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Nupage sample reducing agent

Manufactured by Thermo Fisher Scientific
Sourced in United States, United Kingdom

The NuPAGE Sample Reducing Agent is a laboratory reagent used to prepare protein samples for electrophoresis. It functions by reducing disulfide bonds in proteins, which helps to denature and unfold the protein structure. This facilitates more accurate separation and analysis of the individual protein components within the sample.

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249 protocols using nupage sample reducing agent

1

Extraction and Analysis of Nuclear Proteins from Drosophila Embryos and S2 Cells

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Embryos (12–24 h) from BioTAP-N Br140 transgenic flies were collected and dechorionated by immersion in 50% bleach for 3 min, rinsed with distilled water, and dried. Embryos (0.2 g) were suspended in 150 µL of nuclear extraction buffer (10% sucrose, 20 mM HEPES at pH 7.6, 10 mM NaCl, 3mM MgCl2, 0.1% Triton X-100) supplemented with 0.1 mM PMSF in a 1.5-mL tube and homogenized on ice with a motorized pestle. Nuclear extraction buffer was added up to 1 mL, and the lysate was centrifuged at 2000g for 5 min at 4°C. The nuclear pellet was resuspended in 150 µL of nuclear extraction buffer, and homogenization and centrifugation steps were repeated. The final crude nuclear pellet was resuspended in 600 µL of Novex Tris-glycine SDS sample buffer (Invitrogen), including NuPAGE sample-reducing agent (Invitrogen), and then boiled for 10 min. For S2 cells, ∼5 × 106 cells expressing BioTAP transgenes were harvested; washed with PBS; lysed with 200 μL of Novex Tris-glycine SDS sample buffer (Invitrogen), including NuPAGE sample-reducing agent (Invitrogen); and then boiled for 10 min.
Twenty microliters was used for each Western blot. PAP antibody (1:1000; Sigma, P1291) diluted in TBST + 5% milk was used to detect the Protein A epitope of the BioTAP tag, and Clarity Western ECL substrate (Bio-Rad) was used for detection.
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2

Protein Aggregates Removal and Detection

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Full medium and RPMI-1640 (without FBS) were centrifuged at 20,000× g for 40 min at 4 °C to remove any pre-existing protein aggregates. Then 5 μl of r8-PNA (200 μM) or 5 μl of r8-PNA (200 μM) plus 20 μl of enhancer (r8-PNAmm) (200 μM) were added to 1000 μl of pre-centrifuged cell medium (with and without FBS). Samples were incubated at 37 °C for one hour, and then centrifuged at 20,000× g for 40 min at 4 °C. The supernatant was removed from each tube and 1000 μl PBS was added to each as a washing step followed by centrifugation at 20,000× g for 40 min at 4 °C. After three washing steps, 13 μl water, 5 μl protein-loading buffer (NuPAGE LDS Sample Buffer, Thermofisher Scientific, Roskilde, Denmark), and 2 μl reducing agent (NuPAGE Sample Reducing Agent, Thermo Fisher Scientific) were added to each tube and after mixing and incubating at 70 °C for 10 min, the samples were run on 4–12% precast midi gel (NuPAGE Bis-Tris Gels, Thermo Fisher Scientific) at 200 volt for 30 min. Subsequent silver gel staining was used to detect proteins on the gel.
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3

CRISPR-Mediated Gene Disruption Efficiency

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The sgRNAs were compared for their efficiency in facilitating CRISPR-mediated disruption of the target gene expressed from a co-transfected plasmid in Cos1 cells (ATCC, Manassas, VA, CAT#CRL-1650). Cos1 cells were maintained in DMEM supplemented with 10% heat-inactivated FBS, 1% penicillin–streptomycin (Gibco, 15070-063), and 2 mM L-glutamine. FuGENE HD (Promega, San Luis Obispo, CA, E2311) was used for transfection according to the manufacturer’s instructions. Briefly, the GFAP or MOG overexpression plasmid, Cas9 expression plasmid, and sgRNA plasmid were mixed in a 1:4:5 ratio to a total of 0.5 µg, and incubated with 1.5 µL of FuGENE HD in 25 µL Opti-MEM (Thermofisher, 31985962) prior to adding to the cultured cells. Twenty-four hours after transfection, cell lysates were harvested in 200 µL Novex Tris-Glycine SDS Sample Buffer (1.6×, Thermofisher, LC2676) with NuPage Sample Reducing Agent (Thermofisher, NP0009) and heated at 70 °C for 5 min (ThermoMixer C, Eppendorf). Lysates were sonicated at a force of 4 for 20 strokes (60 Sonic Dismembrator, Fisher Scientific). The lysates were subjected to western blotting analysis.
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4

