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7 protocols using rabbit anti ym1

1

Immunohistochemical and Flow Cytometry Analysis of Neuroinflammation

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Lipopolysaccharide (Escherichia coli 0111:B4) was obtained from InvivoGen. Recombinant mouse IL4 and IL4I1 were obtained from R&D Systems. The following antibodies were used for immunohistochemistry. Primary antibodies: rat anti-CD11b (1:100; AbD Serotec), rabbit anti-Ym1 (1:100; StemCell Technologies), mouse anti-iNOS (1:50; BD Pharmingen), rabbit anti-Olig2 (1:300; Millipore), mouse anti-CC1 (1:300; Millipore), mouse anti-Nkx2.2 (1:100; DSHB), mouse anti-GFAP (1:400; Sigma), rat anti-Tenascin-C (1:100, Abcam), rabbit anti-NF200 (1:100; Sigma), mouse anti-SMI-32 (1:1000; Calbiochem), mouse anti-IST-9 (1:200; Abcam). Secondary antibodies: Alexa Fluor® 488 Goat Anti-Rabbit IgG (1:1000), Alexa Fluor® 488 Goat Anti-Rat IgG (1:500), Alexa Fluor® 594 Goat Anti-Mouse IgG (1:1000), Alexa Fluor® 594 Chicken Anti-Goat IgG (1:500) and Alexa Fluor® 594 Goat Anti-Rat IgG (1:500). Flow cytometry primary antibodies: PE/Cy7 anti-CD4 (BioLegend), Brilliant Violet 711 anti-T-bet (Biolegend), PE anti-RORγt (BD Pharmingen) and PerCP/Cy5.5 anti-Gata3 (BioLegend), anti-NOS2 PE (Santa Cruz Biotechnology) and anti-CD11b APC/Cy7 (Biolegend). LIVE/DEAD® Fixable Yellow Dead Cell Stain Kit (Invitrogen) was used to monitor cell death.
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2

Immunohistochemical Analysis of Ym1 Expression

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Immunohistochemistry was performed on 60 μm coronal sections and standard immunostaining techniques were employed. Sections were incubated with rabbit anti-Ym1 (1:600, Stemcell Technologies Inc., Vancouver, BC), washed in 1 × PBS (3 times) and incubated with biotinylated anti-rabbit IgG antibody (Vector Laboratories, Burlingame, CA) for 2 hours at room temperature. Sections were incubated in avidin-biotin-horseradish peroxidase solution (Vectastain elite ABC kit, Vector Laboratories) for 1 hour and then reacted with 3,3′-diaminobenzidine (Vector Laboratories) for color development and mounted for immunohistochemical analysis using a Leica DM4000B microscope (Leica Microsystems, Exton, PA, USA).
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3

Western Blot Analysis of Arginase-1 and Ym1

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Proteins from ipsilateral cortical tissue were extracted using RIPA buffer, equalized, and loaded onto 5–20% gradient gels for SDS PAGE (Bio-Rad; Hercules, CA). Proteins were transferred onto nitrocellulose membranes, and then blocked overnight in 5 % milk in 1 × TBS containing 0.05 % Tween-20 (PBS-T). The membrane was incubated in mouse anti-arginase 1 (N-20) (1:1000; BD Transduction Laboratories), rabbit anti-Ym1 (1:1000; Stem Cell Technologies, Vancouver, BC), or rabbit anti-GAPDH (1:2000; Sigma) overnight at 4°C, then washed three times in TBS-T, and incubated in appropriate HRP-conjugated secondary antibodies (Jackson ImmunoResearch Laboratories, West Grove, PA) for 2 h at room temperature. Membranes were washed three times in TBS-T, and proteins were visualized using SuperSignal West Dura Extended Duration Substrate (Thermo Scientific, Rockford, IL). Chemiluminescence was captured ChemiDoc™ XRS+ System (Bio-Rad), and protein bands were quantified by densitometric analysis using BioRad Molecular Imaging Software. The data presented reflects the intensity of target protein band normalized based on the intensity of the endogenous control for each sample (expressed in arbitrary units).
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4

