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42 protocols using alexa fluor 568

1

PLA-Based Detection of HIV-1 Rev Interactions

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H1299 cells were grown, fixed and permeabilized as described for immunofluorescence. Samples were overnight hybridized with 50 ng of a Globin DNA probe (5′-GGCCTCACCACCAACTTCATCCACGTTCACCTTGCAAAAA-3′) conjugated to digoxigenin in the 3′ end. Afterwards, samples were saturated with PBS 3% BSA, 0.1% saponine and incubated for 2 h with mouse monoclonal anti-digoxigenin (DI-22, Sigma) and rabbit polyclonal anti-NCL (ab22758, Abcam) primary antibodies diluted in blocking solution. The proximity ligation assay (PLA) was carried out using the Duolink PLA in situ kit (Sigma) following the manufacturer's protocol. For co-staining of HIV-1 Rev protein in PLA samples, chicken polyclonal anti-HIV-1 Rev antibody (ab36623, Abcam) and goat anti-chicken IgY conjugated to Alexa Fluor® 568 (Abcam) were added to primary antibodies and Duolink secondary antibodies mixes, respectively. For co-staining of NCLΔNLS or nucleolus, samples were incubated for 45 min with mouse monoclonal anti-HA-Tag antibody conjugated to Alexa Fluor® 488 (6E2, Cell Signaling) or anti-Fibrillarin antibody conjugated to Alexa Fluor® 488 (EPR10823B, Abcam) after the PLA amplification step.
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2

Quantifying Nuclear p65 Localization

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The cells were fixed with 4% paraformaldehyde for 15 min and then permeabilized with methanol at −20 °C for 10 min. After blocking with 1% bovine serum albumin, the primary antibody against p65 (8242S; Cell Signaling Technology) was applied at a 1:400 dilution for 1 h. Then, the secondary antibody conjugated with Alexa Fluor 568 (Abcam, Cambridge, UK) was applied at a 1:1000 dilution with 3 μM Nuclear Green DCS1 (Abcam) for 30 min. After mounting on glass slides, the subcellular localization of p65 and the nucleus was visualized with FL2 (orange-red) and FL1 (green) detectors, respectively, using Nikon BioStation IM (NIKON, Tokyo, Japan) [14 (link),26 (link)]. The brightness of green and orange-red fluorescence was quantified using ImageJ software (National Institutes of Health, Bethesda, MD, USA). The amount of p65 in the nucleus was calculated as the ratio of the brightness of orange-red fluorescence to that of the corresponding green fluorescence.
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3

Immunofluorescence Assay for HIF-1α and UCHL1 in 2D Cell Culture

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For HIF‐1α and UCHL1 staining in 2D culture, cells treated with each condition were washed with PBS (−) and fixed in 4% paraformaldehyde at room temperature for 15 minutes, followed by permeabilization with 0.1% Triton X‐100 for 10 minutes on ice. The coverslips were blocked with 3% BSA for 12 hours and incubated with anti–HIF‐1α (1:500; BD Biosciences) and anti–UCHL1 (1:500; R&D Systems) antibodies for 1 hour at 4°C. After three 5‐minute washes with PBS (–), samples were probed with goat anti–rabbit polyclonal secondary antibody (Alexa Fluor 488, 1:1000; Abcam) or goat anti–mouse polyclonal secondary antibody (Alexa Fluor 568, 1:1000; Abcam) mixed with 4′,6‐diamino‐2‐phenylindole (DAPI) (1:5000, Roche) at room temperature for 1 hour. The coverslips were mounted onto slides with Dako Fluorescence Mounting Medium (Agilent). Fluorescence was detected by fluorescence microscopy (Olympus).
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4

