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24 protocols using goat anti mouse 800cw

1

Reagents and Antibodies for Protein Detection

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Unless otherwise stated, all (bio)chemicals and reagents were from Sigma-Aldrich (Dorset, UK). Tissue culture reagents and buffers were from Thermo Fisher Scientific (Paisley, UK). Molecular biology enzymes and reagents were from New England BioLabs (Hitchin, UK). Primers were ordered at Eurofins Genomics (Ebersberg, Germany). For western blotting, the following primary antibodies were used: mouse antitubulin (ab7291; 1:4000; Abcam, Cambridge, UK); rabbit anti–hexa-histidine tag (6xHis, ab9108; 1:4000; Abcam); and sheep anti–green fluorescent protein (produced in house). Secondary antibodies (800CW goat anti-mouse, 680RD goat anti-mouse, 800CW donkey anti-rabbit, and 800CW donkey anti-goat) and 680LT streptavidin were purchased from LI-COR (Cambridge, UK) and were all used at 1:10,000. Acetyl–norleucine–substance P (Ac-Nle-SP) and probe 1 were synthesized as described here.
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2

SDS-PAGE Protein Gel Analysis Protocol

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Prior to SDS-PAGE analyses, media samples were treated with 100 mM iodoacetamide (Acros Organics) in the dark for 1–2 h to prevent disulfide shuffling, or 100 mM dithiothreitol for 1 h at room temperature to reduce disulfides. All samples were then treated with 6× gel loading buffer (300 mM Tris, pH 6.8, 15% glycerol, 6% SDS, and 10% (w/v) bromophenol blue) and boiled for 10 min prior to protein gel electrophoresis. Samples were then separated by SDS-PAGE using 12% polyacrylamide gels and analyzed by immunoblotting using a LiCor  Odyssey imager for detection. Nitrocellulose blots were probed with primary antibodies (diluted in 5% bovine serum albumin) obtained from the following suppliers: Santa Cruz: HA probe (1:200; sc-7392); Agilent Technologies: rat Anti-DYKDDDDK (1:2000; 200474); and Sigma: β-actin (1:5000; A1978). Secondary antibodies were obtained from LiCor Biosciences: 800CW goat anti-mouse, 800CW goat anti-rat, 680LT goat anti-mouse, and 680LT goat anti-rat. All secondary antibodies were used at a dilution of 1:10,000 in 5% non-fat milk. Uncropped scans of selected immunoblots are supplied in Supplementary Fig. 7.
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3

Western Blot Analysis of Protein Samples

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Samples were run on 6, 9, 11, or 13% polyacrylamide gels and transferred to supported 0.45-μm nitrocellulose membranes (GE Healthcare). Membranes were blocked with 5% fat-free milk in Tris-buffered saline/Tween-20. Antibodies used were rabbit anti–glucose-6-phosphate dehydrogenase (G6PDH; A9521; Sigma-Aldrich), mouse monoclonal anti-GFP (11814460001; Roche Diagnostics, Rotkreuz, Switzerland), rabbit anti-GFP (TP401; Torrey Pines Biolabs, Secaucus, NJ), mouse monoclonal anti–FLAG-M2 (F1804; Sigma-Aldrich), 800CW goat anti-rabbit (926-32211; LI-COR Biosciences, Lincoln, NE), 800CW goat anti-mouse (926–32210; LI-COR Biosciences), 680LT goat anti-rabbit (926–68021; LI-COR Biosciences), and 680LT goat anti-mouse (926-68021; LI-COR Biosciences). Membranes were scanned using an Odyssey CLx imaging system and analyzed using the Image Studio Lite 4.0.21 software (LI-COR Biosciences). For Mup1 degradation assays, full-length Mup1-GFP and free GFP were detected with mouse monoclonal anti-GFP antibody on a single membrane and brightness and contrast adjusted separately due to differences in transfer efficiency.
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4

