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6 protocols using alexa fluor 790

1

Investigating Autophagy and Inflammation Pathways

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ABT-263 (Navitoclax), 3-MA (3-methyladenine) and Rapamycin (Sirolimus) were purchased from Selleck Chemicals (TX, USA). The primary Rabbit monoclonal antibodies of Bcl-2, Bax, Beclin-1(Becn), Atg5, LC-3, Trem-2, and Tubulin-α conjugated with Alexa Fluor® 790 were acquired from Abcam (Cambridge, UK). The secondary antibodies Goat anti-Rabbit IgG H&L (Alexa Fluor®680) was purchased from Abcam as well. The DAPI (4′, 6-diamidino-2- phenylindole) was obtained from Beyotime (Shanghai, China). The F4/80-PE anti-mouse antibody, PE Rat IgG2a isotype and biotin anti-mouse CD16/32 antibody were purchased from Biolegend (San Diego, CA). The Phallodin-iFluor 633 Conjugate was purchased from ATT Bioquest® (Sunnyvale, CA). The cell culture reagents, RPMI 1640 and FBS (fetal bovine serum) were purchased from Biological Industries (Cromwell, CT). The RT2 First Strand kit and Profiler PCR Array (PAXX-084) and SYBR Green qPCR master mix were purchased from Qiagen (Hilden, Germany). Proteome Profiler Array of Mouse cytokine (ARY006) was purchased from R&D systems, Inc. (MN, USA).

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2

Protein Quantification and Western Blotting

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Total protein from patient derived frozen tissue samples (Affiliated Dermatology Laboratory) were isolated using RIPA buffer (50 mM Tris HCl, pH 8.0; 150 mM NaCl; 1% NP-40; 0.5% sodium deoxycholate; 0.1% SDS; HALT (Protease and Phosphatase Inhibitor), DNaseI and DTT following an established protocol (21 (link)). Forty micrograms of total protein from each sample were resolved on either a 10% (FOXP3) or 4-20% (all other proteins) Mini-PROTEAN® TGX™ Precast Protein gel (Bio-Rad), transferred to a low fluorescent PVDF membrane, and blocked using 5% NFDM (non-fat dry milk, 1X TBS, 0.1% Tween 20) for one hour at room temperature. Primary antibodies in 1% NFDM used were 1:200 rabbit monoclonal histone H3 antibody (D1H2) (Cell Signaling Technology), 1:1000 rabbit anti-GAPDH (Cell Signaling Technology), 1:200 mouse monoclonal CFH (OX-24) (Abnova, OX-24), 1:200 mouse monoclonal IFN-γ (Santa Cruz Biotechnology), and 1:200 mouse monoclonal antibody FOXP3 (F9) (Santa Cruz Biotechnology). 1:10,000 AlexaFluor® 790 (Abcam) or 1:5,000 HRP-conjugated (Santa Cruz Biotechnology) were used as secondary antibodies. All blots were performed in triplicate and relative protein expression was measured using either an Odyssey® CLx (LI-COR Biotechnology) or ChemiDoc XRS (BioRad) imaging system. Band intensities were normalized to either GAPDH or H3 using Image J software (NIH).
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3

Western Blot Analysis of Larval Brain

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Ten third instar larval brains per well were run on 10% SDS-PAGE gel and transferred to nitrocellulose membrane. Membranes were imaged on the Odyssey Infrared Imaging System (LI-COR). Primary antibodies used were mouse anti-β-tubulin (1:3000, DSHB E7), rabbit anti-SNF5 (1:3000, Abcam ab126734) and rabbit anti-Snr1 (1:1000, this study). Secondary antibodies used were donkey anti-rabbit Alexa Fluor 680 (1:10,000, Jackson ImmunoResearch) and donkey anti-mouse Alexa Fluor 790 (1:25,000, Abcam).
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4