Immunofluorescent Localization of IGF2BP2 and IGF2BP3

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Immunofluorescence staining was performed to detect the expression of IGF2BP2 and IGF2BP3. In brief, the tissue samples were deparaffinization, blocked at room temperature for 60 min with a blocking solution (5% BSA/0.1% Triton X-100 PBS), and stained with the primary anti-IGF2BP2 (1:200; 11601-1-AP; Proteintech) and anti-IGF2BP3 (1:200; 14642-1-AP; Proteintech) antibodies. The samples were then washed with Tris-buffered saline for 30 min, and incubated with the secondary goat anti-rabbit IgG H&L (Alexa Fluor® 568) (1:200, ab175471; Abcam) and goat anti-mouse IgG H&L (Alexa Fluor 488) (1:200, ab150113; Abcam) antibodies for 30 min at 37 °C in the dark. After washing in PBS, DAPI staining was performed for 5 min, to counterstain the nuclei (28 (link)). Finally, the samples were sealed in 50% glycerin and imaged on a fluorescence microscope (DP72, OLYMPUS, Japan).
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5

Immunohistochemical Analysis of Cellular Signaling

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After fixation in acetone for 10 min, the sections were treated with normal donkey serum for 50 min. Subsequently, the sections were incubated with primary antibody (p-GSK3β, PTEN, and cleaved caspace-3, respectively) at 4°C overnight. The next day, the sections were then incubated with secondary antibodies conjugated to Alexa Fluor 488 or Alexa Fluor 568 (1 : 200; Abcam), followed by nuclei counterstaining with 4′,6-diamidino-2-phenylindole (DAPI, 2 mg/ml). The slides were then examined using a fluorescence microscope (Leica TCS SP5).
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6

Evaluating H.cordata and 2-undecanone on B[a]P-induced DNA damage

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BEAS-2B cells were seeded on confocal dishes and exposed to the vehicle (water), B[a]P (5 μM) alone, B[a]P (5 μM) plus H.cordata (12.5, 25, or 50 mg/mL), or B[a]P (5 μM) plus 2-undecanone (25, 50, or 100 μM) for 48 h, respectively. After the incubation, the cells were fixed in cold methanol, permeabilized with 0.1% TritonX-100 and blocked with 5% bovine serum albumin. Then, the cells were incubated with a p-H2A.X (1:100) or a Nrf2 (1:100) antibody for 1 h and then stained with a secondary fluorescent antibody (1:200; Alexa Fluor 568, Abcam Inc. Cambridge, MA, USA). Finally, the cells were incubated with DAPI for another 20 min. Fluorescence signals were detected using a Leica TCS SP8 confocal fluorescence microscope (Leica, Germany). The relative fluorescence of p-H2A.X in the cells was analysed by ImageJ software.
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7

Immunomodulatory Nanoparticle Protocol

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Pluronic F127 (P2443) was purchased from Sigma-Aldrich and ropivacaine (R413090) was obtained from Mackline, while Imiquimod (HY-B0180A) and doxorubicin (Dox, HY-15142) were purchased from MCE. Butorphanol (H20020454) was purchased from Hengrui. Anti-mouse CD45-PE-cy7 (103114), anti-mouse CD11c-APC-cy7 (117323), anti-mouse CD3-APC-cy7 (100221), anti-mouse CD8a-APC (100711), anti-mouse CD16/32-TruStain FcX (101320), anti-mouse CD86-APC (105011), anti-mouse CD11b-PE (101207), anti-mouse Gr1-APC (108411), anti-mouse CD4-PE (100408) and anti-mouse Foxp3-AF488(126406) antibodies were purchased from BioLegend. Anti-mouse CD80-FITC (FW0149), anti-mouse MHC-I-APC (FW2919), and anti-Rb Phospho-p38 (Thr180/Tyr182) (DL3485) were purchased from Elabscience. Anti-LC3 (ab192890) and anti-P62 (ab109012) antibodies and Alexa Fluor 568 and Alexa Fluor 488 secondary antibodies were purchased from Abcam. BD™ Cytometric Bead Array (CBA) Mouse TNF Flex Set (558299), Mouse IFN-γ Enhanced Sensitivity Flex Set (562233) and Mouse Enhanced Sensitivity Master Buffer Kit (562246) were purchased from BD Bioscience.
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8

