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Nupage mops sds buffer

Manufactured by Thermo Fisher Scientific
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NuPAGE MOPS SDS buffer is a ready-to-use buffer solution designed for use in electrophoresis of proteins. It is compatible with the NuPAGE protein gel electrophoresis system.

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13 protocols using nupage mops sds buffer

1

CLIP-seq Sample Preparation and Analysis

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The IP samples were denatured 10 min at 70 °C and fractionated on 10% acrylamide Bis-Tris gel with NuPAGE MOPS-SDS buffer (Invitrogen). Protein–RNA complexes were transferred onto a nitrocellulose membrane with NuPAGE transfer buffer (Invitrogen) for 1 h, 30 V at room temperature. The region corresponding to N–RNA complex was excised. The RNA was eluted from the membrane by digesting the protein with proteinase K (Sigma, Saint Louis, MO, USA) in PK Buffer (4 mg/mL proteinase K, 200 mM Tris-HCl pH 7.5, 100 mM NaCl, 20 mM EDTA, and 2% SDS) for 30 min at 55 °C. RNAs were purified by phenol–chloroform extraction followed by ethanol precipitation. RNA concentration in each sample was determined by Qubit microRNA assay (Invitrogen). Size-matched samples, which are the stringent CLIP-seq controls recommended by the ENCODE project (https://www.encodeproject.org/ accessed 30 November 2021), were used in this study. These size-matched samples, which are not selected by IP of N, were prepared side-by-side with the IP samples (Figure 1A).
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2

Protein Extraction and Western Blot Analysis

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In order to obtain total protein extracts, cells were lysed using either Laemmli lysis buffer (4% SDS, 20% glycerol, 120 mM Tris-HCl, pH 6.8) or RIPA buffer (150 mM NaCl, 1.0% IGEPALâ CA-630, 0.5% sodium deoxycholate, 0.1% SDS, and 50 mM Tris-HCl, pH 8.0) supplemented with protease and phosphatase inhibitors and denatured for 10 min at 70 C. In order to prepare chromatin enriched protein fractions, cells were incubated with Pre-extraction Buffer (0.025 M HEPES-NaOH, pH 7.4, 0.05 M NaCl, 1 mM EDTA, 3 mM MgCl 2 , 0.3 M Sucrose, 0.5% Triton X-100) supplemented with protease inhibitors for 10 min on ice prior to lysis. Proteins were resolved by SDS-PAGE using NuPage 4-12% Bis-Tris 1 mm gel and NuPage MOPS SDS buffer (Invitrogen), at 200 V for 1 h. Proteins were transferred to PVDF membrane by semidry transfer for 1 h and 10 min at 65 mA. Membranes were blocked in 5% milk or BSA in TBS-0.1% Tween 20 for 30 min, and incubated with primary antibodies overnight at 4 C and secondary antibodies for 1 h at RT. Antibodies used are listed in the Key resources table. Primary antibodies were used at a dilution 1:1000 unless otherwise stated, while secondary antibodies were used at a dilution 1:5000. The signal was visualized with ECL substrate in an Amersham imager 600 (GE Healthcare).
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3

SDS-PAGE Protein Separation and Visualization

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NuPAGE® (6 μL) LDS sample buffer (Invitrogen, Thermo Fisher Scientific, UK) was added to a solution (20 μL) of the protein to be tested. The mixture was vortexed for 3–5 s and loaded onto a Novex® Bis-Tris 4–12% precast gel (Invitrogen, Thermo Fisher Scientific, UK) mounted in an electrophoresis tank. The pre-stained molecular weight standard (5 μL) was added to the first well. Running buffer (NuPAGE® MOPS SDS buffer diluted in distilled water, 1:20 v/v; Novex®, Life Technologies, UK) was added into the tank. A voltage of 200 V and current of 70 mA were applied and the experiment allowed to run for 50 min. The gel was removed, stained using Coomassie blue for 1 h, and then washed with distilled water for 1 h.
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4

Proteomic Analysis of Worm Embryos

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Samples were purified from worm embryos as above and eluted in 50 μl Laemmli buffer, of which 30μl was resolved by SDS-polyacrylamide gel electrophoresis (SDS-PAGE) using NuPAGE Novex 4-12% Midi Bis-Tris gels (NP0321, Life Technologies) with NuPAGE MOPS SDS buffer (NP000102, Life Technologies). Subsequently, gels were stained with ‘SimplyBlue SafeStrain’ colloidal Coomassie (LC6060, Invitrogen), and each lane was cut into 40 slices that were digested with trypsin before processing for mass spectrometry (MS Bioworks, USA). Data were analyzed using Scaffold software (Proteome Software Inc, USA).
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5

Evaluating Signaling Pathways in 3D Tumor-Stromal Interactions

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HT29 CSCs were 3D-cultured in Matrigel as described above for 4 days alone or in the presence of JUG-EGCs. Tumorspheres were then extracted from Matrigel using the Cell Recovery Solution (Corning) according to the manufacturer's protocol. JUG-EGCs were incubated for 3 days with or without TEC-CM (HT29 cell conditioned medium) in the presence or absence of CAY10526 (10 µM). Cells were lysed with 2X Laemmli buffer with 5% β-Mercaptoethanol heated to 60 °C. Samples were processed for electrophoresis using NuPAGE MOPS SDS buffer (Life Technologies) and separated on 4–12% or 12% Bis-Tris gels (Life Technologies). Proteins were transferred onto nitrocellulose membranes using the iBlot System (Life Technologies). After blocking, blots were incubated overnight at 4 °C with primary antibodies diluted in 1X TBS with 5% BSA and 0.1% Tween for ERK (1:500, Cell Signaling), pERK (1:500, Cell Signaling), EGFR (1:500, Cell Signaling), pEGFR (1:4000, Cell Signaling), mPGES-1 (1:200, Santa cruz), Cox2 (1:1000, Invitrogen) and GAPDH (1:1000, Cell Signaling). Immunoblots were probed with appropriate horseradish peroxidase-conjugated secondary antibodies for 1 h at room temperature (Thermo Scientific) and visualized by chemiluminescence (Clarity Western ECL Substrate; Bio-Rad) using a Gel-Doc imager and the Image Lab Software (Bio-Rad).
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6

