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13 protocols using ki67 sp6

1

Antibody Characterization for Immunostaining

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Antibodies for immunostaining and western blotting were used as per the manufacturer’s recommendations. The following antibodies were used within this study: β-tubulin (Cell Signalling Technology, Cat # 2146 (1:1000)), Cleaved Caspase-3 [Asp175] (Abcam, Cat # ab49899 (WB 1:500, IHC 1:1500)), CDKN2A/p19ARF (Abcam, Cat # ab80 (1:1000)), cMYC [Y69] (Abcam, Cat # ab32072 (WB 1:1000, IHC 1:500)), Cyclophilin B (Cell Signalling Technology, Cat # 43603 (1:1000)), GFAP [GA5] (Millipore, Cat # MAB3402 (1:1000)), GFP (Abcam, Cat # ab13970 (1:1000)), HSF1 (Abcam, Cat # ab61382 (1:1000)), HSP70 (Abcam, Cat # ab2787 (1:1000)), HSP90 [EPR16621] (Abcam, Cat # ab203085 (1:1000)), Ki67 [SP6] (Abcam, Cat # ab16667 (1:2000)), n-MYC [NCM II 100] (Abcam, Cat # ab16898 (1:250)), NPR3 (Abcam, Cat # ab97389 (1:250)), Olig-2 (Millipore, Cat # AB9610 (1:1000)), OTX2 (R&D Systems, Cat # AF1979 (1:500)), p21 (Abcam, Cat # ab109199 (1:1000)), Synaptophysin [SY38] (Millipore, Cat # MAB5258 (1:500)), TUJ1 (Covance, Cat # MMS-435P (1:500)), β-actin (Santa Cruz Biotechnology, Cat # sc-47778 (1:1000)), CDKN2A/p16INK4A (Abcam, Cat # ab211542 (1:1000)), anti-mouse IgG secondary HRP (VWR, Cat # NXA931 (1:1000)), anti-rabbit IgG secondary HRP (GE Healthcare, Cat # NA934 (1:1000)), and Lamin B1 (Abcam, Cat # ab16048 (1:1000)).
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2

Immunohistochemical analysis of proliferation and apoptosis in melanoma

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Immunohistochemical (IHC) staining was performed after chemical dewaxing of two 3 μm thick sections using antibodies against Ki-67 (SP6) (Abcam, Cambridge, UK) and cleaved caspase-3 (Cell Signaling, Danvers, MA, USA). Ki-67 and cleaved caspase-3 stainings are indicators for proliferation and apoptosis indexes, respectively. IHC staining was carried out by adding 100 μL of DAB+chromogen diluted at 1:50 in substrate buffer [EnVision+ Dual Link System-HRP (DAB+)] for 10 min. Finally, tissue specimens were washed in phosphate buffer saline (PBS), the nuclei counterstained with hematoxylin and mounted using Eukitt® for microscopic examination. Positively stained melanoma cells, in which Ki-67 and cleaved caspase-3 highlight in brown the nucleus and the cytoplasm respectively, were quantified using ImageJ software (National Institutes of Health, Bethesda, MD, USA).
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3

Immunohistochemical Analysis of Immune Cells

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Immunohistochemistry was performed as previously described [28] (link). Briefly, specimens were rehydrated, endogenous peroxidase activity blocked, and incubated either with anti-F4/80 (BM8) for 45 min or anti-Gr-1 (RB-8C5), anti-Ly6C (HK1.4), anti-Ly6G (1A8, BioLegend, CA, USA) and anti-IL-17a (Abcam, England) overnight at 4 C, or Ki67 (SP6, Abcam) for 2 h. Labeling was visualized via HRP-conjugated secondary antibody with DAB precipitate (Abcam). Positive labeling was imaged and quantified as previously described [28] (link).
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4

Immunohistochemical Analysis of Tumor Samples

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IHC staining was performed on tumor samples resected day 35 post-inoculation of 143B cells or day 28 post-inoculation of LM8 cells, as previously described [55 (link)]. IHC staining was performed using primary antibodies against cleaved caspase-3 (Asp175) (5A1E) (#9664, 1:2000), cleaved caspase-8 (Asp387) (D5B2) (#8592, 1:1000), Beclin-1 (D40C5) (#3495, 1:400), LC3-I/II (D3U4C) (#12741, 1:2000), CD31(#77699, 1:100) each purchased from Cell Signaling Technology (Danvers, MA, USA), Ki-67 (SP6) (ab16667, 1:100; Abcam, Cambridge, UK), and VEGF (A-20) (sc152, 1:50; Santa Cruz Biotechnology, Inc. Dallas, TX, USA). The Dako Liquid DAB + Substrate Chromogen System (Glostrup, Denmark) was used as substrate-chromogen according to the manufacturer’s specifications. The immunostained specimens were counterstained with hematoxylin.
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5

