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26 protocols using ba 1100

1

Immunohistochemical Analysis of EGFR and Cytokeratin 5

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EGFR and cytokeratin 5 immunostaining were performed using a rabbit anti-EGFR antibody (1:200 dilution; Cat. # ab32077, Abcam) and a rabbit anti-cytokeratin 5 antibody (1:200 dilution; Cat. # ab64081, Abcam). All sections were rinsed in PBS, incubated for 10 min in PBS containing 3% hydrogen peroxide, and immersed for 30 min in blocking reagent (Dako Protein Block, S0909, Dako). Sections were then incubated with primary antibody at 4°C for 24 h followed by biotinylated horse anti-rabbit IgG secondary antibody (1:300 dilution; BA1100, Vector Laboratories) for 30 min at room temperature and rinsed in PBS for 3 changes for 5 min each. Tissue sections were processed using the (ABC) solution for 30 min (Vector Laboratories, Burlington, ON), and visualized with 3,3’-diaminobenzidine (0.5 mg/ml; Sigma-Aldrich Canada, Oakville, ON). Negative control staining (without addition of primary antibody) was performed on adjacent sections. Counterstaining of EGFR and cytokeratin 5 stained sections was performed using hematoxylin. Slides were then dehydrated through 70–100% alcohol, cleared with xylene, and cover slipped for microscopic examination.
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2

Comprehensive Immunohistochemical Profiling of Tumor Samples

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All xenograft and patient tumor specimens were fixed in 10% formalin and embedded in paraffin, then IHC was performed on 5 µm sections. Briefly, sections were first deparaffinized and rehydrated, and then antigens were retrieved in citrate buffer. After blocking the endogenous peroxidase with 0.3% hydrogen peroxide for 20 min and proteins with 5% serum for 1 h, sections were incubated overnight at 4 °C with 1:400 diluted primary antibody against SV2A (HPA007863, Sigma -Aldrich, St. Louis, MO, USA), SSTR2 (ab134152, Abcam, Waltham, MA, USA), SSTR5 (ab28618, Abcam, Waltham, MA, USA), PSMA (ab19071, Abcam, Waltham, MA, USA), CgA (ab45179, Abcam, Waltham, MA, USA), or SYP (ab32127, Abcam, Waltham, MA, USA). Next, the sections were incubated with biotinylated anti-rabbit or anti-mouse secondary antibodies (#BA-1100 and #BA-2000, Vector Laboratories Burlingame, CA, USA) at room temperature for 1h. After washing for 10 min three times in PBS, the sections were incubated with ABC-HRP complex (#PK-4000, Vector Laboratories Burlingame, CA, USA) for 1 h. Then slides were developed with 3,3′-diaminobenzidine (SK-4105, Vector Labs, Burlingame, CA, USA). All the slides were mounted after counterstaining with hematoxylin. Staining signals were photographed at high-power fields (×40) using an Olympus BX51 Microscope (Olympus, Tokyo, Japan).
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3

Histological Staining and Quantification

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Paraffin sections (as illustrated in Supplementary Fig. 5a) were subjected to Masson-Trichrome-Goldner staining (Merck Millipore, Darmstadt, Germany) to label collagen fibres. For immunohistochemistry, antigens were retrieved with target retrieval solution (Dako, Hamburg, Germany) and blocked with serum derived from the same animal as the secondary antibody (Vector laboratories, Burlingame, USA). The following primary antibodies were used: CD45 (1:100; 553076, BD Pharmingen, Heidelberg, Germany), F4/80 (1:200; MCAP497, AbD Serotec, Puchheim, Germany), αSMA (1:200; ab5694, Abcam, Cambridge, UK) and CD31 (1:100; ab28364, Abcam). Appropriate secondary antibodies (BA-1100, BA-4001; Vector Laboratories) were added and amplified with TSATM Indirect (Perkin Elmer, Rodgau, Germany) prior to DAB-labelling (Dako). Positively stained cells or areas were quantified by two independent, blinded investigators applying 20 standardized high-power-fields (Supplementary Fig. 5b) using an Axiostar Plus Microscope (Carl Zeiss, Jena, Germany) and ImageJ software (National Institutes of Health, Bethesda, USA).
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4

