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19 protocols using troma 1

1

Immunostaining Protocol for Mammary Explants

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Explants were harvested and transferred to wells of a 24-well plate. The protocol for immunostaining was adapted from Kogata N & Howard BA44 (link). Briefly, explants were fixed in 4% paraformaldehyde for 1 h, blocked and permeabilized for 1 h at room temperature. The explants were incubated with primary antibodies overnight and then with secondary antibodies for 4 h at 4 °C. Primary antibodies used were cytokeratins (K) 8 (rat, 1:100) (Troma-I, Developmental Studies Hybridoma Bank) and K14 (rabbit, 1:200) (RB-9020, Thermo Fisher). The secondary antibodies (1:1000) used were Cy2-conjugated donkey anti-rat and RRX-conjugated donkey anti-rabbit (Jackson Immunoresearch). Images were acquired using a Zeiss LSM510 confocal microscope.
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2

Placental Immunostaining and Quantification

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Fresh frozen (12 µm) or paraffin wax-embedded (5 µm) serial placental sections were immunostained using anti-CD31 (BD550274, BD Pharmingen, 1:50), anti-MCT1 (Ab1286-I, Millipore Sigma, 1/1000), anti-MCT4 (Ab3314-P, Abcam, 1:400), anti-Tpbpa (Ab104401, Abcam, 1:200) and anti-Ck8 (Troma-I, Developmental Studies Hybridoma Bank, 1:7) antibodies. Images were acquired using a NanoZoomer Digital Pathology Scanner and NDPView software (Hamamatsu Photonics). The precise middle sections of E9.5 whole implantations were identified in the serial sections and the Tpbpa-positive cell surface was quantified using NDPView 2 software.
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3

Immunohistochemical Analysis of Regenerative Glands

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Formalin-fixed paraffin-embedded sections (6 μm) were subjected to H&E staining and immunohistochemistry. Antibodies to CK8 (Troma-I, Developmental Studies Hybridoma Bank, Iowa, USA), αSMA (DAKO), ERα (Abcam plc), PR (Abcam), Ki67 (Thermo Fisher Scientific), and pSTAT3 (Abcam, ab76315) were used. For cell counting, numbers of cells on 3 randomly selected sections were manually counted by microscopic images at ×40 magnification. For the quantitative analysis of regenerating glands and stromata, 3 randomly selected sections were analyzed using Leica Laser Microdissection LMD software v7.5.1 (Leica Microsystems GmbH).
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4

Immunohistochemical Analysis of Implantation Sites

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Implantation sites were fixed in 10% formalin overnight, embedded in paraffin, 8 μm sections were rehydrated, antigen retrieval was performed, non-specific binding was blocked, and specific immunostaining was conducted as described below. In the case of Crry staining, antigen retrieval was performed in 10 mM citric acid (anhydrous) (Sigma-Aldrich), 0.05% Tween-10, pH 6.0 in a pressure cooker for 3 min. Blocking and staining were performed in 1% BSA, 10% donkey serum, 5% mouse serum in PBS. Rabbit anti-Crry (1:1000) (provided by V. Michael Holers, Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO) was placed in blocking buffer overnight. Donkey anti-rabbit HRP (Jackson Immunoresearch) was used at 1:200. Staining was visualized with diaminobenzidine (DAB).
For trophoblast staining, 7.5 dpc implantation sites were collected as described above. Antigen retrieval was accomplished with 10 mM Tris EDTA pH 9.0 for 3 min in a pressure cooker. Staining was accomplished with TROMA-I (1:50 dilution of hybridoma supernatant) (Developmental Studies Hybridoma Bank, Univ. of Iowa) and goat anti-rat light chain horseradish peroxidase (HRP). Staining was visualized with DAB. Controls employed a second Ab only.
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5

Immunostaining for Trophoblast and Crry

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Implantation sites were fixed in 10% formalin overnight, embedded in paraffin, 8 μm sections were rehydrated, antigen retrieval was performed, non‐specific binding was blocked, and specific immunostaining was conducted as described below. In the case of Crry staining, antigen retrieval was performed in 10 mmol/L citric acid (anhydrous; Sigma‐Aldrich), 0.05% Tween‐10, pH 6.0 in a pressure cooker for 3 minutes. Blocking and staining were performed in 1% BSA, 10% donkey serum, and 5% mouse serum in PBS. Rabbit anti‐Crry (1:1000; provided by V. Michael Holers, Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO) was placed in blocking buffer overnight. Donkey anti‐rabbit HRP (Jackson Immunoresearch) was used at 1:200. Staining was visualized with diaminobenzidine (DAB).
For trophoblast staining, 7.5 dpc implantation sites were collected as described above. Antigen retrieval was accomplished with 10 mmol/L Tris‐EDTA pH 9.0 for 3 minutes in a pressure cooker. Staining was accomplished with TROMA‐I (1:50 dilution of hybridoma supernatant; Developmental Studies Hybridoma Bank, University of Iowa) and goat anti‐rat light chain horseradish peroxidase (HRP). Staining was visualized with DAB. Controls employed a second Ab only.
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6

