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147 protocols using anti ki67

1

Comprehensive Immunohistochemical Analysis of Tissue Samples

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To check for levels of p53 expression and cleaved PARP (indicator of apoptosis), the tissues were sectioned to 14-μm thickness, fixed with 4% paraformaldehyde, and blocked with blocking buffer for 1 hr. This was followed by treating with anti-p53 (Sigma; P 8999) or anti-cleaved PARP (Thermo Fisher Scientific; 44-698G) antibodies overnight in blocking buffer. On subsequent day, the sections were treated with fluorescent secondary antibodies. Sections were imaged on a Zeiss LSM 700-405 confocal microscope.
To check for levels of TNF-α (pro-inflammatory cytokine), ki67 (cell proliferation), CD68 (activated microglia), and cleaved PARP (apoptosis), the tissues were sectioned in 4- to 5-mm blocks and submitted as individual cassettes for paraffin embedding at Emory Winship Pathology Core Lab. Tissues from paraffin-embedded blocks were sectioned at 5-μm thickness. IHC was performed using DAB chromogenic kit (Wako) following the manufacturer’s protocol. Antibodies used were anti-TNF-α (Boster Biologics; PA 1079), anti-p53 (Sigma; P8999), anti-cleaved PARP (Thermo Fisher Scientific; 44-698G), anti-ki67 (Thermo Fisher Scientific; MA5-15690), and anti-CD68 (AbD Serotec; MCA 341R). Whole-slide scanning was done using Hamamatsu’s Nanozoomer 2.0 HT.
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2

Characterization of Intestinal Cell Types

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Immunofluorescence staining was performed and assessed as described previously [17 (link)]. Primary antibodies included rabbit monoclonal anti-ki67 (Thermo scientific), rabbit polyclonal antisera against murine colonic mucin Muc2 (1:50; a gift from Jan Dekker), rabbit polyclonal antisera against TFF3 (1:200; a gift from D. Podolsky), polyclonal rabbit anti-VIP (Immunostar), goat polyclonal anti-carbonic anhydrase (CA) I (Santa Cruz), rat anti-BrdU monoclonal antibody (1:200, AbD Serotec) and rabbit anti-serotonin (5HT) (Antibodies incorporated). For immunohistochemistry of longitudinal muscle myenteric plexus preparations, colon tissues were prepared as described previously [22 (link)]; primary antibodies included polyclonal rabbit anti-VIP (1:1000; Immunostar), rabbit anti-neuronal nitric oxide synthase (NOS—1:500; Transduction), rabbit anti-substance P (SP—1:1000; Immunonuclear Corp), and goat anti-neuropeptide Y (NPY—1:1000; a gift from Thue Schwartz).
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3

Cryosection Immunofluorescence Assay

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Mouse tissue was cryopreserved using O.C.T. and cut into 5 µm sections. Cryosections were fixed in ice‐cold methanol/acetone. After blocking in 10% goat serum with 0.1% Triton X‐100, sections were incubated with primary antibodies diluted in 10% goat serum at 4°C overnight. Following primary antibodies were used: anti‐CD31 (550274, BD Biosciences, 1:50), anti‐cleaved caspase 3 (9664, Cell Signaling Technology, 1:100), anti‐ColIV (2150‐1470, Bio‐Rad, 1:250), anti‐ERG (ab93513, Abcam, 1:1,000), anti‐α‐SMA (C6198, Sigma‐Aldrich, 1:200), anti‐Ki‐67 (14‐5698‐82, Thermo Fisher Scientific, 1:100) or FITC‐Isolectin B4 (L2895, Sigma‐Aldrich, 1:100). DAPI and fluorophore‐conjugated secondary antibodies were added before embedding the sections in fluorescent mounting medium (DAKO). Images were acquired using a confocal microscope (Zeiss LSM 700) and analysis was done using Fiji software.
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4

Comprehensive Antibody Validation Protocol

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Santa Cruz Biotechnology: anti-SMO H-300 (sc-13943, IHC), anti-SMO N-19 (sc-6366, WB), anti-GLI1 H-300 (sc-20687, IHC), anti-actin I19 (sc-1616, WB), anti-NRP2 (sc-13117, IHC and WB), anti-p-ERK1/2 (sc-101761, WB) and anti-ABCG2 (sc-25821, WB). Abcam (Cambridge, UK): anti-SHH (ab53281, IHC), anti-GAPDH (ab8245, WB) anti-OCT4 (ab19857, WB and IHC) and Phospho—(Ser/Thr) (ab17464, WB-IP). Cell Signalling (Leiden, The Netherlands): anti-GLI1 (L42B10, WB). Thermo Fisher Scientific: Anti-KI-67 (RM-9106, IHC). EMD Millipore (Milan, Italy): Anti-human nuclei (MAB-1281, IHC) and anti-phospho-serine (#16-455 Kinase assay).
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5

