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10 protocols using af647 donkey anti rabbit

1

Immunohistochemical analysis of mouse brain

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Anesthetized mice were transcardially perfused with PBS followed by 10% Formalin. Skulls containing whole brains where kept overnight at RT in 10% Formalin. Brains were removed the following day and incubated in 10% Formalin overnight at 4C and then dehydrated in 30% sucrose for 3 days. Brains were hemisected sagittally, frozen in OCT, and cut in 12 µm sagittal sections using a Leica CM1860 UV cryostat (Leica Biosystems, Wetzlar, Germany). Primary antibodies include: Goat anti-GFP (Abcam, Cambridge, UK), Rabbit anti-CD8α (Sino Biological Inc., Beijing, China) and anti-CD4-PE (GK1.5, BioLegend). Secondary antibodies against goat (bovine anti-goat AF488) and rabbit (donkey anti-rabbit AF647) were purchased from Jackson ImmunoResearch (West Grove, PA). Images were acquired using a Leica DM4000 B LED microscope (Leica Biosystems, Wetzlar, Germany).
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2

Phenotyping Antigen-Specific T Cells

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Phycoerythrin (PE)-conjugated MHC Dextramer reagents and PE-conjugated MHC Tetramer reagents were obtained from Immudex (Denmark). The MHC multimer reagents used in this study are shown in Supplementary Table 1. CD3 (clone UCHT1) - FITC, CD8 (clone RPA-T8) - BV510, and CD4 (clone RPA-T4) - PECF594 (BD Biosciences, San Diego, CA). Unconjugated NFAT1 (Cell Signaling, Danvers, MA), and donkey anti-rabbit AF647 (Jackson ImmunoResearch Laboratories Inc., West Grove, PA). DAPI (Life Technologies, Carlsbad, CA).
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3

Immunofluorescence Antibody Protocol

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The following primary antibodies were used: mouse IgG1 anti-SIRT3 antibody (1:200; Novus Biologicals; RRID:AB_2818991); goat anti-Oncomodulin antibody (OCM; 1:1000; Santa Cruz; RRID:AB_2267583), rabbit anti-Myosin7a (MYO7; 1:200; Proteus; RRID:AB_10013626) mouse anti-CTBP2 (aka C-Terminal Binding Protein 2; 1:200; BD Transduction Laboratories; RRID:AB_399431), and mouse anti-GRIA2 (aka GluR2/GluA2; 1:2000; Millipore; RRID:AB_2113875). The following secondary antibodies were purchased from Jackson Immuno Research: Donkey Anti-Mouse AF488 (1:500; RRID:AB_2340849), Donkey Anti-Rabbit AF594 (1:500; RRID:AB_2340622), Donkey Anti-Rabbit AF647 (1:200; RRID:AB_2340625), Donkey Anti-Goat AF647 (1:200; RRID:AB_2340438), Goat Anti-Mouse AF594 (IgG1, 1:500; RRID:AB_2338885), AF488 Goat Anti-Mouse (IgG2a, 1:500; RRID:AB_2338855). For the images in Fig 1, an AF568 Goat Anti-Mouse (IgG1, 1:200, Thermo Fisher, RRID: AB_2535766) was used.
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4

Immunofluorescent Analysis of Mouse Tumors

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Mouse tumors were embedded for 4 hours in 4% paraformaldehyde overnight in 30% sucrose and mounted in OCT medium. Fifty-micrometer-thick sections were cut and fixed in 4% paraformaldehyde for 20 min. After washing and permeabilization [0.5% PBS/BSA + Triton X-100 (1/400e, AppliChem); 20 min, room temperature], sections were stained overnight at 4°C using a rat anti–Lyve-1 antibody (1/300e; Novus) and a rabbit anti–cleaved casp-3 (1/100e; Cell Signaling Technologies). Alexa Fluor 546–labeled goat anti-rat (1/1000e; Invitrogen) and donkey anti-rabbit AF647 (1/1000e; Jackson ImmunoResearch) and Alexa Fluor 488–labeled anti-CD45.1 (1/100e; BioLegend, clone A20) antibodies were incubated for 2 hours at room temperature. Sections were mounted with DAPI Fluoromount-G (SouthernBiotech).
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5

Immunohistochemical Analysis of Heart Tissue

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Heart tissues were fixed in 4% formalin for 4 h at room temperature and then embedded in paraffin. For staining slides were blocked in 5% donkey serum followed by 1 h of incubation with the primary antibody, washing 3 times for 5 min in PBS, and subsequent incubation of the secondary antibodies for 45 min. Following DAPI (4′,6′-diamidino-2-phenylindole) staining (Roche, 1:10.000) the slides were mounted with ProLong Gold (Invitrogen, cat. no. P10144). The following antibodies were used: anti-ACTA2(aSMA)-Cy3 (C6198,1:250, Sigma-Aldrich), anti-SEMA3G (HPA001761, 1:100, Sigma-Aldrich), AF647 donkey anti-rabbit (1:200, Jackson Immuno Research).
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Immunofluorescence Staining of Mouse Kidney

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Mouse kidney tissues were fixed in 4% formalin for 2 h at RT and frozen in OCT after dehydration in 304%4 sucrose overnight. Using 5–10 μm cryosections, slides were blocked in 5% donkey serum followed by 1-h incubation of the primary antibody, washing three times for 5 min in PBS, and subsequent incubation of the secondary antibodies for 45 min. Following DAPI (4′,6-diamidino-2-phenylindole) staining (Roche, 1:10,000) the slides were mounted with ProLong Gold (Invitrogen, #P10144). Cells were fixed with 3% paraformaldehyde followed by permeabilization with 0.3% TritonX. Cells were incubated with primary antibodies and secondary antibodies diluted in 2% bovine serum albumin in PBS for 60 or 30 min, respectively. The following antibodies were used: anti-Runx1 (HPA004176, 1:100, Sigma-Aldrich), AF647 donkey anti-rabbit (1:200, Jackson Immuno Research).
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7

