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116 protocols using a31572

1

Renal Subcapsular Graft Cryosection Immunostaining

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Slides containing renal subcapsular graft cryosections were blocked (10% horse serum and 0.1% Triton X-100 in PBS) at room temperature for 1 h and stained with anti-collagen I (Abcam, ab34710, 1:500) and anti-collagen II (Abcam, ab185430, 1:500) antibodies at 4 °C overnight. After washing in PBS (3 × 10 min), anti-Rabbit Alexa Fluor 555 (Invitrogen, A31572, 1:500) and anti-Mouse Alexa Fluor 647 (Invitrogen, A31571, 1:500) secondary antibodies were incubated for 1 h at room temperature. After washing in PBS (3 × 10 min), slides were mounted with ProLong™ Gold Antifade Mountant with DAPI (Invitrogen, P36931). For long bone and calvarial staining, the following antibodies were used: anti-PDPN (eBioscience, 17-9381-41, 1:50), anti-CADM1 (abcam, ab3910, 1:100), anti-FOXP1 (Sigma-Aldrich, ABE68, 1:100), anti-FOXP2 (Abcam, ab16046, 1:200), anti-Rabbit Alexa Fluor 555 (Invitrogen, A31572,1:500) and anti-Rat Alexa Fluor 647 (Invitrogen, A21472, 1:500). Images were acquired with Olympus fluorescence inverted microscope (IX73) and analyzed by ImageJ software.
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2

Nuclear Localization Analysis of STAT1, PARP9, and DTX3L

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For analysis of nuclear localization, U3A-STAT1-PARP9-DTX3L cells were treated with leptomycin B56 (link) and IFN-β, then were fixed for 8 min at −20 °C with methanol and then incubated with mouse antibody to STAT1 (1:100 dilution; 1; BD Biosciences) and Alexa Fluor 488–labeled donkey anti-mouse (A-21202; Thermo Fisher Scientific), rabbit anti-PARP9 (40-4400; Thermo Fisher Scientific) and Alexa Fluor 647–labeled goat anti-rabbit (A-21246; Thermo Fisher Scientific), or rabbit anti-DTX3L (A300-834A; Bethyl) labeled with Alexa Fluor 555–labeled donkey anti-rabbit (A-31572; Thermo Fisher Scientific) and then with DAPI. For experiments on the co-localization of EMCV 3C and DTX3L, U3A-STAT1-PARP9M-DTX3LM cells were fixed and then were incubated with rabbit antibody to EMCV 3C (ref. 45 (link)) and Alexa Fluor 555–labeled donkey anti-rabbit (A-31572; Thermo Fisher Scientific) and with goat anti-DTX3L (sc-102496; Santa Cruz) and Alexa Fluor 633–labeled donkey anti-goat (A-21082; Thermo Fisher Scientific), and with mouse anti-STAT1 (1; BD Biosciences) and Alexa Fluor 488–labeled donkey anti-mouse (identified above), and then with DAPI. Cells were imaged using a Zeiss LSM 750 confocal microscope.
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3

Neddylation Pathway Transfection Assay

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Transfection was performed using Lipofectamine 2000 (Invitrogen, 11668-019) following the manufacturer’s protocol by combining reagent (µL) with DNA (µg) at a 2:1 ratio. DMSO was purchased from Sigma-Aldrich (D2650). MLN4924 was purchased from Active Biochemicals (A-1139).
Antibodies rabbit anti-CUL1 (ab75812), rabbit anti-CUL3 (ab194584), rabbit anti-NEDD8 (ab81264), and rabbit anti-CSN4 (ab12322) were purchased from Abcam. Donkey anti-rabbit secondary antibodies conjugated to Alexa Fluor 488, 555, or 647 were purchased from Invitrogen (A-21206, A-31572 and A-31573, respectively).
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4

