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17 protocols using ab279653

1

Histological Analysis of Colitis in Mice

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Colon tissues were washed with PBS, fixed in 4% paraformaldehyde and embedded in paraffin. Tissue sections of the whole colon were subjected to hematoxylin & eosin (H&E) and periodic acid Schiff (PAS) staining (Solarbio, Beijing, China). These procedures were performed according to the manufacturer’s protocols. The stained sections were imaged under a Leica DM6 microscope (Leica, Wetzlar, Germany). Histological scoring was performed in a blinded fashion by two pathologists. Colitis was scored based on the combined scores of inflammatory cell infiltration (score 0–4), ulceration (score 0–4) and area of crypt distortion (score 0–4).
For IHC, 4% paraformaldehyde-fixed and paraffin-embedded colon tissue sections were deparaffinized and hydrated with decreasing concentrations of ethanol. Tissue sections were stained for Ki67 using mouse anti-Ki67 antibodies (ab279653), F4/80 using rabbit anti-F4/80 antibodies (ab16911) and iNOS using rabbit anti-iNOS antibodies (ab3523); the antibodies were obtained from Abcam (Cambridge, MA, USA). Images were taken using a Leica DM6 microscope (Leica). The investigators examined the lesions in a blinded fashion.
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2

Immunofluorescence Analysis of LSC Proliferation

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LSCs were cultured in six-well plates and treated with SP or AKT inhibitor MK-2206 for 5 days. The samples were then fixed with 4% paraformaldehyde and permeabilized with 0.1% Triton X-100 for 30 min followed by blocking using 5% goat serum for 30 min at room temperature. Incubation with the following antibodies was performed at 4°C overnight: anti-Ki67 (1:50, Cat#ab279653, Abcam) and anti-DeltaNp63 (1:50, Cat#ab203826, Abcam). Next, incubation with Alexa Fluor-conjugated secondary antibodies (1:500, Cat#A-21422/A-11008, Thermo Fisher Scientific) was carried out. The nuclei were stained using DAPI (Cat#FD9637, Fude Biological Technology). Finally, the cells were visualized using a laser scanning confocal microscope-LSM 880 with Airyscan (ZEISS, Oberkochen, Germany).
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3

Immunohistochemical Analysis of Colon Tumors

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Tumors and colon tissues of the mice were fixed with 4% paraformaldehyde, embedded in paraffin, and cut into 5 μm sections. Immunohistochemical staining of the tissue sections was conducted as previously described [48 (link)]. Antibodies against ki67 (ab279653, 1:1000, Abcam, Cambridge, UK) and CD44 (37259, 1:100, Cell Signaling Technology, Beverly, MA, USA) were used. Additionally, the colon tissues were stained with hematoxylin and eosin (H&E) for histological analysis. Multiple fields of each tissue section were randomly selected for IHC (200×) and histopathological (40×) analyses.
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4

Immunohistochemical Analysis of Tumor Tissues

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The tumors from mice were paraffin-embedded and cut into 5 μm sections. After antigen retrieval, the sections were blocked in the primary antibody anti-ki-67 (ab279653, 1:1000, Abcam) or anti-PGK1 (ab233135, 1:500, Abcam). The sections were incubated in the second antibody and stained with diaminoaniline (DAB). At last, a fluorescence microscope (Axio Imager A2, Carl Zeiss AG, Germany) was used to take photos.
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5

Quantification of Ki67 Expression in Tumor Cells

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The expression of KI67 was detected by Immunohistochemistry. The sections were isolated from tumor tissues and then treated with conventional deparaffinization, rehydration, and blocking of endogenous peroxidase activity for 15 min. Sections were pretreated for the purpose of antigen retrieval by microwaving, and then washed with PBS. Sections were incubated for 2 h at room temperature with anti-KI67 (ab279653, Abcam, USA), after which sections were rinsed with PBS, developed with DAB, counterstained with hematoxylin, cleared with xylene, and observed under a light microscope. A mean percentage of positive tumor cells was determined in at least five areas at × 400 and assigned to one of five of categories: (a) 0. < 5%; (b) 1. 5–25%; (c) 2. 25–50%; (d) 3. 50–75%; and (e) 4. > 75%. According to cell staining intensity score: (a) cell no color, 0 points; (b) straw colored, 1 point; (c) brownish-yellow, 2 points; and (d) tan, 3 points. Divided into 4 levels based on cell staining intensity score: (a) negative, 0-1points; (b) weak positive, 2-3 points; (c) positive, 4-5 points; (d) string positive, 6-7 points.
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6

