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18 protocols using glycine

1

Chromatin Immunoprecipitation and qPCR Analysis

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Cells were cross-linked with 1% Formaldehyde Solution (Sigma-Aldrich) for 15 min at 37 °C, quenched by 125 mM Glycine (Sangon Biotech, Shanghai, China) for 5 min at room temperature, and sonicated to shear DNA. CHIP assay was performed with CHIP Assay Kit (Beyotime) according to the manufacturer’s protocol. Chromatin fragments were precipitated with anti-AR (#51533, CST, 1:100 dilution) or a control non-immune IgG (#7074, CST, 1:100 dilution). The precipitate was eluted and analyzed by QPCR using TB Green Premix Ex TaqTM kit (Taka ra) and the Applied Biosystems QuantStudio instrument (Thermo Fisher). The primers of CHIP-QPCR were listed in Table S2.
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2

Preparation of Aqueous Solutions for Biological Experiments

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Ciprofloxacin, glucose, cysteine, glycine, threonine, histidine, vitamin B and GSH were purchased from Sangon Biotech Co., Ltd. (Shanghai, China). Sodium dihydrogen phosphate (NaH2PO4), disodium hydrogen phosphate (Na2HPO4), hydroxypropylmethyl cellulose (HPMC), boric acid (H3BO3), phosphoric acid (H3PO4), glacial acetic acid (HAc), sodium hydroxide (NaOH) and sodium chloride (NaCl) were obtained from Dingguo ChanGSHeng Biotechnology Co., Ltd. (Beijing, China). Ultrapure water with a conductivity of 18.25 MΩ cm -1 was applied for all experiments and produced by an Aquapro AWL-0502-P ultrapure water system (Chongqing, China).
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3

Construction and Maintenance of Plasmid PET24a(+)-SA-hGM-CSF

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Plasmid PET24a(+)-SA-hGM-CSF was constructed and maintained in our laboratory. The human erythroleukemia cells (TF-1) and prostate cancer cell line LNCaP as well as PC-3 were purchased from the cell bank of Chinese Academy of Sciences (Beijing, China), and maintained in DMEM/F12 (HyClone,USA). containing 10% (v/v) fetal bovine serum (Gibco,USA), 1% penicillin/streptomycin(Gibco). The mouse bladder cancer cell line (MB49) was purchased from American Type Culture Collection (ATCC), and cultured in RPMI1640 (Gibco) supplemented with 10% fetal bovine serum (Gibco), 1% penicillin/streptomycin(Gibco), at 37°C, in 5% CO2 humidified incubator. Tris (hydroxymethyl) aminomethane, Sodium chloride, Sodium dodecyl sulfate, Ethylenediaminetetraacetic acid, Urea, Glycine, and L-Arginine were obtained from Sangon Biotech Shanghai Co Ltd. The other reagents used in this study were of analytical grade and are commercially available.
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4

Cloning, Expression, and Purification of Proteins

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The plasmid pET30a(+)-6× His-SC, pET28a(+)-6× His-ST-GFP, and the competent Escherichia coli (E. coli) strain BL21(DE3) were obtained from our laboratory. Na2HPO4·12H2O, NaH2PO4·2H2O, CaCl2, NaCl, HCl, NaOH, and ethanol were purchased from Sinopharm (Beijing, China). EDC, Sulfo-NHS, kanamycin sulfate, agar, isopropyl-β-D-thiogalactopyranoside (IPTG), imidazole, glycine, 2-(N-morpholino)ethanesulfonic acid (MES), BSA, SDS-PAGE preparation kit, Bradford reagent, and carboxyl-SMBs (300 nm in diameter) were purchased from Sangon Biotechnology (Shanghai, China). A 0.1 M phosphate-buffered saline solution (PBS, pH 7.4) was prepared with 29 mg/mL Na2HPO4·12H2O, 2.965 mg/mL NaH2PO4·2H2O, and 8.766 mg/mL NaCl in distilled water, and the pH was adjusted to 7.4 by 1.0 M HCl. PBS (0.02 M) was prepared with 5.8 mg/mL Na2HPO4·12H2O, 0.593 mg/mL NaH2PO4·2H2O, and 29.22 mg/mL NaCl in distilled water, and the pH was adjusted to 7.4 by 1.0 M HCl. HisTrap™ HP 5 mL columns were obtained from GE Healthcare (Pittsburgh, PA, USA). Amicon® Ultra-15 centrifugal filter devices were purchased from Merck Millipore (Darmstadt, Germany).
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5

Quantitative ChIP Analysis of RBP-Jκ Binding

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Quantitative ChIP analysis was performed as previously described 20 (link). Cells were cultured to 80-90% confluency and then crosslinked with 1% formaldehyde (Sigma) at RT for 10 min. After neutralization with glycine (125 nmol/L, Sangon), cells were lysed in SDS lysis buffer. The antibody against FLAG (Sigma) was used to pull down the DNA and protein complex, and the purified DNA was subjected to qRT-PCR. We designed primers encompassing the predicted RBP-Jk binding sites in promoter regions of SLUG and GAS1. Subsequently, 1% of total chromatin supernatant before immunoprecipitation was used as input. The primers used were provided in Table S4.
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6

