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14 protocols using ab5706

1

Protein Expression Analysis in Tumor Cells

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Proteins were extracted from cultured cells, and tumor tissues of tumor-bearing mice using, respectively, 0.1 ml and 1.0 ml radioimmunoprecipitation assay reagent containing 1% phenylmethanesulfonyl fluoride to prevent protein degradation. Protein extracts were subjected to SDS-PAGE and analyzed using the following primary antibodies: TGF-β1, Smad2/3 (sc-398844, Santa Cruz Biotechnologies), P-smad2/3, E-cadherin (ab1416, Abcam), N-cadherin (ab6528, Abcam), cytokeratin (CK) (ab9377, Abcam), β-catenin (ab32572, Abcam), α-SMA (ab124964, Abcam), MMP-7 (ab5706, Abcam), and β-actin (TA-09; ZSGB-BIO, Beijing China). After that, the membranes were incubated with secondary antibodies at 4°C overnight, washed in PBST thrice for 10 min each time, and incubated with the corresponding secondary antibody. The dilution ratio was determined as recommended. Protein levels were measured using the Image-Pro Plus system version 6.0. Band intensity was quantified using the ImageJ software version 1.34. All experiments were performed in triplicate.
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2

Protein Expression Analysis in Cancer Cells

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LoVo or SW1116 cells were lysed on ice with the lysis buffer (Beyotime, Shanghai, China) and the lysates were later centrifuged for 15 min at 12,000 × g. The BCA kit (Thermo Fisher Scientific, Waltham, MA, USA) was acquired for evaluating protein concentrations. Protein was subjected to SDS–PAGE (Bio-Rad, Hercules, CA, USA) and transferred to PVDF membranes (Millipore, Billerica, MA, USA). Primary antibodies and secondary antibodies were applied to incubate membranes in sequence. ECL detection system (Applied Biosystems, Foster City, CA, USA) was utilized to visualize protein bands. Primary antibodies against MMP2 (ab97779, Abcam, Cambridge, MA, USA), MMP7 (ab5706, Abcam), N-cadherin (ab76057, Abcam), E-cadherin (ab40772, Abcam), NANOG (ab80892, Abcam), OCT4 (ab181557, Abcam), Gli4 (AV37797, Sigma-Aldrich), PTCH1 (ab53715, Abcam), Shh (ab53281, Abcam), Gli1 (ab49314, Abcam), Gli2 (ab167389, Abcam), and GAPDH (ab9484, Abcam) were used, individually.
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3

Intestinal Organoid MMP7 Characterization

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Small intestinal organoids were cultured for 6 days and removed from
Matrigel using Cell Dissociation Solution as above. Cell lysates were prepared
in RIPA buffer (50 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, 1% NP-40,
0.5% deoxycholate, 0.1% sodium dodecyl sulfate) with protease
inhibitors. After separation by SDS-PAGE, immunoblots were probed for MMP7
(ab5706, Abcam) or GAPDH (sc-32233, Santa Cruz) and visualized with
chemiluminescence. To generate rMMP7, the Mmp7 gene was cloned
into a pET27 vector with a C-terminal Strep tag. Upon expression in E. coli
strain BL21, rMMP7 was purified from solubilized inclusion bodies by affinity
chromatography using StrepTactin Sepharose (IBA GmbH).
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4

Macrophage Extracellular Trap Visualization

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Cocultures were completed and macrophages were fixed as described above. Coverslips were washed once with PBS prior to staining with SYTOX Green (final concentration, 10 μM) (ThermoFisher) for double-stranded DNA (dsDNA), and Hoechst 33342 (final concentration, 5 μM ) (ThermoFisher) for condensed chromatin (nuclei). Additional staining for histones and MMPs was accomplished by blocking cells in 1% bovine serum albumin in PBS for 30 min at 37°C followed by a 1-h incubation at 37°C with antibodies for histone H3 (ab5103; Abcam, Cambridge, MA), neutrophil elastase (ab68672; Abcam), myeloperoxidase (ab9535; Abcam), matrix metalloproteinase 1 (MMP-1) (ab551168; Abcam), MMP-7 (ab5706; Abcam), MMP-8 (ab81286; Abcam), MMP-9 (ab38898; Abcam), or MMP-12 (ab137444; Abcam). Cells were then washed three times with 1% BSA in PBS, followed by a 30-min incubation with an Alexa Fluor 594-conjugated goat anti-rabbit secondary antibody (ThermoFisher) and two additional washes with 1% BSA in PBS prior to mounting coverslips onto glass microscope slides with Aqua Poly/Mount (Polysciences Inc., Warrington, PA). Macrophages were visualized with a Zeiss LSM 710 META inverted laser scanning confocal microscope, and extracellular traps were identified by dsDNA staining that extended into the extracellular environment.
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5

Mdivi-1 Inhibits Mitochondrial Division

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The commercially available mitochondrial division inhibitor, Mdivi-1, was from Sigma-Aldrich (Saint-Louis, MO, USA) and utilized for treating SK-HEP-1 and Huh7 cells, with DMSO (Sigma-Aldrich) as the control group. Translation inhibitor cycloheximide chase was also from Sigma-Aldrich for assessing protein stability. The primary antibodies against cleaved (c)-caspase-3 (ab2302, Abcam), total (t)-caspase-3 (ab13847, Abcam), c-caspase-6 (ab2326, Abcam), t-caspase-6 (ab185645, Abcam), Bax (ab32503, Abcam), Bcl-2 (ab32124, Abcam), E-cadherin (ab40772, Abcam), N-cadherin (ab76057, Abcam), MMP2 (ab37150, Abcam), MMP7 (ab5706, Abcam), DRP1 (ab184247, Abcam), PDI1 (ab4644, Abcam), CDK1 (ab18, Abcam), H-RAS (G12V) (ab140571, Abcam), LZTR1 (ab106655, Abcam), c-Myb (ab109127, Abcam), and GAPDH (ab245356, Abcam), as well as secondary antibodies were all obtained from Abcam (Cambridge, MA, USA). Antibodies against p-DRP1 (S616) (#3455S, Cell Signaling Technology, Danvers, MA, USA), p-ERK1/2 (#4370S, Cell Signaling Technology), and ERK1/2 (#4695S, Cell Signaling Technology) were obtained from Cell Signaling Technology (Danvers, MA, USA).
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6