Immunofluorescence Staining of Tumor Sections

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Tumor samples were fixed in 4% paraformaldehyde on ice for 2 hrs before being paraffin embedded. Paraffin sections (5um) were stained with antibodies for smooth muscle actin (SMA) and Keratin 8, which label basal and luminal epithelial cells, respectively. Primary antibodies used were: rabbit anti-SMA (AbCAM 5694, 1:250), and rat anti-Keratin 8 (Troma-I) (Developmental Studies Hybridoma Bank, University of Iowa, 1:250). Secondary antibodies were: biotinylated rabbit-anti-rat IgG (Dako Cytomation E0468) and biotinylated rabbit IgG (Vector BA-1000). The fluorophore was a streptavidin fluorescein (Vector SA-5001). Hoechst-33342 dye (Invitrogen H1399) was used for nuclear DNA counterstaining, and slides were visualized using a Zeiss wide-field fluorescent microscope equipped with AxioVision 4.8 software.
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7

Immunofluorescence Staining of Tumor Sections

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Tumor samples were fixed in 4% paraformaldehyde on ice for 2 hrs before being paraffin embedded. Paraffin sections (5um) were stained with antibodies for smooth muscle actin (SMA) and Keratin 8, which label basal and luminal epithelial cells, respectively. Primary antibodies used were: rabbit anti-SMA (AbCAM 5694, 1:250), and rat anti-Keratin 8 (Troma-I) (Developmental Studies Hybridoma Bank, University of Iowa, 1:250). Secondary antibodies were: biotinylated rabbit-anti-rat IgG (Dako Cytomation E0468) and biotinylated rabbit IgG (Vector BA-1000). The fluorophore was a streptavidin fluorescein (Vector SA-5001). Hoechst-33342 dye (Invitrogen H1399) was used for nuclear DNA counterstaining, and slides were visualized using a Zeiss wide-field fluorescent microscope equipped with AxioVision 4.8 software.
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8

Histological Analysis of Lung Metastases

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Tissues were fixed in formalin or EAF (ethanol, acetic acid, and formalin mixture) and paraffin‐embedded, followed by hematoxylin and eosin (H&E) staining according to routine protocols. For the postmortem analysis of lung metastases, paraffin‐embedded lungs were sectioned and H&E‐stained at five different levels throughout the lungs. Immunohistochemistry was performed using rabbit anti‐cytokeratin‐5 (1:500, PRB‐160P; Covance, Princeton, NJ, USA), rat anti‐cytokeratin‐8 [1:1500, Troma‐I; Developmental Studies Hybridoma Bank (DSHB), Iowa City, IA, USA], rabbit anti‐ERα (1:1000, sc‐542; Santa Cruz Biotechnology, Dallas, TX, USA), and rabbit anti‐PR (1:300, RM‐9102; Thermo Fisher Scientific, Waltham, MA, USA).
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9

Immunostaining of Frozen Tissue Sections

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Frozen tissues were sectioned at 10 μm thickness and placed onto charged slides for immunostaining as previously described [11 (link)]. Primary antibodies against E-cadherin (1:500, R&D systems, AF 748) and Keratin (K) 8 (1:500, Developmental Studies Hybridoma Bank, TROMA-1) were used. Alexa Fluor 488- or 647-conjugated secondary antibodies (1:500, Jackson Immunoresearch) were utilized for visualizations. Slides were mounted with Prolong® Diamond antifade mounting medium (Fisher Scientific, P36970).
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10

Immunohistochemical Analysis of Colonic Tissue

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Colonic frozen sections (4 μm thick) were stained with anti-Ki67 (Abcam, Cambridge, MA, USA), rabbit anti-CHI3L1 (Affinity Bioreagent, Golden, CO), rat anti-F4/80 (Serotec, Raleigh, NC, USA), -CD4 (eBioscience, San Diego, CA, USA), -CD11b (BD Pharmingen, San Jose, CA, USA), or -cytokeratin 8, TROMA–1 (Developmental Studies Hybridoma Bank at the University of Iowa (Iowa City, IA) antibodies, as well as normal rabbit Ig using the avidin-biotin-complex system (Vector laboratories) as previously described [12 (link)].
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