Western Blot for Apoptosis Markers

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Protein extracts were mixed with NuPAGE LDS Sample Buffer (ThermoFisher NP0007), NuPAGE Sample Reducing Agent (ThermoFisher NP0004) and heated for 10 min at 70 °C. Protein (10ug/lane) was resolved on NuPAGE Novex 4–12% Bis-Tris Protein Gels, 1.0 mm, 15-well (ThermoFisher NP0323BOX) and transferred using a Mini-Trans-Blot Cell onto 0.22Um PVDF membranes (ThermoFisher 88520). Membranes were blocked with Membrane Blocking Solution (ThermoFisher 000105) for 1 hour at room temperature (22 °C). The membranes were then incubated overnight at 4 °C with primary antibodies at the following dilutions: anti-Caspase 3 (CST 9661) 1:1000, anti-PARP2 (CST 9542) 1:1000, anti-Actin (CST 4970) 1:5000. The membranes were then washed four times with PBS and 0.5% Tween20 (TBST) and incubated with horseradish peroxidase-conjugated secondary antibody (anti-rabbit NA934) 1:15000 for 1 h at room temperature. The membranes were then washed four times with TBST and were visualized with Lumina Forte Western HRP substrate (Millipore WBLUF0500).
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5

Affinity Purification of GFP, RFP, and Ubiquitin

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Cleared cell lysates were incubated with 10–20 μl of GFP–Trap or RFP–Trap agarose affinity peptide beads (Chromotek) for 2 h at 4 °C. Beads were washed 5× with wash buffer (20 mM Tris-HCl, pH 7.5–8.0, 2 mM EDTA, 150 mM NaCl, 10% (v:v) glycerol, 1% (v:v) Triton X-100, 0.5% (w:v) CHAPS and 1× EDTA-free cOmplete protease cocktail inhibitor). The beads were heated in NuPAGE LDS sample buffer (Thermo Fisher Scientific) plus NuPAGE sample reducing agent (Thermo Fisher Scientific) for 10 min at 100 °C, before being spun at 17,000g for 1 min at 4 °C. For ubiquitin immunoprecipitation, cleared lysates were incubated with ubiquitin–Trap beads (catalog no. UBA01, Cytoskeleton) for 2 h at 4 °C. Beads were washed 5× and incubated with 4× NuPAGE LDS sample buffer at 22 °C for 5 min and spun at 17,000g for 1 min.
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6

Evaluating SPIO NPs and ASOs in Neuroblastoma

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SK-N-DZ, SK-N-BE, DMEM and EMEM were purchased from ATCC (Manassas, VA, USA). 1% Minimum Essential Medium Non-Essential Amino Acids Solution, Ham’s F-12 Nutrient Mix, A532, azide, Slide-A-Lyzer MINI Dialysis Units, Nanodrop 2000, Opti-MEM, Ab-Alexa488, DAPI, NuPAGE Sample Reducing agent and SuperSignal™ West Pico Chemiluminescent kit were all purchased from Thermo Fisher Scientific (Waltham, MA, USA). SPIO NPs were purchased from Ocean Nanotech (San Diego, CA, USA). ASOs were synthesized and provided by Ionis Pharmaceuticals (Carlsbad, CA, USA). 5’-DBCO-TEG phosphoramidite, Zetasizer Nano ZS, FC500 and Centro LB 960 Microplate Luminometer were from Glen Research (Sterling, VA, USA), Malvern (UK), Beckman Coulter (Brea, CA, USA) and Berthold Technologies (Oakridge, TN, USA), respectively. Anti-MXD3 monoclonal mouse Ab, rabbit anti-histone Ab, AV conjugated to FITC, PI and Caspase 3/7 Glo kit were purchased from Neuromab (Davis, CA, USA), Abcam (Cambridge, UK), BD Biosciences (San Jose, CA, USA), Roche (Nutley, NJ, USA) and Promega (Madison, WI, USA), respectively. Image J was from NIH (Bethesda, MD, USA).
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7

Quantification of ECM Proteins in Isolated Microvesicles

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Isolated MV were lysed in M-PER™ Mammalian Protein Extraction Reagent (Item78505, ThermoFisher) with protease inhibitors (Item78439, ThermoFisher). Total protein content of the lysates was measured by bicinchonic acid assay. A portion (20 µg total protein) of each sample was reduced using NuPAGE™ Sample Reducing Agent (ThermoFisher), resolved by PAGE, transferred to nitrocellulose, and probed with 2–5 µg/mL of primary antibody as previously described [36 (link)]. Antibodies used were rabbit pAbs recognizing laminin (Item L9393, Millipore-Sigma), col IV (Item ab6586, Abcam), fibronectin (Item AB2033, Millipore-Sigma), or TSG-6 (RAH-1; [37 (link)]). A rat monoclonal antibody recognizing human HSPG2 (perlecan) (Item ab2501, Abcam) was also used. Primary antibodies bound to the blots were visualized with the appropriate horseradish peroxidase‐conjugated secondary antibodies (Jackson Immuno Research, West Grove, PA) (1 µg/mL), visualized by enhanced chemiluminescence (GE Healthcare Life Sciences, Pittsburgh, PA), scanned, and quantified using ImageJ as previously described [36 (link)].
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8