Comprehensive Autophagy Signaling Antibody Panel

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The following primary antibodies were used in this study: anti-AMPK antibody (#2532S; Cell Signaling Technology), anti-p-AMPK antibody (#2535S; Cell Signaling Technology), anti-LC3 I/II (#4108S; Cell Signaling Technology), anti-P62/SQSTM1 (#8025S; Cell Signaling Technology), anti-Beclin1 (ab62557; Abcam), anti-NRAGE (sc-136552; Santa Cruz Biotechnology), anti-GAPDH (#5174; Cell Signaling Technology), anti-Ulk1 (#2707773; Millipore), anti-p-Ulk1 (Ser758; #2571270; Millipore), anti-ATG13 (#13468S; Cell Signaling Technology), anti-p-ATG13 (S355; #43533S; Cell Signaling Technology), anti-PI3k (#4263S; Cell Signaling Technology), and anti-mTOR (#2643610; Millipore). Secondary antibodies used for western blotting were as follows: 800CW goat anti-mouse and 800CW goat antirabbit, purchased from LI-COR Biosciences. Hydroxychloroquine (HCQ), purchased from Sigma, was diluted in phosphate-buffered saline (PBS, pH 8.0) at a stock concentration 5 M.
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5

Western Blot Analysis of PIP5K1γ Expression

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Protein from cultured fibroblasts was harvested and lysates were blotted as previously described.111 (link) anti-PIP5K1γ (ABS190; 1:300; Sigma) and anti-β-actin (MA1-91399; 1:1000; Thermo-Fisher) were applied to transferred membranes overnight at 4°C. Blot bands were detected by Sapphire Biomolecular Imager (Azure Biosystems) after 1 h incubation in the following secondary antibodies: goat anti-rabbit 680RD (P/N 926–68071, 1:10,000; LI-COR), goat anti-Mouse 800CW (P/N 925–32210, 1:10,000; LI-COR). Images were processed on ImageJ using the BioImporter plugin tool to calculate the protein expression for each band. Protein abundance was first normalized to beta-actin intensity then normalized to control cell intensity.
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6

Western Blot Analysis of NSG1 and NSG2 Proteins

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Brains from wild‐type and NSG1 KO mice were homogenized in 5 mM CHAPS, 50 mM Tris–HCl, 150 mM NaCl, 1× proteinase inhibitor with a Kontes microtube pellet pestle while kept on ice. Detergent‐insoluble material was removed by centrifugation at 13,000× g for 10 min. Aliquots of supernatants were mixed with SDS sample buffer (125 mM Tris–HCl, pH 6.8, 20% glycerol, 4% SDS, 0.02% bromophenol blue, and 125 mM dithiothreitol) and incubated at 50°C for 20 min. The samples were separated on a 10% NuPage Bis‐Tris gel (Invitrogen) using a MES buffer system (Invitrogen), transferred to nitrocellulose membranes using the Trans‐Blot Turbo Transfer System (Bio‐Rad), blocked in Odyssey Blocking Buffer (LI‐COR), and probed simultaneously with the primary antibodies: mouse anti‐NSG1 (Santa Cruz; sc‐390654, 1:1000) and rabbit anti‐NSG2 (Abcam; ab189513, 1:1000) followed by incubation with the IRDye conjugated secondary antibodies: goat antimouse800CW (LI‐COR; 926‐32210, 1:10,000) and goat antirabbit680RD (LI‐COR; 926‐68071, 1:10,000). The Odyssey CLx infrared imaging equipment was used to detect infrared signals.
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7

Immunoprecipitation and Immunoblotting Protocol

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Immunoprecipitation and immunoblotting analyses were performed as previously described.40 (link) The following secondary antibodies were used, goat anti-mouse 800CW, goat anti-rabbit 800CW, goat anti-mouse 680LT or goat anti-rabbit 680 (all from LI-COR Biosciences GmbH, Lincoln, NE, USA). The membranes were scanned using Odyssey Imager from LI-COR Biosciences GmbH.
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8

