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7 protocols using rabbit anti nf kb p65

1

Immunostaining protocol for protein analysis

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For immunostaining, tissues were fixed in Zn-formalin for 24 hr and embedded in paraffin. Sections were deparaffinized, rehydrated, and prepared by antigen retrieval for 6 min each, and then blocked in 5% donkey serum for 1 hr at room temperature, incubated with either Rabbit anti-BNIP3 antibody at 1:100 (A5683, Abclonal), Rabbit anti-NF-kB-p65 1:400 (8242S, Cell Signaling Technology), Rabbit anti-Phospho-c-jun 1:200 (3270S, Cell Signaling Technology), Rat anti-ki67 1:100 (14-5698-82, ebiosciences), Rabbit anti-pRB-Ser807/811 1:400 (8516, Cell Signaling Technology), anti-p21 1:1000 (ZRB1141, Sigma), Rat anti-Phospho H3 1:1000 (H9908, Sigma), or Goat anti-GFP (ab6673, Abcam) at 1:250 overnight at 4°C, washed, incubated with secondary antibody AF594-anti-rabbit (A-21207, Invitrogen), Alexa594 anti-rat (A-21209, Invitrogen), and Alexa488 anti-goat (11055, Invitrogen) antibodies at 1:200 for 1 hr at room temperature, counterstained with DAPI, washed, and mounted. Slides were visualized and imaged using an Olympus IX71 inverted multicolor fluorescent microscope and a DP71 camera using ×400 magnification. MFI was calculated by measuring average intensity over a fixed threshold for all images. NF-kB staining was imaged via Zeiss LSM880 confocal microscope using ×63 oil-immersion objective, and intensity was measured on 0.8 µm z-sections.
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2

Immunofluorescence analysis of nuclear proteins

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The primary antibodies used in immunofluorescence were rabbit anti‐γ‐H2Ax (Cell Signalling), mouse anti‐cGAS (Santa Cruz Biotechnology), rabbit anti‐lamin B1(Cell Signalling), rabbit anti‐NFkB (p65) (Cell Signalling) while the secondary were Cy3 or FITC–conjugated goat anti‐rabbit or mouse IgG (Sigma‐Aldrich Chemicals). DAPI were used for nucleus staining. The coverslips with the immune‐labelled cells were mounted with an anti‐fade mounting medium (Biomeda, Collegno, Italy) and analysed under a Bio‐Rad MRC 1024 ES confocal laser scanning microscope (Bio‐Rad) equipped with a 15‐mW Krypton/Argon laser source. The cells were observed with a Nikon Plan Apo X60 oil immersion objective (Nikon Instruments, Rome, Italy) at 595 nm. Series of optical sections (X‐ and Y‐steps: 512 × 512 pixels) were then obtained through the depth of the cells, with a thickness of 1 μm at intervals of 0.8 μm (Z‐step). A single composite image was obtained by superimposition of 20 optical sections for each sample. Total NFkB fluorescence intensity and Mander's coefficient (M1), used to assess NFκB p65 colocalization with the nucleus (DAPI), were determined by ImageJ software.
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3

Protein Extraction and Western Blotting

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Ductular structures were manually picked up, cleaned with 5%FCS DMEM and protein extracted with RIPA (Sigma) according to the manufacturer’s instructions. Protein content was quantified using a BSA standard and Pierce reagent before being resolved using SDS/PAGE and blotted onto nitrocellulose membrane. Membranes were blocked with 5% BSA on T-PBS during 1 h at room temperature. Membranes were incubated at 4 °C overnight with primary antibody (mouse anti-β actin (Sigma), rabbit anti-p-Smad2 (Ser465/567)/Smad3 (Ser 423/4225) (Cell Signalling) or rabbit anti-NF-kB p65 (Cell Signalling)). Appropriate HRP-labelled secondary antibodies were used (Dako or CST) and signal detected with ECL reagent (Amersham). In order to use the same membrane with different antibodies, stripping was performed with mild stripping buffer during 10 min at room temperature. Membrane was blocked again with 5% BSA on T-PBS during 1 h and re-incubated with the desired antibody overnight. All uncropped western blots can be found in Supplementary Figure 14.
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4