Immunoprecipitation of TMEM41B Protein

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TMEM41B KO HAP1 cells reconstituted with full length TMEM41B fused to tagRFP (infected and uninfected) were collected and lysed in nonyl phenoxypolyethoxylethanol (NP-40) buffer (10 mM HEPES, pH 7.5, 150 mM KCl, 3 mM MgCl2, 0.5% NP-40) supplemented with cOmplete Mini EDTA-free protease inhibitor tablet (Millipore/Sigma: 11836170001) and 0.1 mM phenylmethylsulfonyl fluoride (PMSF) (Millipore/Sigma: 10837091001). Protein concentrations were determined by BCA assay as described above. Per sample, 50 μL (1.5 mg) Dynabeads Protein A for Immunoprecipitation (ThermoFisher Scientific: 10001D) were prepared and linked to 5 μg antibodies (rabbit anti-tagRFP and normal rabbit IgG control) according to the manufacture’s protocol. 100 μg of whole cell lysate (WCL) were incubated with beads-antibody complexes for 70 min at RT followed by wash steps according to the manufacture’s protocol. The resulting beads-antibody-antigen complexes were subsequently treated with elution buffer, mixed with NuPAGE® LDS Sample Buffer (ThermoFisher Scientific: NP0008) and NuPAGE® Sample Reducing Agent (ThermoFisher Scientific: NP0009) as per manufacturer’s instructions and denatured for 15 min at 70°C. The precipitated proteins within the eluted fractions were resolved by western blot as described above.
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9

Western Blot Analysis of STAT3 Phosphorylation

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Whole cell lysates were prepared using RIPA Lysis and Extraction Buffer (Thermo Fisher Scientific), supplemented with Phosphatase and Protease Inhibitor Cocktail tablets (Roche). NuPAGE LDS sample buffer and NuPAGE sample reducing agent (both from Thermo Fisher Scientific) were both added to protein samples according to the manufacturer’s instructions. Protein (30 μg) was separated by polyacrylamide gel electrophoresis using a Bis-Tris buffer system (Novex NuPAGE (4–12%), Thermo Fisher Scientific), prior to transfer to a 0.45 μm PVDF membrane (Immobilion-FL, Merck Millipore, Bayswater, VIC, Australia), and processed for fluorescence-based detection. The following primary antibodies and dilutions were used: pSTAT3 (Y705), 1:500 (Cell Signaling Technology, Danvers, MA, USA); total STAT3, 1:1000 (Cell Signaling Technology); GAPDH: 1:2000 (Sigma Aldrich, Castle Hill, NSW, Australia). The appropriate fluorescent secondary antibody (LI-COR Biosciences, Lincoln, NE, USA) was used and bands visualized and quantified using an Odyssey imaging system (LI-COR). Original western blots can be found at Figure S5.
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10

Western Blot Analysis of Cellular Markers

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Cell lysis was carried out with RIPA lysis buffer (50 mM Tris pH 7.5, 150 mM NaCl, 1% NP-40, 0.5% Na-deoxycholate, 0.1% SDS) supplemented with FPIC (Fast Protease Inhibitors cocktail; Sigma-Aldrich; Cat#: S8830-20TAB). The lysates were reduced in NuPAGE LDS Sample Buffer (Thermo Fisher; Cat#: NP0007) supplemented with NuPAGE Sample Reducing Agent (Thermo Fisher; Cat#: NP0009), separated by polyacrylamide gel in NuPAGE MOPS SDS Running Buffer (Thermo Fisher; Cat#: NP0001) and transferred into nitrocellulose membrane (Amersham; Cat#: 10600007). Membranes were blocked in 5% milk powder in PBST Buffer (1× PBS, 0.2% Tween 20) and incubated overnight at 4°C with the primary antibodies against SETDB1 (Abcam; Cat#: ab107225), H3 (Santa Cruz Biotechnology; Cat#: sc-8654), H3K9me3 (Abcam; Cat#: ab8898), H3K27me3 (Diagenode; Cat#: C15410069), Lamin A/C (Proteintech; Cat#: 10298-1-AP), Lamin B1 (Abcam; Cat#: ab16048), E-cadherin (BD Transduction Laboratory; Cat#: 610181), Paxillin (Millipore; Cat#: 05-417), β-actin (Sigma-Aldrich; Cat#: A5441). Membranes were incubated with the appropriate LI-COR IRDye secondary antibody (LI-COR Biosciences GmbH) and revealed by Odyssey Fc imaging system (LI-COR Biosciences GmbH). The images obtained from the slot blot assay were analyzed with the Image Studio Lite 5.2.5 software.
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