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7 protocols using af594 anti rabbit

1

Multiplexed Immunofluorescence Staining Protocol

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The cryosections were fixed in in ice-cold acetone for 10 min followed by 3 x 5 min washes in PBS. Then, the tumor sections were blocked with 10% goat serum (in PBS) for 1 h and incubated for 30 min with Crystal A MausBlock reagent (Innovative Diagnostik-Systeme, Hamburg, Germany) at room temperature, washed 3 x 2 min with PBS. Following, the sections were incubated with Crystal B MausBlock reagent (Innovative Diagnostik-Systeme, Hamburg, Germany) for 5 min at room temperature and washed again 3 x 2 min in PBS. Afterwards, the slides were incubated overnight at 4 °C with mouse MAB1 (1:50, Hydroxyprobe Inc., MA, USA), rat CD31 (1:20, Dianova Research, Hamburg, Germany) and rabbit Carbonic Anhydrase 9 (1:100, Abcam, UK) antibodies diluted in PBS containing 0.1% BSA plus 1% goat at serum plus 0.1% Tween-20. Subsequently, the slides were washed 3 x 5 min with PBS and then were incubated with AF488 anti-mouse, AF594 anti-rabbit and AF680 anti-rat antibodies (1:500, ThermoFisher Scientific, MA, US) diluted in 1% goat serum for 1 h, at room temperature. Then the slides were washed 3 x 5 min in PBS and mounted with coverslips using Prolong Diamond mounting agent (ThermoFisher Scientific, MA, US).
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2

Integrin-β3 and pFAK-Y397 Immunostaining

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After 3-h adherence on RGD-membrane, cells were treated firstly with 4% paraformaldehyde and then 0.1% Triton X-100 treatment for 20 min each at 37 °C. 5% BSA with 10% normal donkey serum (blocking buffer) was used for overnight blocking at 4 °C. Samples were then incubated with the primary antibody in blocking buffer at 4 °C for 48 h. Primary antibody was then washed with PBS, followed by secondary antibody incubation for 2 h in room temperature. Primary antibodies included activated human integrin-β3 antibody (1:25, anti-LIBS2 epitope clone ab62, Millipore MABT27) and pFAK-Y397 (1:50, Thermo Fisher Scientific 44-624G). Secondary antibodies included AF594-anti-mouse (1:1000, Thermo Fisher Scientific A-21203) and AF594-anti-rabbit (1:1000, Thermo Fisher Scientific A-21207).
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3

Integrin and Src Signaling Pathway

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Primary antibodies included anti-pY416Src (CST 2101, 1:1,000 for Western blot [WB]), anti-Src (CST 2109, 1:1,000 for WB), anti-PIK3CA (Abcam ab40776; 1:100 for immunofluorescence [IF], 1:1,000 for WB), SHIP2 (Abcam ab70267; 1:100 for IF, 1:1,000 for WB), anti-AKTIP (Atlas Antibodies HPA046300; 1:1,000 for WB), anti-SNX9 (Atlas Antibodies HPA031410; 1:1,000 for WB), activated human integrin-β3 antibody (Millipore MABT27, LIBS2, epitope clone ab62; 1:50 for IF), anti-pFAK-Y397 (Thermo Fisher Scientific 44-624G; 1:100 for IF, 1:1,000 for WB), anti-FAK (Abcam ab40794; 1:1,000 for WB), anti-tubulin (CST 2146; 1:10000 for WB), and anti-GAPDH (Thermo Fisher Scientific AM4300; 1:10,000 for WB). Secondary antibodies included AF594-anti-mouse (Thermo Fisher Scientific A-21203; 1:1,000 for IF), AF594-anti-rabbit (Thermo Fisher Scientific A-21207; 1:1,000 for IF), AF488-anti-mouse (Thermo Fisher Scientific A-21202; 1:1,000 for IF) and AF488-anti-rabbit (Thermo Fisher Scientific A-21206; 1:1,000 for IF), anti-mouse horseradish peroxidase (HRP) (Santa Cruz sc-516102; 1:2,000 for WB), and anti-rabbit HRP (CST 7074; 1:2,000 for WB).
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4