Quantification of E2F3 and Ki-67 in Colorectal Tumors

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The tumors from the nude mice were fixed in 10% paraformaldehyde at 4°C for 12 h, and then dehydrated in different concentrations of ethanol, permeabilized using xylene and embedded in paraffin. The paraffin-embedded tumor tissues were then sliced (0.5 µm), rehydrated, and were stained with HE at 4°C for 10 min and sealed with neutral gum. For IHC assessment of E2F3 and Ki-67 in colorectal tumor tissues from the nude mice, the DAKO Envision system (Dako; Agilent Technologies, Inc.) was used. Briefly, after paraffin-embedded sections of tumor tissues were heated at 60°C, the sections were incubated with primary antibodies against E2F3 (1:200; cat. no. ab50917; Abcam) and Ki-67 (1:1,000; cat. no. ab279653; Abcam) overnight at 4°C. Then, the sections were incubated with biotin-labeled secondary antibodies (1:1,000; cat. no. ab205718; Abcam) at 37°C for 20 min. Under a light microscope, IHC staining scores for E2F3 were obtained by multiplying the intensity (0, negative; 1, low; 2, medium; and 3, high) with the extent of staining (0, 0%; 1, 0-10%; 2, 10-50%; 3, 50-75%; 4, >75%); the final scores were between 0-12. For evaluation of Ki67, the number of positive cells was calculated in three representative areas of high staining.
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7

Immunohistochemical Analysis of Ki67 Expression

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The excised tumor samples were embedded and fixed. Sections were microwaved in Retrieval Solution (Amyjet, Wuhan, China) at pH 6.0 or pH 9.0 for 7 min, followed by incubation in 3 % H2O2 for 10 min. Nonspecifically bound sites were then blocked with 2.5 % normal horse serum (Vector Biolabs, Burlingame, CA, USA). The sections were incubated with an antibody against Ki67 (#ab279653, Abcam, USA). After incubation with a secondary antibody (#ab125913, Abcam) for 30 min, the sections were stained with 3,3′-diaminobenzidine solution (Sangon Biotech, Shanghai, China) and hematoxylin (Sangon Biotech). Representative areas were viewed under a light microscope (Nikon 90i, Tokyo, Japan).
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8

Comprehensive Immune Signaling Pathway Analysis

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Anti-KI67 (abcam, ab16667), Anti-KI67 (ab279653), Anti-TOMM20 (abcam, ab186735), Anti-FTO (ab126605), Anti-Vimentin (Santa, sc-80975), Anti-COL II (abcam, ab34712), Anti-MMP3 (abcam, ab52915), Anti-MMP13 (abcam, ab39012), Anti-dsDNA (abcam, ab27156), Anti-CMPK2 (Proteintech, 25877-1-AP), Anti-STING (CST.13647), Anti-cGAS (Proteintech, 29958-1-AP), Anti-TBK1 (abcam, ab40676), Anti-p-TBK1 (CST.5483), Anti-p-IRF3 (CST.29057), Anti-IL-1β (abcam, ab315084), Anti-IL-6 (abcam, ab290735), Anti-GADPH (abcam, ab8245).
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9

Intestinal Organoid Immunofluorescence Analysis

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Organoid samples were obtained, fixed in 4% paraformaldehyde at 4℃ for 1 h, dehydrated in 15–30% sucrose for 2 days. The organoid was embedded in OCT and sliced into 8-μm-thick sections. Ileum and organoid sections were stained with primary mAbs against ZO-1 (ab96587, Abcam), Occludin (ab216327, Abcam), Ki67 (ab279653, Abcam), Lysozyme (A0099, Dako), Muc2 (27675-1-AP, Proteintech), and YAP. Images at a 200 × magnification were captured using a Zeiss Axio Imager D2 immunofluorescence microscope. Three to six random fields were quantified per section. Immunohistochemistry was performed as previously described [25 (link)]. The relative intensities of stained proteins were determined by automated image analyses in three to five randomly selected 200 × fields for every sample.
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10

Immunohistochemical Analysis of Cellular Markers

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Paraffin-embedded tissue sections were dewaxed and rehydrated for IHC assay. The sections were water-bathed in antigen retrieval solution (Solarbio) for 1 h, blocked with normal goat serum (Solarbio) at 23°C for 20 min, and then incubated with anti-Ki67 (1 : 5,000, ab279653, Abcam Inc., Cambridge, MA, USA), anti-SUV39H1 (1 : 800, MA1-25505, Thermo Fisher Scientific), and anti-SPP1 (1 : 5,000, NB110-89062, Novus Biologicals, Littleton, CO, USA) at 4°C overnight, and then incubated with the goat antimouse IgG (1 : 1,000, ab205719, Abcam). Thereafter, the sections were cultured with horseradish peroxidase- (HRP-) labeled streptavidin (Solarbio) at 37°C for 20 min, developed with DAB (Solarbio), and counter-stained with hematoxylin (Solarbio) for 1 min. After that, the tissue sections were dehydrated, cleared in xylene, and sealed with neutral resin. The number of IHC-positive cells (brownish) was counted under the microscope. The rate of positive cells was calculated by three pathologists blind to the groups as follows: rate = positive cells/total cells × 100%.
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