Synthesis of Gold Nanoparticles

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HAuCl4.4H2O was purchased from Sinopharm Chemical Reagent Co., Ltd. (Shanghai, China). Cellulase, pepsin, trypsin and AA were obtained from Yuanye Biotechnology Co., Ltd. (Shanghai, China). Histidine, threonine, lysine, glycine, glutathione (GSH), maltose, sucrose, glucose and metal ions were acquired from Sangon Biotechnology Co., Ltd. (Shanghai, China). All reagents were of analytical purity and used directly. Milli-Q purified water prepared by the PR03200 ultra-pure water meter (Zhongshan Keningte Cleaning Supplies Co., Ltd.) was utilized in all experiments.
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7

Sorafenib Cytotoxicity and Apoptosis Analysis

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Sorafenib was purchased from Selleck Chemicals (Houston, TX, USA). The BCA protein assay kit, the Cell Counting Kit-8, and the Annexin V-FITC apoptosis detection kit were purchased from KeyGen Biotech (Nanjing, China). The EdU Apollo567 In Vitro Imaging Kit was purchased from Guangzhou, People's Republic of China. DAPI and paraformaldehyde (PFA) were purchased from GuGe Biotech Co. Ltd. (Wuhan, China). Triton X-100 was purchased from ShenGong Biotech. Co. Ltd. (Shanghai, China). Methanol and ethanol were purchased from Shanghai LingFeng Chemical Reagent Co. Ltd. DMSO, Tween 20 and glycine was purchased from Sangon Biotech Co. Ltd. (Shanghai, China). Skim milk was purchased from Becton, Dickinson (San Diego, CA, USA). Primary antibodies against c-caspase-3, c-caspase-9, and c-PARP were purchased from Cell Signaling Technology (Danvers, MA, USA); GAPDH and SGOL1 were purchased from Abcam (Cambridge, MA, USA).
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8

Fluorescent DNA Probe Synthesis

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Hydrochloric acid (HCl), tris(hydroxymethyl) aminomethane (Tris), MgCl2, NaCl, ZnCl2, ascorbic acid were obtained from Sinopharm Chemical Reagent Co., Ltd. (Shanghai, China). Exo III, guanosine monophosphate, cytidine monophosphate, glycine, and lactose were obtained from Shanghai Sangon Biotechnology Co., Ltd. (Shanghai, China). Melamine was purchased from Aladdin Reagents Co., Ltd. (Shanghai, China). All these chemicals were used without further treatment. All solutions were prepared by using ultrapure water (resistivity  18.2 MΩ cm) obtained from a Milli-Q water purification system (Millipore Corp., Bedford, MA, USA). The HPLC-purified DNA probes were obtained from Shanghai Sangon Biotechnology Co., Ltd. (Shanghai, China) and their sequences were listed as follows:
HP: 5′-GTC TGT TTT TTT TCT CAG ACT CTT TTT TTT-3′
MB-DNA: 5′-AGA AA X AA X ACA GAC-MB-3′
X denotes the AP site of spacer C3.
The MB-DNA and HP were directly used and diluted in 50 mM Tris-HCl (pH = 7.2, containing 100 mM NaCl, 5 mM MgCl2) to give the stock solution of 10 µM.
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9

DF Compound Extraction and Characterization

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Chloral hydrate, sodium chloride injection, normal saline, and methanol were bought from Sinopharm Chemical Reagent Co., Ltd. (Shanghai, China). Glycine, TRIS buffer, and sodium dodecyl sulfate (SDS) was purchased from Sangon Biotech (Shanghai) Co., Ltd. (Shanghai, China). Skim milk powder was purchased from BBI Life Sciences (Shanghai, China). 30% acrylamide and ammonium persulfate (AP) were bought from Beijing Dingguo Changsheng Biotechnology Co., Ltd. (Beijing, China). Tetramethylethylenediamine (TEMED) was provided by Sigma (St. Louis, MO, United States). GeneView (Ste. Genevieve, MO, United States) provided the enhanced chemiluminescence (ECL) Kit. The Milli-Q (18.2 MΩ) ultra-pure water system (Millipore, Billerica, MA, United States) was used to prepare pure water. Mouse serum interferon gamma (IFN-γ), IL-10, IL-12p70, IL-17A, TNF-α, IL-6, monocyte chemoattractant protein-1 (MCP1), and IL-1β enzyme-linked immunosorbent assay (ELISA) kits were purchased from Bender (Gruenberg, Germany).
DF was prepared in our laboratory [Batch No.: 20180522. The DF had a rhodojaponin III content of 41.6% and a rhodojaponin VI content of 13.6%, as determined by the linear curve method (Yao et al., 2019 )]. Dexamethasone was purchased from GlpBio (Batch No.: GC40775. Montclair, CA, United States).
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10

Colorimetric Assay for ATP and AMP

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ATP and AMP were purchased from Aladdin (Shanghai, China) in the form of sodium salt. Magnesium acetate was from Sigma (St. Louis, MO, USA). Bromothymol blue sodium salt, glycine, and other reagents all came from Sangon Biotech Corp. (Shanghai, China). Plastic cuvettes were purchased from Centome Corp. (Chengdu, China).
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