Comprehensive Protein Expression Analysis

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Western blot reagents were obtained from GE Healthcare (Pittsburgh, PA, USA). Fluorescent probes for caspase activity, caspase inhibitors, and annexin V assay kit were from BD Biosciences (San José, CA, USA). Culture media were from Lonza (Basel, Switzerland). MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl tetrazolium bromide) and p38MAPK inhibitor (SB202190) were obtained from Sigma-Aldrich (St. Louis, MO, USA). Primary monoclonal rabbit antibodies against caspase 8 (dilution, 1:1,000; #4927), cleaved-caspase 9 (dilution, 1:1,000; #7237), MMP-2 (dilution, 1:1,000; #4022), MMP-9 (dilution, 1:1,000; #3852), p-p38 (dilution, 1:1,000; #9211), p38 (dilution, 1:1,000; #9212), and TIMP-1 (dilution, 1:1,000; #8946) were purchased from Cell Signaling Technology, Inc. (Danvers, MA, USA). Caspase 3 (dilution, 1:1,000; sc-7148), Bid (dilution, 1:1,000; sc-11423), Bcl-2 (dilution, 1:1,000; sc-783), Bcl-xL (dilution, 1:1,000; sc-634), and Bax (dilution, 1:1,000; sc-526) were purchased from Santa Cruz Biotechnology, Inc. (Dallas, TX, USA), and β-actin (dilution, 1:5,000; #A5441) was obtained from Sigma-Aldrich (St. Louis, MO, USA).
Anti-Ki67 (dilution 1:200) and Click-iT Tunel colorimetric IHC detection kit were from Thermo Fisher (Waltham, MA USA). DAB kit was provided from Vector laboratories (Burlingame, CA, USA).
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6

Immunohistochemical Analysis of Tumor Markers

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Formalin-fixed, paraffin-embedded sections were dewaxed. Heat induced epitope retrieval was performed in a water bath containing citrate buffer (Dako North America, Carpinteria, CA, USA), blocked with 1% hydrogen peroxide and then treated for 30 min with CAS-Block (Invitrogen, Carlsbad, CA, USA) before primary antibody incubation. The primary antibodies were rabbit monoclonal anti-Ki-67 (1:200 dilution; Thermo Fisher Scientific) and rabbit monoclonal anti-CD31 (1:75 dilution; Abcam). Staining signals were detected using the Starr Trek Universal horseradish peroxidase (HRP) Detection System (Biocare Medical, Pacheco, CA, USA). Immunohistochemistry slides were scanned with a 3DHITECH PANNORAMIC Midi slide scanner, and images were captured using PANNORAMIC Viewer software (3DHITECH, Budapest, Hungary).
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7

Detecting Gal-3 Expression in MSCs

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Immunostainings for detection of Gal-3 expression were performed in MSC plated on coverslips. The cells were fixed with paraformaldehyde 4% and incubated overnight at 4°C with the primary antibody goat anti-Gal-3, diluted 1 : 400 (Santa Cruz Biotechnology, Dallas, TX, USA). On the following day, sections were incubated for 1 h with phalloidin conjugated with Alexa Fluor 488 (1 : 200; ThermoFisher Scientific) mixed with the secondary antibody anti-goat IgG Alexa Fluor 568 (1 : 1000; ThermoFisher Scientific). Proliferating cells were evaluated by KI67 staining (anti-Ki67 1 : 1000; ThermoFisher Scientific), followed by anti-rabbit IgG Alexa Fluor 568 (1 : 1000 ThermoFisher Scientific). Dead cells were stained with PI (BD Biosciences). Nuclei were stained with 4,6-diamidino-2-phenylindole (VECTASHIELD mounting medium with DAPI H-1200; Vector Laboratories, Cambridgeshire, UK). The presence of fluorescent cells was determined by observation using an A1+ confocal microscope (Nikon).
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8

Immunohistochemical Analysis of Tumor Tissues

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Tumors removed from the mice were fixed in 4% paraformaldehyde overnight, embedded in paraffin, sectioned at 4 μm thickness and then were stained with HE and immunohistochemistry (IHC) assay. For IHC, sections were incubated with the primary antibody at 4°C overnight and the secondary antibody at room temperature for 30 min before staining. Slides were observed using a microscope (OLYMPUS, CX41) and staining was expressed by positive area. The primary antibodies used in the assay are listed as follows: anti-Ki67 (1:100, Thermo Fisher Scientific, RM-9106-S1), anti-PTEN (1:100, #9559), anti-p-AKT (1:100, #4060), anti-p-S6K (1:100, #9206) were purchased from Cell Signaling Technology (Danvers, MA, USA).
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9

Immunophenotyping of Cardiac Tissue

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Serial 8 µm frozen sections from LV tissue were fixed in 1% paraformaldehyde for 10 min at room temperature and post-fixed in Ethanol/Acetic acid (2:1) for 5 min at 20 °C. Sections were blocked with PBS BSA 1% for 1 h before immunolabeling with primary antibodies against: α-SMA (Abcam), and Ki67 (anti-Ki67; ThermoFischer Scientific). A fluorescent secondary antibody tagged alexa-red-555 was used against the primary antibody. Stained sections were scanned using an epifluorescence Zeiss Axiocam microscope equipped with a digital camera. The α-SMA + and Ki67 + mean fluorescence was calculated with NIH ImageJ software (NIH) in each section, comparing it with the size of the whole area.
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10

Immunohistochemical Analysis of Transcription Factors

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The following antibodies were used for immunochistochemistry: anti-Foxm1 [42] (link), [45] (link), anti-SPDEF [46] (link), anti-Ki67 (Thermo Scientific) and anti-phospho-Histone H3 (pH 3) antibody (Santa Cruz).
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