Immunohistochemical Analysis of Tumor Samples

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Fixed tumors and organs were embedded in paraffin and unstained slides were prepared for immunostaining or stained with H&E. IHC staining was performed as previously described (21 (link)). Primary antibodies included rabbit anti-Ki67 (1:400), rabbit anti-CD31 (1:100) (#9027; #77699, Cell Signaling Technology), rabbit anti-cleaved PARP (1:50) and rabbit anti-cleaved-caspase-3 (1:200), detected by a biotinylated horse anti-rabbit IgG antibody (BA-1100, Vector Laboratories Inc., Burlingame, CA) secondary antibody. Anti-human-specific mitochondria IHC staining (AbCAM, Cambridge, MA, cat# ab92824) was performed at a 1:1000 dilution to visualize metastases. All slides were developed with DAB Impact (Vector Labs, Burlingame, CA), counterstained in Gill’s hematoxylin (Vector Labs) and mounted with Cytoseal XYL mounting media. Tissue images were acquired with a Keyence BZ-X700 microscope. Quantification of metastatic burden was performed by digital scanning of whole stained slides using a Pannoramic FLASH III system (3D Histech), followed by manual counting of metastatic lesions present in the tissue section. Quantification of Ki67-, CD31-, cleaved-PARP- and cleaved-caspase-3-positive tumor cells was performed by calculating the area of positive cells in 4–5 representative fields per section using the Keyence Hybrid Cell Count module.
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5

Proliferating Cells in Stented Arteries

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A subset of slides from the animals treated with BMS (n=4) and AAV2iNOS eluting stents (n=4) were immunostained with anti-Ki67 antibody (1:100) to determine the prevalence of proliferating cells in the neointima, media and adventitia of the stented arterial segments. A secondary horse anti-rabbit biotinylated antibody (Vector labs, BA-1100), Vectostain ABC Elite peroxidase kit (Vector labs, PK-6100) and 3, 3’ diaminobenzidine chromogen (Vector labs, SK-4105) were used as recommended by the manufacturer for color development. The slides were counterstained with Gill-3 hematoxylin, mounted and photographed at 200x. The number of Ki-67 –positive cells in individual arterial compartments was determined for each image (Image J) by counting cell nuclei after converting the image into a black and white 16-bit image and adjusting threshold to visually match the original image. The number of proliferating cells was then normalized by the area of the respective arterial compartment in the captured image, and averaged over 4 images obtained for each slide.
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6

Immunohistochemistry for NeuN and ID1

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Immunohistochemistry for NeuN (a neuronal marker) and ID1 was performed using a published procedure (28 (link)). The sections were incubated in mouse anti-NeuN (1:800; MAB377; EMD Millipore, Billerica, MA, USA) or rabbit anti-ID1 (1:200; sc-488; Santa Cruz Biotechnology, Inc.) as primary antibodies, and in biotinylated horse anti-mouse (1:200; BA-2001; Vector Laboratories, Inc., Burlingame, CA, USA or rabbit anti-goat immunoglobulin G (1:200; BA-1100; Vector Laboratories, Inc.) and streptavidin peroxidase complex (VECTASTAIN® Elite ABC kit 1:200; Vector Laboratories, Inc.) as secondary antibodies. The antibodies were finally visualized with 3,3′-diaminobenzidine tetrahydrochloride. A negative control test was performed to establish the specificity of the immunostaining using pre-blocking serum (S-1000; Vector Laboratories, Inc.) instead of primary antibody. The negative control test showed no immunoreactivity in structures observed.
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7

Immunohistochemical Analysis of Gap Junctions

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Regarding the antigen retrieval, tissue sections were exposed to microwaves for 15 min at 600 W in 10 mM sodium citrate while H9c2 cells were treated with 0.2%, triton-X100/PBS (Sigma-Aldrich) for 10 min. Then the samples were incubated for 10 min in 3% H2O2/methanol in order to block endogenous peroxidases, treated for 20 min at 37 °C with PBS-blocking solution containing 1% normal goat serum (NGS, Vector, Burlingame, CA, USA), 0.1% bovine serum albumin (BSA, Sigma-Aldrich), 0.1% triton-X100 for blocking non-specific binding. and then incubated overnight at 4 °C with primary antibodies diluted in a 1%BSA/2%FBS/PBS solution (RαCx26-Ct 1:400, RαCx26-cl 1:200, RαCx43 1:200, RαCx32 1:200 and MαMyo 1:750). Detection was accomplished by sequential treatments with biotinylated anti-rabbit or anti-mouse immunoglobulins (1:200, BA-1100 or BA-2000, Vector), streptavidin-peroxidase complex (Vector) and 3.3’diaminobenzidine tetrahydro-chloride (DAB Dako Italia SRL, Milan, Italy). The specificity of secondary antibodies was obtained by performing the experiments omitting the primary antibodies. Sections were then counterstained with Harris’ hematoxylin (Fluka, Buchs, Switzerland) and examined by means of a Leica DMRB light microscope at 20x or 40x magnification; representative images were captured by DFC480 digital camera (Leica Microsystem, Cambridge, UK).
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8