Immunohistochemical Analysis of Activated Notch1, Microglia, and Neurons

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Four-micron-thick brain coronal sections were prepared as described earlier, deparaffinized in xylene, rehydrated via alcohol gradients, and washed with PBS (0.01 M, pH 7.4). Following antigen retrieval, the sections were blocked in 5% bovine serum albumin for 30 min at room temperature (RT) and incubated with primary antibodies as follows: rabbit anti-activated Notch1 (1:200; Ab52301, Abcam, Cambridge, UK); goat anti-Iba1 (1:300; Ab5076, Abcam); mouse anti-CD68 (1:200; Ab31630, Abcam); rabbit anti-NeuN (1:200, 24307T, Cell Signaling Technology, Danvers MA, USA) overnight at 4 °C. The next day, the slices were washed with PBS and incubated with secondary antibodies: donkey anti-goat Alexa 488 (1:500; A11055, Invitrogen), donkey anti-rabbit Alexa 555 (1:500; A31572, Invitrogen), donkey anti-mouse Alexa 488 (1:500; A21202, Invitrogen), donkey anti-goat Alexa 555 (1:500; A21432, Invitrogen), goat anti-mouse Alexa 555 (1:500; A21422, Invitrogen), and donkey anti-rabbit Alexa 488 (1:500; A21206, Invitrogen) for 1 h at RT. After washing with PBS three times, the sections were stained by 4′6-diamidino-2-phenylindole for 10 min at room temperature and observed under a fluorescence microscope (Leica-DMI8, Leica Microsystems, Wetzlar, Germany).
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5

Immunofluorescence Staining of Ovarian Tissue

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Immunostaining was performed according to previously described protocols (60 (link)). Briefly, the collected ovaries were fixed with 4% (w/v) PFA for 12 to 24 hours, dehydrated, embedded in paraffin, and cut into 8-μm sections. After deparaffinizing and gradually hydrating the sections, they were put into 0.01% sodium citrate buffer (pH 6.0) and then subjected to microwave antigen retrieval for 16 min. The sections were blocked with 10% donkey serum (Jackson ImmunoResearch) at room temperature for 1 hour, and then the tissue sections were incubated with primary antibodies overnight at 4°C. Next, the sections were thoroughly washed in PBS, incubated with the secondary antibody at room temperature for 1 hour, then stained with Hoechst 33342 (B2261, Sigma-Aldrich) for 1 min. The main primary antibodies used in immunofluorescence are as follows: goat anti-FOXL2 (1:300 dilution; IMG-3228, Novus Biologicals) and DDX4 (1:300 dilution; ab27591, Abcam). Second antibody dilution: donkey anti-goat Alexa Fluor 488 (1:150 dilution; A11055, Invitrogen) and donkey anti-rabbit Alexa Fluor 555 (1:150 dilution; A31572, Invitrogen). Images were acquired on a Nikon Eclipse Ti digital fluorescence microscope, Leica (DMi8), or Andor Dragonfly spinning-disc confocal microscope. The image data were analyzed by the software ImageJ. Image merging was by using the color-merge channels function in ImageJ.
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6

Immunohistochemistry of Neurotransmitter Markers

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The primary antibodies used for immunohistochemistry were as follows: mouse anti-PV (1:1,000, 235, Swant), rabbit anti-SST (1:2,000, T-4103, Peninsula), mouse anti-RELN (1:1,000, MAB5364, Millipore), rabbit anti-VIP (1:500, 20077, Immunostar), goat anti-SATB1 (1:100, sc5889, Santa Cruz), anti-RFP (1:500, 600–401-379, Rockland), and rat anti-BrdU (1:500, OBT0030G, Accurate Chemicals). The secondary antibodies used for immunohistochemistry, all raised in donkey and used at 1:2,000 dilution, were as follows: anti-mouse Alexa Fluor 488 (A21202, Invitrogen), anti-mouse Alexa Fluor 555 (A31571, Invitrogen), anti-rabbit Alexa Fluor 555 (A31572, Invitrogen), anti-goat Alexa Fluor 488 (A11055, Invitrogen), anti-rat Alexa Fluor 647 (712–606-153, Jackson Immunoresearch), and anti-rat Alexa Fluor 488 (A21208, Invitrogen).
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7