Multicolor Immunohistochemistry for Murine Skin

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Skin pieces were snap-frozen, and slides were fixed with acetone and blocked overnight with 10% goat serum, 1% BSA, and 2.5% mouse serum in PBS at room temperature. The primary antibodies from BD were used at 1:100 dilutions: Gr1 (RB6-8C5), CD4 (H129.19), and CD8 (53-6.7). The antibodies from eBioscience were used at 1:50 dilution: CD11c (N418) and F4/80 (BM8). Biotinylated anti–rat IgG (Vector Laboratories) or anti–hamster IgG (Vector Laboratories) was used as a secondary antibody. Alkaline phosphatase kit and Vector Red substrate (Vector Laboratories) were used for visualization of the results. The tissues were counterstained with hematoxylin. Images were taken by the digital slide scanner Scanscope (Aperio) and analyzed by Aperio software. Cell number was calculated per 1 mm2. The antibodies specific for γδ T cells (GL-3), cytokeratin-14 (LL002), and Ki67 (SP6) were purchased from Abcam, and the staining was evaluated on an E600 upright microscope.
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6

Immunofluorescence Staining of Paraffin Sections

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Paraffin sections were deparaffinized in xylene, hydrated in a graded series of ethanol, and blocked by incubation with 1% BSA in PBS for 2 h. The following primary antibodies were used at 4 °C overnight at the indicated dilutions: α-SMA (1:100; Biolegend); IL-6 (1:30; Invitrogen); Ki67 (SP6; 1:200; Abcam); pan-cytokeratin (AE1/AE3 + 5D3; 1:200; Abcam); E-cadherin (1:200; R&D Systems, Wiesbaden, Germany); N-cadherin (1:200; BD Transduction Laboratories, Franklin Lakes, NJ, USA); and collagen type 1 (1:200; Invitrogen). After washing with PBS, sections were incubated for 2 h at room temperature in secondary antibodies (Alexa Fluor 488 goat anti-mouse IgG, 1:400; Alexa Fluor 488 goat anti-rabbit IgG, 1:400; Alexa Fluor 488 Donkey anti-Goat IgG, 1:400; Alexa Fluor 594 goat anti-mouse IgG, 1:400; and Alexa Fluor 594 goat anti-rabbit IgG, 1:400). All secondary antibodies were purchased from Invitrogen. Phase-contrast images were acquired on a Zeiss LSM 880 inverted Confocal Laser Scanning Microscope (Carl Zeiss, Oberkochen, Germany).
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7

Immunohistochemical Analysis of Tumors

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Tumours excised at 4 h were fixed in 4% paraformaldehyde for 24 h and paraffin-embedded. Consecutive sections were processed for immunohistochemical analysis of primary antibodies (1/100) as follows: Ki-67 (SP6, Abcam), hydroxynonenal (4HNE, Abcam) and cleaved-caspase-3 (Cell Signaling). Positive cells were counted in five high-power fields of three sections from each group.
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8

Immunohistochemical Evaluation of Autophagy

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IHC staining was performed as previously described (45 (link)). IHC staining with primary antibodies against LC3-I/II (D3U4C) (#12741, 1:2000), Beclin-1 (D40C5) (#3495, 1:400) (Cell Signaling Technology, Danvers, MA, USA) and Ki67 (SP6) (ab16667, 1:100) (Abcam, Cambridge, UK) was performed using the Dako Liquid DAB+Substrate Chromogen System (Glostrup, Denmark) according to the manufacturer’s specifications, followed by counterstaining with hematoxylin.
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9

Multiparametric Analysis of Cell Markers

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The following antibodies were used: KIF20A(L-13) (Santa Cruz, sc-104954), KIF20A (OriGene, AP01361PU-N), Alpha-tubulin(TU-01) (ThermoFisher, MA1-19162), Ki67(SP6) (Abcam, Ab16667), Active caspase 3 (BD Biosciences, 559565), and NeuN (Millipore, MAB377). Secondary antibodies were purchased from Jackson ImmunoResearch Laboratories (Cy3, Cy5, and Cy2 AffiniPure conjugated) and Click-iT®EdU Alexa Fluor®594 image kit (ThermoFisher Scientific) was used.
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10

Flow Cytometry and Immunohistochemistry Analyses

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Flow cytometry analyses were performed on single-cells suspensions from spleen, bone marrow, lymph nodes as previously described (20 (link)). Antibodies include: CD43(S7), CD5(53-7.3), CD138(281.2), CD21/35(7G6), CD23(B3B4), CD11b/Mac-1(M1/70) and IgK from BD Pharmingen (San Diego, CA); B220(RA3-6B2), CD19(eBio1D3), CD8a(53-6.7), CD4(L3T4), CD3ε(145-2C11) and TCRβ(H57-597) from eBioscience (San Diego, CA); Ter119 and Gr1(RB6-8C3) from BioLegend (San Diego, CA); IgM and IgD from Southern Biotech (Birmingham, AL) and PNA from Vector Labs (Burlingame, CA). Immunohistochemistry (IHC) staining was performed on formalin fixed, paraffin-embedded tissue sections as described previously using the following antibodies: B220, CD3, PAX5, BCL6, IRF4 and CD138 (21 (link)). Immunofluorescence on paraffin-embedded tissues was performed using antibodies against Ki67 (SP6, Abcam, Cambridge, MA), and B220 (RA-3B62, BD Pharmingen). Images were acquired with a Nikon Eclipse 80i microscope (Nikon, Melville, NY) and processed on NIS-Elements AR 3.10 software (Nikon, Melville, NY).
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