c-Fos Immunohistochemistry in PVN and PFC

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Animals were perfused with saline, followed by 4% paraformaldehyde (PFA) solution and brains were dissected out and stored in 4% PFA. Brains were sectioned on a vibratome (Leica VT1000 S, U.S.A.) at 40-μm thickness. Free-floating sections spanning the PVN of the hypothalamus (−0.58 to −1.22 mm from Bregma, five to six sections per animal) and PFC (2.46–1.34 mm from Bregma, five to six sections per animal) were subjected to processing for c-Fos immunohistochemistry. Briefly, sections were blocked in 10% horse serum, followed by overnight incubation with rabbit-anti-c-Fos antibody (1:500, Catalog number CST-2250S, Cell Signaling Technology). Sections were washed and incubated with a biotinylated horse-anti-rabbit IgG secondary antibody (1:500, Catalog number BA-1100, Vector Laboratories). Signal amplification and visualization involved exposure to an avidin–biotin complex solution (ABC solution, Vector Laboratories) followed by 3,3′-Diaminobenzidine (DAB) substrate (Sigma, U.S.A.). Sections were mounted and visualized at 200× magnification (Zeiss Axioskop, Germany). c-Fos positive cells were counted per section by an experimenter blinded to the treatment conditions.
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9

Immunohistochemical Analysis of NOD1 in Colon Cancer

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Human colon cancer TMA from USBioLab (Maryland, USA) was deparaffinized using xylene and rehydrated using graded ethanol (100%, 95%, 70%, 50%) and distilled water. Antigen retrieval was performed using pH 6 citrate buffer in pressurized heater for 16 min. After cooling, samples were permeated using 2% Triton X-100/TBS for 30 min. Endogenous peroxidase, avidin and biotin were blocked using 3% hydrogen peroxide, avidin and biotin blocking solutions in 2% normal horse serum (NHS) (Vector Labs #SP-2001, #S-2000). TMAs were incubated with anti-NOD1 (1:200) or NHS for vehicle control at 4 °C overnight. The next day, after washing with 0.05% TBST, biotinylated secondary antibody (Vector Labs #BA-1100), streptavidin-HRP, DAB chromogen (Vector Labs VECTASTAIN Elite ABC kit #PK-6100, ImmPACT DAB Peroxidase substrate #SK-4105) and Hematoxylin (Sigma-Aldrich) were sequentially added before slide dehydration in graded ethanol and xylene and coverslip with Permount mounting medium (Fischer Scientific). After drying, the specimens were examined twice by a Royal College-certified pathologist (Dr. R. McClure) who is blinded and have no prior knowledge of the study. Each core staining intensity was scored as “3-Strong-staining”, “2-Some-staining” or “1-No-staining”.
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10

Proliferating Cells in Stented Arteries

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A subset of slides from the animals treated with BMS (n=4) and AAV2iNOS eluting stents (n=4) were immunostained with anti-Ki67 antibody (1:100) to determine the prevalence of proliferating cells in the neointima, media and adventitia of the stented arterial segments. A secondary horse anti-rabbit biotinylated antibody (Vector labs, BA-1100), Vectostain ABC Elite peroxidase kit (Vector labs, PK-6100) and 3, 3’ diaminobenzidine chromogen (Vector labs, SK-4105) were used as recommended by the manufacturer for color development. The slides were counterstained with Gill-3 hematoxylin, mounted and photographed at 200x. The number of Ki-67 –positive cells in individual arterial compartments was determined for each image (Image J) by counting cell nuclei after converting the image into a black and white 16-bit image and adjusting threshold to visually match the original image. The number of proliferating cells was then normalized by the area of the respective arterial compartment in the captured image, and averaged over 4 images obtained for each slide.
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