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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5

Antibodies and Compounds for Ferroptosis Study

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The primary antibodies for SLC7A11 (12691 (Cell Signaling Technology), ab175186 (Abcam) and 26864‐1‐AP (Proteintech), Flag tag (14793; Cell Signaling Technology), ACSL4 (ab155282; Abcam), Streptavidin (3419; Cell Signaling Technology), GPX4(ab125066; Abcam), LAMP2 (66301‐1‐Ig; Proteintech), Anti‐4Hydroxynonenal (ab48506; Abcam), GAPDH (ab8245; Abcam), andβ‐actin (ab8226; Abcam) were commercially available. The following secondary antibodies were used in immunofluorescence assays: AF488‐anti‐Mouse (Invitrogen), AF594‐anti‐rabbit (Invitrogen), AF594‐anti‐mouse (Invitrogen), AF568‐anti‐rabbit (Abcam), AF647‐anti‐rabbit (Abcam), and AF647‐anti‐mouse (Abcam). Small‐molecular compounds such as Sorafenib (HY‐10201), Erastin (HY‐15763), Bafilomycin (HY‐100558), MG132 (HY‐13259), Cycloheximide (HY‐12320), Chlorquinaldol (HY‐17589A), Z‐VAD‐FMK(HY‐16658B), Necrosulfonamide (HY‐100573) and Ferrostatin‐1 (HY‐100579) were all from MCE. 2‐BP (21604) was from Sigma–Aldrich.
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6

Monocyte Activation Profiling by Flow Cytometry

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Immature floating BMDC were harvested, stained with Fixable Viability Dye eFluor 780 (Thermo Fisher Scientific, 65-0865-18), and then anti-CD11C (BD Biosciences, 749039), anti-Ly6C (Biolegend, 128014), and anti-CD206 (Biolegend, 141716) antibodies for 30 min at 4 degree. For P-IRF3 and P-p65 detection, human monocytes stimulated with CXCL4 and/or ORN8L for the times indicated in the figure legends were fixed with 4% Paraformaldehyde (PFA) in PBS for 15 min at room temperature (RT). After washing with PBS, cells were permeabilized with 0.05% digitonin for 10 min and blocked with 3% BSA for 30 min at RT. Next, cells were stained with anti-P-IRF3-AF488 (1:50, Cell Signaling, 73981S) or anti-p-p65 (1:1600, Cell Signaling, 3033S) antibodies for 2 h. Secondary anti-rabbit-AF594 (1:2000, Thermofisher Scientific, A-11012) antibodies were added to the cells for 30 min after P-p65 antibody staining. After washing, the cells were analyzed using BD FACSymphony A3 Cell Analyzer and Flowjo software.
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7

Immunofluorescence Staining of Kidney Tissue

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Kidney tissues were obtained from percutaneous needle biopsy in cold PBS. Tissues were mounted on Surgipath FSC22 Frozen Section Compound (Leica, IL, USA) and stored at − 80 °C until the section of the tissues. As the first step for staining, tissues were fixed with cold acetone. After blocking, primary and secondary antibodies were applied to tissue section and incubated for an hour at room temperature, respectively. Coverslip was mounted on the tissue slides after application of ProLong™ Diamond Antifade Mountant with DAPI (Life Technologies, OR, USA) applied to the tissue slides. The antibodies used for the staining were as follows: anti-c-Kit antibody (host: rabbit, polyclonal) from Biorbyt (Cambridge, UK), anti-CD3 antibody (rat, polyclonal) from Abcam (Cambridge, UK), and anti-rabbit AF594 (donkey, polyclonal) and anti-rat AF488 (donkey, polyclonal) from ThermoFisher Scientific (IL, USA). Slides were imaged by confocal microscopy, FV3000 (Olympus, Tokyo, Japan) and analyzed with FV10-ASW 4.0 Viewer (Olympus, Tokyo, Japan).
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