Western Blot Analysis of Epithelial-Mesenchymal Transition

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Twenty to forty micrograms of each protein sample and control protein (either P-cadherin or HeLa cell lysate) were resolved on a 4–20% Mini-PROTEAN® TGX™ Precast Protein gel (Bio-Rad, Hercules, CA, USA) based on their molecular weights, transferred to a PVDF membrane, and blocked using 5% non-fat dry milk (NFDM, 1X TBS, 0.1% Tween 20) for one hour. Primary antibodies used: 1:1000 rabbit anti-phospho (S838 + S840) E-cadherin (Abcam, Cambridge, UK), 1:500 rabbit anti-E-cadherin (Abcam, Cambridge, UK), 1:250 mouse anti-vimentin (Santa Cruz Biotechnology [SCBT]), 1:500 rabbit anti-TGF-β (anti-TGFβ1/2/3; SCBT), and 1:1000 rabbit anti-GAPDH (Cell Signaling Technology) in non-fat dry milk. Primary antibodies were omitted as a negative control. A 1:10,000 dilution of either AlexaFluor® 790 (Abcam, Cambridge, UK) or an HRP-conjugated secondary antibody was used. All blots were performed in triplicate and relative expression was measured using either an Odyssey® CLx (LI-COR Biotechnology, Lincoln, NE, USA) or ChemiDoc XRS + (Bio-Rad, Hercules, CA, USA) imaging system. Band intensities of phosphorylated E-cadherin, E-cadherin, vimentin, and TGF-β were normalized to GAPDH and analyzed using ImageJ (NIH).
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5

Western Blot Analysis of Autophagy Markers

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Cells were incubated in DMEM medium in the presence or absence of 300‐nM Bafilomycin A1 (Solarbio Life Sciences) for 3 hr, then cell pellets were extracted using RIPA lysis buffer (10‐mM Tris pH7.4, 150‐mM NaCl, 1% NP‐40, 0.5% sodium deoxycholate, 1‐mM PMSF, and protease inhibitor cocktail). Gels were blotted onto PVDF membranes. The primary antibodies used for western blotting were anti‐Actin (1:10000; proteintech, China), anti‐LC3 (1:3000; Abcam), anti‐p62 (1:2000; Abcam), and anti‐Flag M2 (1:1000; Sigma), the secondary antibodies used for western blotting were anti‐rabbit IgG, horseradish peroxidase (HRP)‐linked (1:10000; proteintech) or anti‐rabbit IgG, CF680 (1:10000; Sigma), anti‐mouse IgG, HRP‐linked (1:10000; proteintech) or anti‐mouse, Alexa Fluor 790 (1:10000; Abcam).
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6

Western Blot Analysis of Autophagy and Apoptosis Markers

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The total protein of the cells or spleen tissue were extracted using 1% Triton X-100 (Beyotime) with 1x protease inhibitor cocktail (Beyotime), and then the concentration of protein was quantified using the Bradford protein assay kit (Beyotime). Twenty micrograms of protein was separated by SDS-PAGE and transferred to a PVDF membrane (0.22 μm, Bio-Rad, USA). After blocking with QuickBlock buffer (Beyotime), the membranes were incubated and shaking gently overnight at 4 °C with the primary antibody against LC-3 (1:2000), Bcl-2 (1:2000), Bax (1:2000), Beclin-1 (Becn; 1:2000), Atg5 (1:2000), Trem-2 (1:1000). All the primary and secondary antibodies were purchase from Abcam Inc.(UK). After washing with TBS-T extensively, the PVDF membranes were incubated with an appropriated Alexa Fluor® 680-conjugated secondary antibody (1:10000) for 1 h at room temperature on the next day. The bands were detected and analyzed with Odyssey CLx (LI-COR, USA) system. After the detection the PVDF membranes were stripped and incubated with Tubulin-α conjugated with Alexa Fluor® 790 (1:10000, Abcam, UK) for 2 h at room temperature, and detected the band for the loading control to normalized the interested proteins. The intensity of these bands were quantified with Image Studio software (LI-COR, version 5.2.5).

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