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20 protocols using ab15580

1

Immunohistochemistry Analysis of Xenograft Samples

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Xenograft sections (4μm) were cut and stained with hematoxylin and eosin. Immunohistochemistry was performed using the following antibodies and dilutions: FLI1 1:50 (Abcam, ab15289), STAG2 1:25 (Santa Cruz, sc81852), Ki67 1:500 (Abcam, Ab15580), cleaved CASP3 1:250 (Cell Signaling, #9661) and CD99 1:1 ready-to-use (Agilent, IS057).
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2

Immunohistochemical Analysis of Cell Signaling

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For IHC, paraffin-embedded sections were stained with antibodies against p62 (Enzo Life Sciences, PW9860-0100), Ki67 (Abcam, ab-15580), pS6 (Cell Signaling, 4858S), p42/44 MAPK (p-ERK) (Cell Signaling, 4376), and 4-hydroxynonenal (4-HNE) (Abcam, ab46545) as described previously [30 (link)].
For quantification of IHC for Ki67, pS6, p-ERK and 4-HNE, 6–10 representative images from each treatment group were obtained and scored using the ImageJ software.
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3

Immunostaining of Cardiac Tissue

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Cells cultured in vitro were fixed in 4% paraformaldehyde at room temperature for 25 min or heart tissues were dissected and fixed in 4% paraformaldehyde at 4°C overnight. The fixed heart tissues were washed three times with PBS and equilibrated in 30% sucrose at 4°C for 2 days before freezing and cryosectioning. Eight micrometer frozen sections were prepared. Cells or tissue sections were blocked with 5% BSA and 5% goat serum and then stained with the respective primary antibodies at 10 ug/ml at 4˚C overnight. Anti-mouse primary antibodies used: COLA1 (abcam, ab34710), cTnT (abcam, ab8295), pH3 (Millipore, 06-570), Ki67 (abcam, ab15580) or cCASP3 (Cell signaling technology, 9661). Alexa-Fluor-488- or Alexa-Fluor-546-conjugated secondary antibodies (Invitrogen) were used at room temperature for 30 min in the dark. For cell death analysis, an in situ cell death detection kit by TUNEL was also used per manufacturer's instruction (Roche, 1256792910). Slides were mounted with DAPI-containing fluorescence mounting medium (Dako) and fluorescence was detected with an upright fluorescence microscope, inverted fluorescence microscope or confocal microscope (all Leica). Images were processed with the ImageJ software and cTNT coverage was analyzed based on this formula: cTNT+ area/total area.
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4

Immunohistochemistry for Angiogenesis Markers

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Sections were heated in citric acid buffer (pH 6.0) at 100 °C for 10 min for antigen retrieval. Sections were then treated with 0.3% hydrogen for 30 min and blocked with 5% normal goat serum containing 0.05% Triton X‐100 (T‐PBS). Sections were then incubated overnight at 4 °C with the following primary antibodies diluted in T-PBS: anti-Eph-B4 (Abcam, ab64820), anti-Ephrin-B2 (Novus, NBP1–49857), anti-Ki67 (Abcam, ab15580), or anti-cleaved caspase-3 (cell signaling, #9661).
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5

Immunohistochemical and Immunofluorescent Liver Analysis

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Paraffin-embedded liver tissue was cut into 5 μm sections, which were stained with Sirius Red to visualize fibrosis or performed immunohistochemical staining according to the protocols provided by manufacturers of the respective antibodies. Snap-frozen tissues embedded in O.C.T. were cut into 8 μm sections, which were used for immunofluorescent staining according to the protocols provided by manufacturers of the respective antibodies. The following primary antibodies were used: CK19 for immunohistochemical staining (AbCam; EP1580Y, 1/200), CK19 for immunofluorescent staining (DSHB; TROMA-III; 1:50), Ki67 (AbCAM; Ab15580; 1:100), YAP (Cell Signaling;14074; 1:100). The secondary antibodies used were: Envision anti-rabbit (DAKO; K4002) for immunohistochemical staining, Alexa488-conjugated rabbit secondary antibody and Alexa568-conjugated rat secondary antibody for immuno-fluorescent staining. The immunofluorescent images were visualized using Leica AF 6000 Modular 146 Systems (Leica Biosystems Newcastle). The presented images are representative of at least three independent experiments.
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6

