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47 protocols using ab62341

1

Immunohistochemistry of Maxillary Samples

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Maxillae were dissected and fixed in 4% PFA overnight. Samples were decalcified in 19% EDTA until soft enough to cut (~7 days). Processed samples were then dehydrated with 30% sucrose followed by embedding in OCT on dry ice with ethanol. Cryosections were fixed by 4% PFA. Sections were then subject to permeabilisation by 0.2% Triton X-100 (Sigma, X100), heat-induced antigen retrieval, and blocking with 3% BSA. Sections were stained by the following antibodies: anti-RFP (Abcam, Ab62341), anti-CD34 (Abcam, Ab81289 and Ab8158), anti-CD31 (Abcam, Ab7388 and Ab24590), anti-GFP (Abcam, Ab13970), anti-Arg1 (Abcam, Ab92274), anti-Met (Abcam, Ab51067), anti-HGF (Abcam, Ab83760), and anti-Ki67 (Abcam, Ab16667). Secondary antibodies included Alexa Fluor 488 (Invitrogen, A11039), Alexa Fluor 568 (Invitrogen, A11077), Alexa Fluor 633 (Invitrogen, A21052), and Alexa Fluor 488 (Invitrogen, A11008). Tyramide signal amplification (NEL744001KT, PerkinElmer) was performed for weak signals. Hoechst 33342 (Invitrogen 62249, 1:500) was used for DNA staining. Slides were mounted using Citifluor AF1 (EMS, 171024-AF1) and cover-slipped for microscopy. Zeiss Apotome or Leica TCS SP5 systems was used for acquiring images. ImageJ and Adobe Photoshop were used for image processing.
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2

Immunochemical Analysis of Cell Markers

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For immunochemical analysis, cells were fixed with 4% paraformaldehyde or 100% ethanol for 15–30 min at room temperature. After incubating with blocking buffer (PBS containing 0.05% Tween 20 (Sigma) and 10% goat or donkey serum) for 30–60 min at room temperature, the cells were incubated with primary antibodies at 4°C overnight. After incubation with primary antibodies, the cells were washed with PBS three times, and incubated with Alexa 488, 555 and 647-conjugated secondary antibodies (Thermo Fisher) and 10 mg/ml Hoechst 33258 (Sigma) for one hour at room temperature. Primary antibodies used in the current study are as follows: anti-NANOG (1:500; 1E6C4; Cell Signaling), SSEA4 (1:500; MAB4304; Merck), TRA-1-60 (1:500; MAB4360; Merck), βIII-tubulin (1:400; 2G10; Abcam), αSMA (1:1000; 1A4; Sigma), SOX17 (1:200; AF1924; R&D Systems), HNF3β/FOXA2 (1:500; D5606; Cell Signaling), RFP (1:500, ab62341, Abcam) and VGLUT2 (1:500, ab79157, Abcam).
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3

Antibody Characterization Protocol

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The antibodies used in the study included GAPDH (14C10, Cell signalling), Ku80 (ab3107, Abcam), RFP (ab62341, Abcam), Codanin-1 (17597-1-AP, Proteintech and H00146059-M01, Abnova). The antibodies for GFP (S268B) and C15ORF41 (S722D) were generated by the Division of Signal Transduction Therapy at the University of Dundee in sheep. Secondary HRP conjugated antibodies (anti-sheep #31480, anti-rabbit #31460 and anti-mouse #31430) were purchased from Pierce. Secondary fluorescent antibodies were used in Figure 2A and Figure 3: donkey anti-sheep Alexa-Fluor 680 #A21102 from Thermo Fischer and donkey Alexa-Fluor anti-rabbit 800 #926-32213 from LiCOR.
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4

Lineage Tracing with Rosa Reporter Mice

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For lineage tracing, RosaRFP reporter mice (https://www.jax.org/strain/007908) were used [43 (link)] and mated to Six3 HET and GnRHcre mice to create the Six3HET:RosaRFP:GnRHcre line. IHC was performed with the anti-RFP antibody (1:1000, Abcam, catalog number: ab62341, RRID: AB_945213).
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5

Immunostaining and Imaging of Mouse Spinal Cords

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Spinal cords were recovered and stained as previously described60 (link),75 (link). Following terminal anesthesia by pentobarbital, mice were perfused transcardially with 10% formalin (Sigma). Spinal cords and brains were removed, post-fixed overnight, transferred to buffered 30% sucrose for 48 h, embedded in O.C.T. Compound (Tissue-Tek, Sakura-Finetek/VWR) and cryostat-sectioned at 30 μm. Serial horizontal sections of spinal cord containing the lesion sites and brain containing the viral injection sites were cut and processed for immunostaining. The following primary antibodies were used: anti-GFAP (DAKO Z0334, 1:1000, free-floating), anti-GAP43 (1:1000, Benowitz lab), anti-Synaptophysin (Synaptic Systems 101004, 1:1000, free-floating), and RFP (1:500, Abcam ab62341, free-floating). BDA tracing was visualized with streptavidin-HRP (1:300, PerkinElmer SAT704A001EA) antibodies plus Cy3-TSA (1:200, PerkinElmer SAT704A001EA). Sections were cover-slipped using Prolong Diamond Antifade Mounting media with DAPI (ThermoFisher) to stain cell nuclei. Each section was imaged on ZEISS LSM 880.
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6