Spinal Cord Injury Immunofluorescence Protocol

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To collect the spinal cords after contusion injury or sham operation mice, mice were anesthetized and then rapidly perfused transcardially with 0.9% saline, followed by 4% PFA. Then, the spinal cords were cryoprotected in 30% sucrose for 3 d at 4°C, before being sectioned. Serial cryostat sections (14 mm thick) were obtained. For immunofluorescent staining, the sectioned slices were permeabilized with 0.3% Triton X-100 in PBS for 30 min and then blocked with 5% BSA for 1 h. After incubation with goat anti-CD31 Alexa Fluor 488-conjugated antibody (1 : 100, R&D, USA), rabbit anti-ki67 (1 : 200, Invitrogen, USA), and rabbit anti-Nrf2 (1 : 200, Proteintech) overnight at 4°C, the sectioned slices were incubated with secondary antibodies anti-rabbit Alexa Fluor 488 or Alexa Fluor 568 (1 : 400, Abcam) for 1.5 h. The slices were mounted with Fluoroshield™ with DAPI (GeneTex Inc.). Signals were analyzed by a fluorescence microscope (Zeiss Apotome 2). Positive cells were quantified using the ImageJ software.
Cell samples were fixed with 4% PFA for 20 min, permeabilized with 0.2% Triton X-100 for 15 min, and blocked with 5% BSA for 30 min and then incubated with primary antibodies overnight at 4°C, followed by secondary antibody incubation for 1.5 h. After washing with PBS, cells were stained with DAPI.
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9

3D Spheroid Imaging and Analysis

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Five days after plating in ULA spheroid microplates, cells were stained with a mixture of 1 mmol/L of Calcein‐AM, 1 mmol/L of EthD‐1 and 20 μmol/L of Hoechst 33342 for 4 hours and then imaged. Images were acquired with a confocal fluorescence microscope (Nikon) at room temperature. For 3D staining, spheroids were washed with PBS (−) and fixed in 4% paraformaldehyde at room temperature for 20 minutes and then permeabilized with 0.3% Triton X‐100/PBS (−) and protease inhibitors for 20 minutes on ice. Samples were blocked with 3% of BSA/1% Triton X‐100/PBS (−) at room temperature for 1 hour and incubated at 4°C with primary antibodies against HIF‐1α (1:400; BD Biosciences) and anti–UCHL1 (1:400; R&D Systems) overnight. After three washes with 0.1% Triton X‐100/PBS (−), samples were probed with goat anti–rabbit polyclonal secondary antibody (Alexa Fluor 488, 1:500; Abcam) or goat anti–mouse polyclonal secondary antibody (Alexa Fluor 568, 1:500; Abcam) mixed with DAPI (Roche) at room temperature for 1 hour. Images were acquired with a confocal fluorescence microscope (Nikon) at room temperature. Fluorescent intensity was quantified using cellSens software (Olympus).
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10

Hippocampal Single-Cell Isolation and Characterization

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We prepared hippocampal single-cell suspensions as described previously.23 (link) After removing the red blood cells and counting the cells, single-cell suspensions were incubated for 30 min on ice with the following antibodies: anti-Iba1 antibody (Alexa Fluor® 568, ab221003, Abcam, UK), anti-CD16 (PE, 12–0161-82, eBioscience, USA) and anti-arginase 1 (Alexa Fluor 700, 12–0161-82, eBioscience, USA). For the apoptosis assay, we used Annexin V-FITC/PI Apoptosis Detection Kit (40302ES60, YEASEN, China) according to the manufacturer’s protocol. Flow cytometry was used to detect the fluorescence and data analyzed using Flowjo 7.6.2.
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