Western Blot Analysis of Ischemic Brain

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Total protein extracts were obtained from the ipsilateral hemisphere of the brain 3 day after cerebral ischemia by homogenization in a 1X Cell Lysis Buffer (included in the Ray Biotech kit) with Protease inhibitor cocktail (Sigma). Non-specific binding was blocked by pre-incubation of the nitrocellulose membrane in PBS containing 0.1% tween 20 (PBS-T) and 5% skimmed milk for 1 ​h. The nitrocellulose was then incubated overnight at 4 ​°C with antibodies against the targeted proteins as follows: 1:500 rabbit anti Iba1 (Wako), 1:500 rat anti Gal- 3 (Cell Signaling), 1:500 rabbit anti Ym1 (Stem Cell technologies), 1:250 rabbit anti IL-4 receptor (Santa Cruz), 1:500 mouse anti phospho-p65 (Cell Signaling) and 1:20 ​000 rabbit anti actin (Santa Cruz). Primary antibody was detected with HRP-conjugated anti-rabbit or anti-mouse antibody (1:2000–1:5000) and blots were developed using an enhanced chemiluminescence detection system (ECL kit; Thermo Fisher Scientific). The density of the specific bands was quantified with Image J software and normalized to β-actin as a housekeeping protein (Lalancette-Hebert et al., 2011 (link)).
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5

Multiparametric Immune Cell Profiling

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Single-cell suspensions were preincubated with FcγR-specific blocking mAb (2.4G2) and washed before staining. Cells were stained with the following antibodies Percp-cy5-conjugated anti-CD45 (eBioscience), APC-conjugated anti-F4/80 (eBioscience), PE-cy7-conjugated conjugated anti-CD11c (eBioscience), FITC–conjugated anti-CD206 (BioLegend), APC-conjugated anti-CD3 (eBioscience), FITC–conjugated anti-CD4 (eBioscience); For intracellular staining, cells were permeabilized (Cytofix/Cytoperm kit; BD Biosciences) and incubated with PE–conjugated anti-IL-4, PE–conjugated anti-IL-5, PE–conjugated anti-IFN-γ (eBioscience), rabbit anti-Ym-1 (Stem Cell Technologies) and PE–conjugated anti-rabbit IgG (eBioscience). Cells were analyzed on a LSRII (BD Biosciences) with FlowJo ver.10 software (TreeStar).
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6

Quantifying Lung Immune Cell Populations

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Single‐cell suspensions of lung tissue were preincubated with FcγR‐specific blocking monoclonal antibody (2.4G2) and washed before staining. To quantify Th2 cells, single cells prepared from lung tissue were stimulated with phorbol 12‐myristate 13‐acetate (100 ng/ml), ionomycin (1 μg/ml), and Golgi stop, then pooled cells from mouse per group were stained with phycoerythrin/cy5 (PE/cy5)‐conjugated anti‐CD3 antibody and fluorescein isothiocyanate (FITC)‐conjugated anti‐CD4, PE‐conjugated anti‐IL‐13, or PE‐conjugated anti‐IL‐4 antibodies. For analysis of macrophages population, cells were stained with the following antibodies: Percp‐cy5‐conjugated anti‐CD45 (eBioscience), FITC‐conjugated anti‐F4/80 (eBioscience), allophycocyanin (APC)‐cy7‐conjugated anti‐CD11c (eBioscience), goat anti‐CD206 (R&D Systems Inc.), rabbit anti‐Ym‐1 (Stem Cell Technologies), APC‐conjugated anti‐goat IgG, or PE‐conjugated antirabbit IgG (eBioscience). Cells were analyzed on an LSRII flow cytometer (BD Biosciences) using FlowJo version 10 software (TreeStar, Inc.).
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7

Western Blot Analysis of Protein Expression

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Tissue samples were prepared using a 7-ml dounce tissue grinder (Wheaton, USA) in complete RIPA buffer (RIPA buffer (Thermo) supplemented with 1 mM sodium orthovanadate, 10 mM sodium fluoride and 1 protease inhibitor tablet (Roche)). WT and AEP−/− MEFs (2 × 105 cells) treated or untreated with the different inhibitors were washed once with ice-cold PBS and lysed using complete RIPA buffer. Tissue and cell lysates were centrifuged at 20,000×g for 10 min and equal amounts of protein loaded on 4–12% NuPAGE gels (Invitrogen) and then transferred onto nitrocellulose membranes (Amersham). Membranes were probed with the following antibodies: rabbit anti-P-STAT3, mouse anti-STAT3, rabbit anti-GAPDH and rabbit anti-LC3 (Cell Signaling), rabbit anti-Ym1 (StemCell Technologies), rabbit anti-EGFR (SantaCruz), rabbit anti-Lamp1, rabbit anti-CtsD, rabbit anti-Fn1 and anti-CtsB (abCam), rabbit anti-TFEB (Bethyl) and rabbit anti-Gns (ProteinTech) and goat anti-OSMRβ (R&D Systems). Sheep anti-AEP was obtained as described previously32 (link) and sheep anti-CtsL and CtsH were generous gifts from Drs Tina Zavašnik-Bergant and Janko Kos (Jožef Stefan Institute, Ljubljana, Slovenia)
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