Tracking Leukocytes in Wound Beds

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During the preparation of PRP and PRF, high quantities of platelets and leucocytes are in the buffy coat or embedded in the fibrin clot after centrifugation. To determine whether these leucocytes remained in the wound beds until the end of study, we used DsRed-transgenic mini-pigs as blood donors [40 (link)], and then, the PRP, PRF and PP prepared from them were applied to the full-thickness wounds created on non-transgenic littermate recipients with the same blood type. Blood types were confirmed in advance by mixing donor and recipient blood, and in the absence of agglutination, blood types were concluded to be the same. Except for the source of blood, the other procedures are the same as described in the above methods. Skin biopsies of wound beds were obtained on day 14 post-wounding. After adequate fixation and paraffin embedding, histological slices were cut and subjected to immunofluorescence (IF) [48 (link)] and immunohistochemistry (IHC) [49 (link), 50 (link)] staining using rabbit anti-DsRed primary antibody (ab62341; Abcam, Eugene, CA, USA) and FITC-conjugated and peroxidase-conjugated secondary anti-rabbit antibodies (ab97063; Abcam, Eugene, CA, USA), respectively.
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7

Antibody Immunofluorescence and ChIP Assays

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The following antibodies were used for immunofluorescence assays: mouse anti-GFP (LGB-1; Abcam), rabbit anti-RFP (ab62341; Abcam); mouse anti-Fibrillarin (38F3; Abcam), mouse anti-HA (HA.11; Covance) and rabbit anti-Rep1 (custom made; directed to a synthetic Rep1 peptide) (31 (link)). A mouse anti-Myc antibody (9E10; Covance) was used in the chromatin immunoprecipitation (ChIP) assays. Antibody dilutions ranged from 1:100 to 1:500 in individual assays, in accordance with initial standardization.
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8

Immunofluorescence Staining of Frozen Tissue Sections

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The explants were embedded in Tissue-Tek O.C.T. compound (Sakura Finetek, Torrance, CA, USA), frozen in liquid nitrogen, and sagittally sectioned (10 μm in thickness). Immunofluorescence (IF) was performed as previously described56 (link)57 (link). Briefly, the sections were post-fixed in 4% PFA for 40 min, washed with phosphate buffer saline (PBS) and 3% glycine, permealized with 0.03% sodium dodecyl sulfate, blocked with 3% goat serum, and then incubated with a primary antibody of rabbit anti-RFP (1:100, ab62341, abcam, Cambridge, MA, USA) at 4 °C overnight. After washes with PBS, the sections were incubated with an Alexa 594-conjugated goat anti-rabbit secondary antibody (1:1000, ab150092, abcam, Cambridge, MA, USA) for 2 h at RT. Then the sections were thoroughly washed and mounted with the ProLong Gold Antifade with DAPI reagent (Life Technologies, Grand Island, NY, USA). The images were taken under a fluorescence microscope (BX51, Olympus Optical Co. Ltd., Tokyo, Japan) as described above.
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9

Immunofluorescent Staining of Cells and Tumors

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Immunofluorescent staining of cells and tumor sections was performed as previously described [70 (link), 71 (link)]. The primary antibodies, employed in this study, were raised against the following antigens: HIF-1α (ab51608; Abcam), FOXC2 (rat anti-mouse FOXC2 antibody, which also cross-reacts with human FOXC2; developed by Dr. Naoyuki Miura, Hamamatsu University School of Medicine, Japan), E-cadherin (61081; BD Biosciences, San Jose, CA, USA), vimentin (MA1-19319; Thermo Fisher Scientific, Asheville, NC, USA), CD31 (ab28364; Abcam), KDR (MA5-15556; Novus, Centennial, CO, USA), RFP (ab62341; Abcam), SV40 large-T antigen (sc-47; Santa Cruz Biotechnology Inc., Dallas, TX, USA). Fluorescently-labeled secondary antibodies were from Thermo Fisher Scientific.
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10

Immunohistochemical and Immunofluorescent Analyses

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For immunohistochemistry staining, formalin-fixed and paraffin-embedded tissue sections were incubated with primary antibodies against MTCO1 (ab14705, Abcam), CD68 (ab955, Abcam), or CD3 (ab16669, Abcam) and then analyzed using streptavidin peroxidase detection system (Maixin) according to the manufacturer’s protocol. Diaminobenzidine (DAB) (Maixin) was used as a horseradish peroxidase (HRP)–specific substrate. For immunofluorescence staining, formaldehyde-fixed cells or kidney sections were performed with primary antibodies against RFP (ab62341, Abcam), CD63 (sc5275, Santa Cruz Biotechnology), IL-10 (ab9969, Abcam), KIM-1 (MA5-28211, Invitrogen), CD68 (ab955, Abcam), iNOS (ab15323, Abcam), CD206 (ab64693, Abcam), and CD3 (ab16669, Abcam), followed by incubation with secondary antibodies. Cell nuclei were stained with DAPI. Immunostained samples were visualized under a confocal microscope (FV1000, Olympus).
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