Proteomic Analysis of Worm Embryos

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Samples were purified from worm embryos as above and eluted in 50 μl Laemmli buffer, of which 30μl was resolved by SDS-polyacrylamide gel electrophoresis (SDS-PAGE) using NuPAGE Novex 4-12% Midi Bis-Tris gels (NP0321, Life Technologies) with NuPAGE MOPS SDS buffer (NP000102, Life Technologies). Subsequently, gels were stained with ‘SimplyBlue SafeStrain’ colloidal Coomassie (LC6060, Invitrogen), and each lane was cut into 40 slices that were digested with trypsin before processing for mass spectrometry (MS Bioworks, USA). Data were analyzed using Scaffold software (Proteome Software Inc, USA).
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7

SDS-PAGE and Western Blotting Protocol

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Protein samples were resolved by SDS–polyacrylamide gel electrophoresis on NuPAGE Novex 4–12% Bis-Tris gels (NP0321 and WG1402A, ThermoFisher Scientific) with NuPAGE MOPS SDS buffer (NP0001, ThermoFisher Scientific), or NuPAGE Novex 3–8% Tris-Acetate gels (EA0375BOX and WG1602BOX, ThermoFisher Scientific) with NuPAGE Tris-Acetate SDS buffer (LA0041, ThermoFisher Scientific). Resolved proteins were either stained with colloidal Coomassie blue dye (‘Instant Blue’, Expedion), or were transferred onto a nitrocellulose iBlot membrane (Invitrogen) with the iBlot Dry Transfer System (Invitrogen).
Antibodies used for protein detection in this study are described in Appendix 1-key resources table. Conjugates to horseradish peroxidase of anti-sheep IgG from donkey (Sigma, A3415), anti-rabbit IgG from donkey (GE Healthcare, NA934), or anti-goat IgG from rabbit (Sigma, A5420) were used as secondary antibodies before the detection of chemoluminescent signals on Hyperfilm ECL (Amersham, GE Healthcare) using ECL Western Blotting Detection Reagent (GE Healthcare).
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8

Antibody Production and Validation

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New antibodies produced in this study are listed in Appendix Table S1 and validated in Figs 3B, 5C, EV2C, and EV4E and Appendix Fig S3. Protein samples were resolved on NuPAGE Novex 4–12% Midi Bis‐Tris gels (NP0301, Thermo Fisher) with NuPAGE MOPS SDS buffer (NP000102, Thermo Fisher). The resolved proteins were transferred onto a nitrocellulose membrane (IB301031, Thermo Fisher) using the iBlot Dry Transfer System (Thermo Fisher).
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9

SDS-PAGE and Western Blotting Protocol

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Protein samples were resolved by SDS–PAGE using the following systems: NuPAGE Novex 4 - 12% Bis-Tris gels (NP0321 and WG1402A, ThermoFisher Scientific) with NuPAGE MOPS SDS buffer (NP0001, ThermoFisher Scientific) or NuPAGE MES SDS buffer (NP0002, ThermoFisher Scientific); NuPAGE Novex 3 - 8% Tris-Acetate gels (EA0375BOX and WG1602BOX, ThermoFisher Scientific) with NuPAGE Tris-Acetate SDS buffer (LA0041, ThermoFisher Scientific). The resolved proteins were either stained with colloidal Coomassie blue dye (‘Instant Blue’, ab119211, Abcam), or else were transferred onto a nitrocellulose iBlot2 membrane (2NR290123-01, ThermoFisher Scientific) with the iBlot2 Dry Transfer System (IB21001, Invitrogen), according to the manufacturer’s instructions.
The antibodies used for immunoblotting in this study are described in Table S5. Chemoluminescent signals were detected by azure-biosystems 300Q with ECL Western Blotting Detection Reagent (17039552, GE Healthcare).
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10

SDS-PAGE and Western Blot Protein Analysis

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Protein samples were resolved by SDS–PAGE using the following systems: NuPAGE Novex 4 ‐ 12% Bis‐Tris gels (NP0321 and WG1402A, Thermo Fisher Scientific) with NuPAGE MOPS SDS buffer (NP0001, Thermo Fisher Scientific) or NuPAGE MES SDS buffer (NP0002, Thermo Fisher Scientific); NuPAGE Novex 3 ‐ 8% Tris‐Acetate gels (EA0375BOX and WG1602BOX, Thermo Fisher Scientific) with NuPAGE Tris‐Acetate SDS buffer (LA0041, Thermo Fisher Scientific). The resolved proteins were either stained with colloidal Coomassie blue dye (“Instant Blue”, ab119211, Abcam), or else transferred onto a nitrocellulose iBlot membrane (NRO11020‐01, Thermo Fisher Scientific) with the iBlot Dry Transfer System (IB1001, Invitrogen), according to the manufacturer’s instructions.
The antibodies used for immunoblotting in this study are described in Appendix Table S1. Chemiluminescent signals were detected on Hyperfilm ECL (Amersham, 66601, GE Healthcare) using ECL Western Blotting Detection Reagent (17039552, GE Healthcare). New antibodies that were generated in this study are validated in Appendix Fig S4.
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