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8 protocols using triton 100

1

Localization of tRF-Trp-CCA-014 in Aged NIH3T3 Cells

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Aged mouse NIH3T3 cells were used to analyse the location of tRF-Trp-CCA-014 and its target genes. First, the probes were designed and synthesized according to the sequences of tRF-Trp-CCA-014 and its target genes. Then, the cells were treated with 4% paraformaldehyde and the cell membranes were permeabilized by Triton-100 (Beyotime, Shanghai, China) for 5 min at 4 °C. Next, the remaining steps were performed according to Xu et al. (2021) [56 (link)]. Finally, photographs were taken using a fluorescence microscope.
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2

In Situ Localization of tRF-Glu-TTC-027 in GC Cells

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After the cells were treated with 4% paraformaldehyde, the cell membranes were permeabilized by Triton-100 (Beyotime, Shanghai, China) for 5 min at 4°C. Next, we added the hybridization solution mixed with Cy3-labelled tRF-Glu-TTC-027 to the permeabilized cells to locate the tRF-Glu-TTC-027 in GC cells. We stained the GC nuclei with DAPI and captured the pictures with a fluorescence microscope.
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3

lncRNA-n346372 Expression in Bladder Cancer

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A Ribo™ lncRNA FISH kit (cat. no. C10910) purchased from Guangzhou RiboBio Co., Ltd. (Guangzhou, China) was employed for RNA FISH to identify the location and expression of lncRNA-n346372 in T24 bladder cancer cells and patients tissue samples, according to the manufacturer's protocol. In brief, cells were cultured (and 4-mm-thick tissue slices were prepared), and fixed in 4% paraformaldehyde for 10 min at room temperature. Cells and tissues were permeabilized with Triton-100 for 5 min at 4°C (Beyotime Institute of Biotechnology, Shanghai, China), and Cy3-labelled n346372 and DAPI-labelled 18S-RNA probes (Guangzhou RiboBio Co., Ltd.) were detected. In the dark, DNA was stained with DAPI for 10 min at room temperature, followed by washing in PBS three times every 5 min. Slides were mounted and examined by confocal fluorescence microscopy (×200; Olympus Corporation, Tokyo, Japan).
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4

Protein Isolation and Western Blot Analysis

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Membrane and cytosolic proteins were isolated with a Membrane and Cytosol Extraction Kit (Beyotime, Haimen, Jiangsu, People’s Republic of China). Triton-soluble and -insoluble proteins were isolated with a lysis buffer containing Triton-100 (Beyotime), and protein concentrations were determined using a BCA protein assay kit (Biosynthesis Biotechnology Co., Ltd, Beijing, People’s Republic of China). Equal amounts of protein were separated by 10% SDS gel electrophoresis under denaturing and nonreducing conditions and then transferred to a nitrocellulose membrane. The membrane was blocked with 5% nonfat milk in Tris-buffered saline and Tween 20 at room temperature for 1 h and then incubated with primary antibody at 4°C overnight. After washing in Tris-buffered saline and Tween 20, the blots were incubated with horseradish-coupled secondary antibody. The signal was detected using enhanced chemiluminescence and recorded on X-ray films. The relative density of the target bands was quantified using Image J acquisition and analysis software.
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5

Metabolic Profiling of TGF-β1-Induced EMT

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Tan IIA (purity > 98%), [U-13C]-glucose, l-serine, l-glycine, l-lactic acid, l-alanine, pyruvate, l-malic acid, succinate, fumarate, l-glutamic acid, citric acid, α-ketoglutaric acid, l-asparatic acid, and l-proline were purchased from Shanghai Yuanye Biotechnology Co., Ltd (Shanghai, China). Recombinant human TGF-β1, Yefluor 488 EdU imaging kit, and cell cycle and apoptosis analysis kit were purchased from Yeasen (Shanghai, China). Sulforaphane (SFN), dimethyl sulfoxide (DMSO) and methoxyamine hydrochloride were purchased from Sigma-Aldrich (St. Louis, MO, USA). d-glucose was purchased from Aladdin (Shanghai, China). Dulbecco's modified Eagle medium (DMEM), minimum essential medium (MEM), and 0.25% trypsin were purchased from Gibco (Carlsbad, CA, USA). Cell counting kit-8 (CCK-8) was purchased from Vazyme (Nanjing, China). SB 204990 was purchased from MedChemExpress (Princeton, NJ, USA). BTA was purchased from Macklin (Shanghai, China). Glucose assay kit was purchased from Elabscience (Wuhan, China). Lactate assay kit was purchased from Nanjing Jiancheng Bioengineering Institute (Nanjing, China). N-tert-butyldimethylsilyl-N-methyltrifluoroacetamide was purchased from Acmec (Shanghai, China). Triton ×100, hoechst33342, antifade mounting medium and 4',6-diamidino-2-phenylindole (DAPI) were purchased from Beyotime (Shanghai, China).
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6

Extracellular Vesicles Isolation Protocol

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The cell supernatant was centrifuged at 500 g × 10 min and 2,000 g × 20 min to remove the floating cells and cell debris, and then centrifuged at 20,000 g × 30 min at 4°C to remove the precipitate and collect the supernatant. After centrifugation at 100,000 g × 70 min, the precipitate was the EVs (Wang et al., 2018 (link)). The EVs precipitate was washed with PBS, centrifuged again at 100,000 g × 70 min, and suspended in 1 mL PBS. The suspension was placed on the top of 30% sucrose cushions to form a clear interface layer, and centrifuged at 100,000 g × 70 min at 4°C. The PBS layer was discarded, and the deuteroxide layer was retained. The deuteroxide was mixed with at least five times the volume of PBS, and centrifuged again at 100,000 g × 70 min to obtain the purified EVs. The EVs were filtered and sterilized with 0.22 μm membrane, and then put into aseptic Ependorf tube. The EVs were grouped and frozen at −80°C. The EVs of some groups were incubated with 1 μg/mL ribonuclease A (Sigma-Aldrich) at 37°C for 30 min or treated with 0.1% Triton × 100 (Beyotime, Shanghai, China) for 30 min (Wang et al., 2018 (link)) for subsequent analysis.
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7

Investigating lncRNA SNHG12 in CAFs-EVs

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Based on a previous study [33 (link)], CAFs-EVs were treated with 1 μg/mL RNase A (Invitrogen) or RNase A in combination with 0.1% Triton × 100 (Beyotime) at normal temperature. Subsequently, the expression patterns of lncRNA SNHG12 were detected by quantitative real-time polymerase chain reaction (qRT-PCR). The experiment was repeated 3 times independently, with at least 3 duplicate wells set for each group of cells in each experiment.
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8

Immunofluorescence Staining of Cultured Cells

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Cultured cells were rinsed with PBS and then fixed with 4% PFA for 20 min. Cells were treated for 5–10 min with 0.5% Triton-100 (Beyotime; cat. no. P0096) and then 4% BSA was added to reduce non-specific staining. Specimens were incubated with primary antibodies (S Table 1) at 37 °C overnight, followed by incubation with secondary antibodies (S Table 1). For the negative controls, the primary antibodies were replaced with PBS and cells were only incubated with the secondary antibodies. The specimens were analyzed and photographed using a Zeiss LSM 780 confocal microscope (Zeiss, Jena, Germany).
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