Immunohistochemical Analysis of Tongue Tumors

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All tumors were harvested at sacrifice and then fixed in 4% paraformaldehyde overnight, and placed in phosphate buffered saline overnight at 4°°C. Tongue tumor tissue sections were made and subjected to immunohistochemistry. Three tumors, 3 to 4 sections per tumor, were used for immunohistochemistry staining analysis using rabbit antibodies for Ki-67 (Abcam Inc.; ab15580), LSD1 (Cell Signaling Technology #2139) OCT4A (Cell Signaling Technology #2840) E-cadherin (BD Transduction laboratories, #610181), MT-MMP1 (Abcam Inc;ab51074) DPAGT1 (Covance Research Products, Inc [20 (link)]) and LOXL2 (GeneTex #GTX105085).
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7

Histological Analysis of Brain Tissues

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For histological analysis, animals were perfused with PBS followed by 4% paraformaldehyde (PFA). Brains were removed and fixed in 4% PFA overnight and then transferred to 70% ethanol and embedded in paraffin. Sections were then stained with hematoxylin and eosin or with Ki67 antibody (Abcam: ab15580) or MYC antibody (Abcam: ab32072). For immunofluorescent staining, brains from PFA-perfused animals were fixed overnight in 4% PFA, cryoprotected in 30% sucrose, frozen in Tissue Tek-OCT (Sakura Finetek), and cut into 12 μm sagittal sections. Sections were blocked and permeabilized for 1 hr with PBS containing 0.1% Triton X-100 and 10% normal donkey serum, stained with primary antibodies (anti-Otx2: Millipore AB9566; anti-Aqp1: Santa Cruz SC-20810; anti-Ki67: Abcam ab15580; pH2A.X: Cell Signaling 9718P) overnight at 4°C, and incubated with secondary antibodies for 1 hr at room temperature. Sections were counterstained with DAPI and mounted with Fluoromount-G (Southern Biotech) before being visualized using a Zeiss LSM 700 confocal microscope.
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8

Histological Characterization of BP Tumors

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Tumor fragments were fixed in 10% formalin overnight and transferred to 70% ethanol. Embedding, sectioning and H&E staining were then performed by Harvard rodent histopathology core. Histological characteristics of BP tumors were examined by independent pathologists at Harvard medical school. IHC staining was performed as described previously75 (link). Antibodies used for IHC staining include anti-BRCA1 antibody (1:1200, Abcam, # ab238983), anti-ERα antibody (1:200, clone SP1, Fisher, # RM9101S0), anti-Ki67 antibody (1:500, Abcam, # ab15580), and anti-HER2 (1:500, clone 29D8, Cell Signaling, # 2165).
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9

Intestinal Cellular Composition and Proliferation

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Specimens were harvested and fixed overnight in 10% formalin/phosphate-buffered saline and embedded in paraffin blocks. The proliferative capacity of the small intestine and apoptosis were determined by immunohistochemistry for BrdU (Abcam, ab6326), Ki67 (Abcam, ab15580) and active caspase-3 (Cell Signaling Technologies, 9579S). The cellular composition of the intestine was determined using antibodies for Dclk1 (Abcam, ab37994), chromogranin A (Abcam, ab15160), Muc2 (Santa Cruz Biotech, sc-15334), lysozyme (Dako, A0099), and synaptophysin (Abcam ab32127). Biotinylated secondary antibodies were applied at 1:1000 dilutions and visualized by using diaminobenzidine peroxidase (DAB) substrate (Invitrogen, Carlsbad, CA). Slides were counterstained with hematoxylin. For immunofluorescent staining, secondary antibodies were applied at 1:500 dilution and nuclei were stained with 4′,6-diamidino-2-phenylindole (DAPI).
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10

Comprehensive Cell Marker Analysis

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Immunohistochemistry and histology was performed as described (35 ). Antibodies specific for CD31 (Cell Signaling, 77699), KI67 (Abcam, ab15580), cleaved caspase-3 (CC3, Cell Signaling, 9661), αSMA (Biocare Medical CM 001), CDH11 (LifeSpan BioSciences, LS-B2308), E-cadherin (Cell Signaling, 3195), Vimentin (Cell Signaling, 5741), equilibrative nucleoside transporter 1 (ENT1, Abcam, ab135756), γH2AX (Novus, NB100–384), CD3 (Invitrogen, MA5–17043), Arginase 1 (Arg1, Cell Signaling, 93668), SOX9 (EMD Millipore, AB5535), PDGFRα (LifeSpan BioSciences, LS-B8655), and β-Galactosidase (Abcam, ab9361) were used.
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