Immunofluorescence Imaging of Skin Cells

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Fresh skin tissues from mice were embedded with OCT (Tissue Tek). Skin sections (6 μm) and HaCaT cells grown on round glass coverslips in 24-well plates were fixed with 4 % paraformaldehyde (PBS) for 10 min. Sections were blocked with 5 % donkey serum for 1 h after permeabilization with 0.3 % Triton X-100 for 15 min at room temperature. Primary antibodies were incubated overnight at 4 °C. After washing with PBS, Alexa Fluor 488-conjugated or 594-conjugated secondary antibody (Thermo Fisher Scientific) was added for 1 h at room temperature. Sections were washed and counterstained with 4′, 6-diamidino-2-phenylindole (DAPI). All images were captured with a Nikon DS-Ri2 (Nikon, Japan). The following primary antibodies were used: Rat anti-CD4 (1:100, eBioscience), Rat anti-CD31 (1:100, eBioscience), Rabbit anti-Ki67 (SolA15) (1:500, eBioscience™, #PA5-114437), Rabbit anti-NF-kB p65 (1:100, Cell Signaling) antibodies.
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5

NF-kB Activation Imaging in Differentiated HL-60 Cells

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Differentiated HL-60 cells were allowed to settle onto poly-L-lysine-coated glass coverslips for 15 mins at 37°C. Cells were pretreated with BB-Cl-amidine (10 uM) for 40 min, stimulated with LPS for 2 hours, and fixed with 2% paraformaldehyde in PBS. Coverslips were blocked with 10% FBS, 1% BSA, 0.05% Triton X-100 and 2mM EDTA in PBS over night. Staining was done with rabbit anti-NF-kB p65 (Cell Signaling, Cat # 8242S) at 1:100 dilution for 2 hours. Antibody binding was detected with Donkey anti-rabbit IgG-AF594 (Jackson Immunoresearch). Draq5 (Cell Signaling) was used to stain DNA. Confocal Microscopy was performed on a Nikon TE2000-U inverted microscope.
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6

Analyzing Nuclear Protein Dynamics via Western Blotting

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Cells were seeded and incubated overnight in culture media. Cells were lysed in Laemmli buffer supplemented with beta-mercaptoethanol and HALT protease and phosphatase inhibitor cocktail (Sigma). Isolation of nuclei from whole-cell lysis adapted a standard centrifugation-based protocol (79 (link)). Briefly, cells were lysed in 0.1% Igepal in PBS supplemented with phosphatase inhibitor cocktail. Nuclear fractions were sedimented by centrifugation. Whole-cell lysates and nuclear fraction were resolved using SDS-PAGE. Western blot was done using a standard protocol, and images were processed and quantified using ImageJ (https://imagej.net/ij/download.html). For phospho-NF-kB experiments cells were serum starved for 4 to 8 h before lysing. Recombinant human TNF-α (R&D systems 210-TA) treatment was done at 20 ng/ml for 15 min before lysing cells. Recombinant human IFN-β (R&D systems 8499-IF-010) was done at 1000 IU/ml for 24 h before lysing cells. Antibodies used include: rabbit anti-JADE3 (Abcam #129495) used at 1:750 to 1:1000, rabbit anti-IFITM3 (Cell Signaling #59212) used at 1:750 to 1:1000, rabbit anti-NF-kB p65 (Cell Signaling #8242) used at 1:1000, rabbit anti-phospho-NF-kB p65 Ser536 (Cell Signaling #3033) used at 1:1000, rabbit anti-H3 (Cell Signaling), anti-Flag horseradish peroxidase (HRP) (Sigma), anti-rabbit IGG HRP (Sigma), and anti-GAPDH HRP (Sigma).
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7

Investigating Necroptosis Signaling Pathways

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Cultured cells were lysed by use of the standard RIPA lysis buffer. Total cellular proteins were then separated by SDS-PAGE gel electrophoresis. The primary antibodies used were mouse anti-RIPK1 (R&D), rabbit anti-RIPK3 (Abcam), rabbit anti-MLKL (Millipore), and rabbit anti-phospho-MLKL (Millipore). The primary NF-kB antibodies, rabbit anti-NF-kB p65, rabbit anti--phospho-NF-kB p65, mouse anti-IkBα, rabbit anti--phospho-IkBα, were obtained from Cell signaling Technology. The secondary antibodies used were goat anti-mouse or rabbit IgG (Jackson Immuno Research).
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