Activation of Mast Cells Signaling Pathways

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Whole cell lysates were prepared from sensitized human skin mast cells (106/sample) that were activated with 100 ng/ml NP-BSA for 5 min at 37°C. Protein equivalents of 5×105 cells/lane were separated by reducing SDS-PAGE and transferred onto nitrocellulose membranes. Two-color staining for Akt, p38 and p42/44 was performed using Odyssey Blocking Buffer (LI-COR Biosciences, Lincoln, NE), and Syk immunoblotting was performed with 5% non-fat dry milk in 25 mM Tris, pH7.4, 0.15 M NaCl, 0.1% Tween-20 (TNT buffer) as previously described [30 (link)]. The primary antibodies used were: rabbit polyclonal anti-p38 MAPK, mouse monoclonal anti-phospho-p38 MAPK (Thr180/Tyr182)(28B10), rabbit polyclonal anti-p44/42 (Erk 1/2), mouse monoclonal anti-phospho-p42/44 (Erk1/2) (E10), rabbit polyclonal anti-Akt, mouse monoclonal anti-Akt (Thr308)(L32A4), rabbit polyclonal antibody against total Syk (Cell Signaling Technology, Danvers, MA), and mouse monoclonal antibody against human phospho-Syk (Tyr525) (R&D Systems, Minneapolis, MN). The secondary antibodies used were goat anti-rabbit IRDye 680RD and goat anti-mouse 800CW (LI-COR Biosciences, Lincoln, NE). The blots were scanned on an Odyssey® CLx Infrared Imaging System (LI-COR Biosciences, Lincoln, NE).
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9

Quantitative Phospho-Protein Profiling

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Following fixation, cells were permeabilized by five times washes in 0.1% Triton X-100 in 1X Tris Buffered Saline (TBS). Cells were blocked for 1 hour at RT in Licor Blocking Buffer (Licor), and hybridized overnight at 4°C in primary antibody (1:250 phospho-eIF4E (Ser209) (Abcam), 1:300 phospho-Akt (Ser473) (Cell Signaling), 1:200 phospho-ERK1/2 (Thr202/Tyr204) (Cell Signaling), 1:400 phospho-4EBP1 (Thr70) (Cell Signaling), 1:500 phosphor-P70 (Thr389) (Cell Signaling), 1: 400 phosphor-S6 (Ser235/236) (Cell Signaling), and 1:400 phosphor-mTOR (Ser2448) (Cell Signaling)). Cells were washed 5 times in TBS with 0.1% Tween-20 and hybridized with 1:5000 Cell Tag (Licor) and 1:800 goat anti-mouse 800CW (Licor) or donkey anti-rabbit 800CW (Licor) for 1 hour at RT. Cells were washed 5 times in TBS with 0.1% Tween-20 and a final wash in TBS. Liquid was decanted from the 96 well plate and the plate was scanned using the Odyssey Imager (Licor) and Image Studio (Licor). We compensated for differences in cell numbers by adjusting the phosphorylation levels (800 channel) by the Cell Tag signal (680 channel). Phosphorylation levels are reported as a ratio to the mean signal in the control cells.
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10

SHH Protein Expression in Limb Development

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Stage 21HH and 24HH legs were homogenised in RIPA buffer (Fisher) containing protease inhibitors, centrifuged, and the supernatant is collected. Protein concentration was estimated using a DC Protein Assay kit (Bio-Rad). Recombinant mouse SHH N-terminus protein (R&D Systems) was used as a positive control. Protein samples were loaded as individual limbs per lane. Proteins were separated by electrophoresis using pre-cast 12% gels (Invitrogen), transferred to nitrocellulose membranes by standard procedures. Membranes were blocked in Odyssey Blocking Buffer (Licor), incubated with 1:100 rabbit anti-SHH H-160 (Santa Cruz, sc9024) 1:2500 mouse anti-γ-tubulin (Sigma, T5326) 4 °C overnight, followed by goat anti-rabbit 680CW (Licor, 926-32221) goat anti-mouse 800CW (Licor, 926-32210) for 1 hour. Membranes were dried and signal detected using an Odyssey Infrared Imager (Licor). Bands were quantified using Image Studio software, and normalised to γ-tubulin protein.
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