Eagle’s Medium, D5796-Sigma Aldrich, Switzerland), 10 vol% FBS (Fetal Bovine Serum, F6765- Sigma Aldrich, Switzerland) and 1 vol% P/S (Penicillin-Streptomycin, P4333-Sigma Aldrich, Switzerland). The cells were grown at 5% CO2, 100% humidity and 37 °C for 5 days untill cells covered over 90% of the flask (3151-Corning, USA). The culture medium was replaced with 4 mL of PBS (Phosphate buffered saline, P5368- Sigma Aldrich, Switzerland) to wash away the dead cells. After dispersing the PBS, 2 mL of trypsin (T4049- Sigma Aldrich) was added to the flask for 3 min to detach the cells. The cells were transferred to a 15 mL tube filled with 8 mL of culture medium and centrifuged. After removing the medium from the tube, fresh medium was added to resuspend cells to a concentration of 103 cells/mL.
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