Immunofluorescence Protein Detection

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The primary protein antibodies to GAPDH (goat pAb; SAB2500450, Sigma), β-tubulin (rabbit pAb; ab6046, Abcam), α-Actinin (rabbit mAb, 6487S, Cell Signaling Technology), ER-α (rabbit mAb; RM9101S, Thermo Fisher Scientific), and mTOR (rabbit,2983S, Cell Signaling Technologies) were used. Secondary antibodies to goat IgG prelabelled with Alexa Fluor 647 (A21447), rabbit IgG pre-labelled with Alexa Fluor 555 or 647 (A31572 and A31573) were purchased from Invitrogen. All primary antibodies were used at a 1:10 dilution in 2% TBST/BSA from stock concentrations and incubated for 2 hours at room temperature, except for anti-GAPDH and anti-ER-α, which were incubated for 3 hours at room temperature. Secondary antibodies were diluted to a 1:20 working concentration in 2% TBST/BSA from stock and incubated for 1 hour at room temperature, protected from light.
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8

Podocyte Identification Protocol

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Previously reported protocols were applied (5 (link), 6 (link)). To identify podocytes, we used a combination of WT1 (Agilent Technologies; IS05530-2) and DACH1 (Sigma-Aldrich; HPA012672) (32 (link)) as primary antibodies; Alexa-Fluor 488, -555, and/or -647 as secondary antibodies (Invitrogen; A21202, A31572, A31571, and A31573, respectively) depending on the experiment; and a DNA marker to identify single nuclei — either DAPI (Sigma-Aldrich; D9542) or DRAQ5 (Abcam; ab108410). Optical images were obtained using inverted laser confocal microscopes (Nikon and LSM800, Zeiss), stored in 1024 × 1024 pixel frames. Each image contained 1 glomerulus.
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9

Immunofluorescence Staining of VDR and Collagen I

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HSFs were fixed in freshly prepared 4% paraformaldehyde for 30 minutes at 4°C and washed three times in PBS for 5 minutes with a 0.1 M PBS blocking solution containing 6% normal donkey serum, 1% bovine serum albumin, and 0.3% Triton X-100 that was applied for 2 hours at room temperature to block nonspecific binding. Primary antibodies against VDR (1:100, 12550; Cell Signaling Technology, Danvers, MA, USA) and Collagen I (1:400, ab88147; Abcam, Cambridge, MA, USA) were diluted in the dilution buffer (containing 3% normal donkey serum, 0.5% bovine serum albumin, and 0.3% Triton X-100 in 0.1 M PBS), which covered the sections during overnight incubation at 4°C. After washing the sections three times with PBS for 5 minutes each, they were incubated with secondary antibodies for 2 hours at room temperature with either donkey anti-rat IgG (H+L) conjugated to Alexa Fluor 488 (1:400, A-21208; Invitrogen) or donkey anti-rabbit IgG (H+L) conjugated to Alexa Fluor 555 (1:400, A-31572; Invitrogen). The secondary antibodies were diluted in the same solution as the primary antibody. Finally, cell nuclei were stained with 4′,6-diamidino-2-phenylindole (Vector Laboratories, Burlingame, CA, USA). The images were captured with a Zeiss LSM 880 confocal microscope (ZEISS, Göttingen, Germany) under a ×20 magnification objective.
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10

Whole-mount antibody staining of fish

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The experiment was performed as previously described (Xu et al., 2015 (link)). In brief, fishes were fixed in 4% PFA at 4°C for 1–2 days. After washing, the fish were either directly subjected to whole-mount antibody staining (for 4 dpf fish) or dissection (for adult fish). The adult skin and other tissues were applied to whole-mount antibody staining as previously described (Barresi et al., 2000 (link); Jin et al., 2006 (link)). The primary antibodies included anti-GFP antibody (ab6658, Abcam), anti-DsRedx antibody (632496, Clontech), and anti-Lcp1 antibody (Jin et al., 2009 (link)). The secondary antibodies were Alexa 488-anti-goat antibody (A11055 Invitrogen) and Alexa 555-anti-rabbit antibody (A31572 Invitrogen). Images were taken under Leica SP8, Zeiss LSM710, or Zeiss LSM880 confocal microscope. The quantification was performed manually.
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