Cryosectioning and Immunostaining of Mouse Heart

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Extracted upper parts of the hearts were fixed for 2 h in 4% paraformaldehyde (Carl Roth) at RT. These parts were then transferred to 30% sucrose solution in PBS and kept at 4 °C overnight to prevent ice crystal formation. Samples were then embedded in Tissue-Tek O.C.T. Compound (Sakura) and quickly frozen and stored at −80 °C until sectioning. In total, 4 μm cryosections were then washed in PBS and permeabilized in PBST-0.1% (PBS with 0.1% Triton X-100 (Sigma-Aldrich). Blocking was performed in 10% BSA in PBS, followed by 1 h incubation of primary antibody. Slides were washed three times for 5 min in PBS and incubated afterwards with secondary antibody for 30 min. Lastly, nuclei were counterstained with 4′,6-diamidino-2-phenylindole (DAPI) staining (Roche, 1:10,000) and slides were mounted with ProLong Gold (Invitrogen, P10144). Used antibodies are listed here: Anti-Mouse CD31 (BD Biosciences, 1:100, 553370), Thrombospondin-4 Antibody (Novus Biologicals, 893655, 1:100) and Ki-67 Monoclonal Antibody (SolA15) (eBioscience, 14-5698-80, 1:100). AF488 donkey anti goat (Jackson Immuno Research, 1:200), and AF647 donkey anti-rabbit (Jackson Immuno Research, 1:200) and AF647 donkey anti-rat (Jackson Immuno Research, 1:200).
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8

Immunohistochemistry of Celiac Ganglia

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The celiac ganglia were dissected from MeAàVMHhM3Dq or mCherry control mice euthanized 2h after CNO administration. The tissue was post-fixed in 4% paraformaldehyde at 4°C overnight, cryo-protected in 30% sucrose (Sigma-Aldrich, 50389) in PBS, embedded in O.C.T Compound (Thermofisher Scientific, Watham, MA; 23–730-572), frozen at −80°C, and sectioned at 10μm thickness. Slides were washed in 0.03% PBT (3 × 5 minutes), incubated in blocking solution overnight at 4°C (2% normal donkey serum, 3% bovine serum albumin in 0.03% PBT), incubated in primary antibodies for 48h at 4°C (Cell Signaling anti-cfos – 1:100; abcam chicken polyclonal to tyrosine hydroxylase [#ab76442] – 1:500), washed in 0.03% PBT (3 × 5 minutes), incubated in secondary antibodies for 2h at RT (Jackson AF-647 donkey anti-rabbit – 1:250; Jackson AF-594 donkey anti-chicken – 1:500), and washed in 0.03% PBT (3 × 5 minutes). After staining, tissue sections were mounted with DAPI counterstain (Fluoromount).
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9

Comprehensive Immunofluorescence Staining of Kidney Tissue

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Kidney tissues were fixed in 4% formalin for 2 hours at RT and frozen in OCT after dehydration in 30% sucrose overnight. Using 5-10 μm cryosections, slides were blocked in 5% donkey serum followed by 1-hour incubation of the primary antibody, washing 3 times for 5 minutes in PBS and subsequent incubation of the secondary antibodies for 45 minutes. Following DAPI (4′,6′-′diamidino-2-phenylindole) staining (Roche, 1:10.000) the slides were mounted with ProLong Gold (Invitrogen, #P10144). The following antibodies were used: anti-mouse PDGFRa (AF1062, 1:100, R&D), anti-CD10 human (clone HI10a, 1:100, biolegend), anti-HNF4a (clone C11F12, 1:100, Cell Signalling), anti-Pan-Cytokeratin TypeI/II (Invitrogen, Ref. MA1-82041), anti-Dach1 (Sigma, HPA012672, 1:100), anti-Col1a1 (Abcam, ab34710, 1:100), anti-ERG (abcam, ab92513, 1:100), anti-CXCL12/SDF-1 (R&D, MAB350, 1:100), AF488 donkey anti goat (1:200, Jackson Immuno Research), AF647 donkey anti-rabbit (1:200, Jackson Immuno Research)
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10

Comprehensive Immunofluorescence Staining of Kidney Tissue

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Kidney tissues were fixed in 4% formalin for 2 hours at RT and frozen in OCT after dehydration in 30% sucrose overnight. Using 5-10 μm cryosections, slides were blocked in 5% donkey serum followed by 1-hour incubation of the primary antibody, washing 3 times for 5 minutes in PBS and subsequent incubation of the secondary antibodies for 45 minutes. Following DAPI (4′,6′-′diamidino-2-phenylindole) staining (Roche, 1:10.000) the slides were mounted with ProLong Gold (Invitrogen, #P10144). The following antibodies were used: anti-mouse PDGFRa (AF1062, 1:100, R&D), anti-CD10 human (clone HI10a, 1:100, biolegend), anti-HNF4a (clone C11F12, 1:100, Cell Signalling), anti-Pan-Cytokeratin TypeI/II (Invitrogen, Ref. MA1-82041), anti-Dach1 (Sigma, HPA012672, 1:100), anti-Col1a1 (Abcam, ab34710, 1:100), anti-ERG (abcam, ab92513, 1:100), anti-CXCL12/SDF-1 (R&D, MAB350, 1:100), AF488 donkey anti goat (1:200, Jackson Immuno Research), AF647 donkey anti-rabbit (1:200, Jackson Immuno Research)
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