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6 protocols using ab14404

1

Immunostaining for Telomere-associated Proteins

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For immunostaining of RAP1, TRF1, TRF2 together with lamin B1, cells grown on coverslips, 24 or 48 h after transfection, were pretreated with extraction buffer (50 mM Tris–HCl, 150 mM NaCl, 1% Trition-X100, 1 mM NaF, 1 mM Na3VO4, 1 mM PMSF, as described in (64 (link)), 2 min on ice before fixation in 2% PFA (10 min)). For single staining with lamin B1, cells were directly fixed in 4% PFA or in ice-cold 100% methanol (10 min). Then, cells were saturated in PBS with 2% BSA-0.05% Tween and stained for 1 h with primary antibodies (mouse anti-TRF1 (Sigma T1348), mouse anti-RAP1 (ab14404, Abcam), mouse anti-TRF2 (Imgenex 124A or Santa Cruz B5) and rabbit anti-lamin B1(ab16048, Abcam), then washed and incubated 1 h with the secondary antibodies (alexa fluor-488 (Life Technologies) or mouse primary antibody and alexa fluor -594 (Life Technologies) for rabbit primary antibody). Nuclei were then counterstained with DAPI and slides were mounted with fluoromount mounting medium (Southern Biotech). Images were acquired on epifluorescence microscope leica DM5500B using a 63×-oil objective and analyzed with ImageJ software.
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2

Proximity Ligation Assay for Telomere-Associated Proteins

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Cells grown on coverslips were fixed in methanol for 10 min, blocked and stained as described above for immunostaining with the following primary antibodies couples: mouse anti-TRF2 (Imgenex 124A) with rabbit anti-lamin B1 (ab16048, Abcam) or mouse anti-RAP1 (ab14404, Abcam) with rabbit anti-lamin B1 (ab16048, Abcam) or mouse anti-HA (HA.11, Biolegend) with rabbit anti-lamin B1 (ab16048, Abcam) or mouse anti-GFP (ab1218, Abcam) with rabbit anti-lamin B1 (ab16048, Abcam) or rabbit anti-Flag (F7425, Sigma) with mouse anti-TRF2 (Santacruz B-5). PLA was performed using the Duolink in situ detection Kit (Sigma) according to the manufacturer's protocol. For some experiments, when indicated in figure legends, PLA was coupled with immunostaining of lamin B1 to detect lamin B1-positive cells. For experiments with Flag-lamin B1 constructs or with HA-TRF2-Linker, anti-Flag and anti-HA antibodies, were used to detect Flag or HA expression intensity, respectively. Digital images were acquired with the SPE confocal microscope using a 63×-objective lens. Images were processed with ImageJ software.
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3

Immunoprecipitation and Western Blot Analysis

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Cells were lysed with NP-40 (GenDEPOT #N1200-050) plus protease inhibitor and phosphatase inhibitor by sonication (Diagenode). Protein levels were measured with a DC protein assay. Each sample with 1000 μg in 500 μl was precleared using 40 μl protein A/G PLUS agarose (Santa Cruz, sc-2003) and incubated for 30 min with gentle agitation. Using a magnetic stand, the samples were cleared from the beads and the supernatant were transferred to a new tube and incubated with 2–5 μg of antibody per sample and incubated overnight at 4°C rotating. The next day, 50 μL of agarose beads were added to each sample and incubated for 2 h at 4°C with gentle agitation. The beads were washed with NP-40 three times for 5 min each. The samples were eluted in a sample buffer for western blot analysis. The following primary antibodies were used for immunoprecipitation (IP): anti-mouse IgG (Abcam #ab37355), anti-rabbit IgG (Abcam #ab172730), RAP1 (Abcam #ab14404), γH2A (Abcam #ab81299), and lamin A/C (Abcam #ab108595).
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4

Protein Expression Analysis of Fibrosis Markers

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The protein levels of α-SMA, COL1A1, Smad2, p-Smad2, PED7A, PED4A, PKA, p-PKA, total Ras-proximate-1 (Rap1), Guanosine-5′-triphosphate (GTP)-Rap1, and exchange protein directly activated by cAMP 1 (Epac1), cAMP-response element-binding protein (CREB) and p-CREB were examined by immunoblotting following the methods described before (Liu et al., 2018 (link)) using the antibodies listed below: anti-α-SMA (ab5694, Abcam), anti-COL1A1 (ab34710, Abcam), anti-Smad2 (ab40855, Abcam), anti-p-Smad2 (ab53100, Abcam), anti-PDE4A (ab14607, Abcam), anti-PDE4B (ab170939, Abcam), anti-PDE4C (ab170939, Abcam), anti-PDE4D (ab171750, Abcam), anti-PKA (BS-0520R, Woburn, MA, United States), p-PKA (ab75991, Abcam), anti-GTP-Rap1 (ab32373, Abcam), anti-Rap1 (ab14404, Abcam), anti-Epac1 (ab109415, Abcam), anti-CREB (ab31387, Abcam), anti-p-CREB (ab32096, Abcam), and anti-Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) (ab8245, Abcam) and then with HRP-conjugated secondary antibody. Enhanced chemilumescent (ECL) substrates (Millipore, MA, United States) were used for signals visualization using GAPDH as an endogenous protein for normalization.
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5

Protein Interaction Analysis by Immunoprecipitation

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The interaction of LRPAP1, LRP1 and IFNAR1 was examined by immunoprecipitation using a protocol described as followed. HEK293T cells were cultured at around 90% confluence in a 100 mm tissue culture dish. Cells were washed with 10 ml of PBS and harvested in 0.5 ml of ice-cold lysis buffer (0.15 mM NaCl, 0.05 mM tris-HCl, pH 7.4, 1% SDS, 1% NP-40) and Protease Cocktail (Roche) and PhoSTOP (Roche). The total extract was pre-cleared with 10 μg normal rabbit IgG (Cell signaling, 2729 S) and 20 μl of protein A/G plus-agarose (Santa Cruz Biotechnology) at 4 °C on a rotor for 1 h. After gently removed protein A/G agarose beads by centrifugation at 500 rcf for 2 min, 0.2 mg of total extract was immunoprecipitated with the indicated antibodies overnight at 4 °C on a rotor. Approximately 20 μl of protein A/G plus-agarose (Santa Cruz Biotechnology) was added at 4 °C for one hour. Then, the beads were washed three times with washing buffer (lysis buffer contained 0.1% NP-40). The pellet was suspended with 40 μl PBS and 10 μl of 5× SDS-PAGE loading buffer and the samples were boiled for 10 min. The supernatant was collected and 20 μg of lysate was loaded onto 10% acrylamide gene electrophoresis and immunoblotting was performed using antibodies against IFNAR1 (Abcam, ab45172), LRP1 (Abcam, ab92544), LRPAP1 (Abcam, ab14404) as described before.
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6

Western Blot Analysis of Cellular Proteins

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For Western blotting analysis, the primary anti-rabbit anti-human RAP1 (1RV 1000, ab14404), SRC (1RV 30000 ab179473 ab109381) and ITGB3 (1RV 1000 ab179473) were all obtained from Abcam, as described above.
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