Protein Expression Profiling of Cancer Markers

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The cell protein samples were extracted in 6-well plates using RIPA lysis buffer with protease inhibitor, then quantitated by BCA kit (Thermo Fisher Scientific), diluted in loading buffer to the same concentration, denatured at 95°C. Then, 20 μg proteins was subjected to SDS-PAGE for 2h and then transferred to PVDF membranes. After being blocked with skim milk, the membranes were co-cultured with primary antibodies against anti-KCNC4 (ab93605, Cambridge, Abcam), anti-MMP2 (ab37150, Abcam), anti-MMP7 (ab5706, Abcam), anti-MMP9 (ab38898, Abcam), anti-Slug (ab27568, Abcam), anti-Twist (ab50887, Abcam) and anti-GAPDH (ab8245, Abcam). Chemiluminescence detection system (GE Healthcare, Chicago, IL, USA) was employed to measure the protein.
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7

Western Blot Analysis of Protein Markers

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Total proteins were extracted through a Total Protein Extraction Kit (KeyGen Biotech, Nanjing, China). Concentrations of protein were examined under BCA commercial kit (KeyGen). Proteins were separated using SDS-PAGE and then moved onto PVDF membranes (Millipore, Carlsbad, USA). Membranes were sealed in non-fat milk and then incubated with given primary antibodies: anti-MMP2 (1:1000, ab37150, Abcam, Cambridge, USA), anti-MMP7 (1:1000, ab5706, Abcam), anti-Bcl-2 (1:1000, ab32124, Abcam), anti-bax (1:1000, ab32503, Abcam), anti-caspase 3 (1:1000, ab13847, Abcam), anti-cleaved caspase-3 (1:1000, ab2302, Abcam), anti-caspase 8 (1:1000, ab25901, Abcam), anti-cleaved caspase-8 (1:1000, ab25901, Abcam), anti-caspase 9 (1:1000, ab32539, Abcam), anti-cleaved caspase-9 (1:1000, ab2324, Abcam), anti-E-cadherin (1:1000, ab15148, Abcam), anti-N-cadherin (1:1000, ab76057, Abcam) and anti-GAPDH (1:1000, ab8245, Abcam). GAPDH was used as a measurement control for other proteins. Moreover, the membranes were co-cultured with goat anti-mouse IgG H&L (Cy3®) preadsorbed (1:2000, ab97035, Abcam) secondary antibodies for 1 h darkness. Chemiluminescence system (Invitrogen) was employed to observe the protein bands.
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8

Intestinal Organoid MMP7 Characterization

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Small intestinal organoids were cultured for 6 days and removed from
Matrigel using Cell Dissociation Solution as above. Cell lysates were prepared
in RIPA buffer (50 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, 1% NP-40,
0.5% deoxycholate, 0.1% sodium dodecyl sulfate) with protease
inhibitors. After separation by SDS-PAGE, immunoblots were probed for MMP7
(ab5706, Abcam) or GAPDH (sc-32233, Santa Cruz) and visualized with
chemiluminescence. To generate rMMP7, the Mmp7 gene was cloned
into a pET27 vector with a C-terminal Strep tag. Upon expression in E. coli
strain BL21, rMMP7 was purified from solubilized inclusion bodies by affinity
chromatography using StrepTactin Sepharose (IBA GmbH).
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9

Protein Extraction and Western Blot Analysis

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RIPA buffer (Beyotime, Shanghai, China) was applied to extract protein from transfected Saos-2 or HOS cells. The protein concentration was quantified by BCA kit (Beyotime). Proteins in same amount were loaded on 10% SDS–PAGE gel (Bio-Rad) and shifted to PVDF membranes (Millipore, Bedford, MA, U.S.A.). Following incubation for 1 h in a closed buffer, blots were incubated with primary antibodies against MMP2 (ab97779, Abcam, Cambridge, MA, U.S.A.), MMP7 (ab5706, Abcam), MMP9 (ab38898, Abcam), E-cadherin (ab76319, Abcam), N-cadherin (ab18203, Abcam), Vimentin (ab92547, Abcam), FUS (ab70381, Abcam), LDHB (ab75167, Abcam), and GAPDH (ab9485, Abcam). Later, secondary antibodies were added and the ECL PLUS/KIT (GE Healthcare, Milwaukee, WI, U.S.A.) was applied for chemiluminescence detection.
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10

Investigating Wnt Signaling Pathway

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RPMI 1640 and fetal bovine serum (FBS) were purchased from Gibco (Grand Island, NY, USA). Antibodies against DKK1 (ab109416), β-catenin (ab32572) and MMP7 (ab5706) were purchased from Abcam (Cambridge, MA, USA). β-actin antibody (sc-47778), goat anti-rabbit IgG-HRP (sc-2004) and goat anti-mouse IgG-HRP (sc-2005) were purchased from Santa Cruz Biotechnology, Inc. (Dallas, TX, USA). MMP7 siRNA (sc-41553) was obtained from Santa Cruz Biotechnology (Santa Cruz, CA, USA).
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