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24 protocols using ab9108

1

Recombinant Slit Protein Production

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Cells infected with 6xHis-tagged Slit-N and Slit-FL recombinant baculovirus were harvested at 1–4 d PI with various MOI. The cell pellets were homogenized, and culture medium was collected. Noninfected cells were prepared similarly as a negative control. Protein production was confirmed by western blotting using 1:1000 rabbit anti-his primary antibody from Abcam ab9108 (Cambridge, Massachusetts) for Slit-N and Slit-FL, 1:250 goat anti-rabbit lgG HRP secondary antibody (Jackson Labs), and SuperSignal West Pico Chemiluminescent Substrate (Pierce, Rockford, Illinois). Images were collected with FOTO/Analyst ImageTech (FOTODYNE, Hartland, Wisconsin).
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2

Quantifying VCAM-1 Expression in Breast Cancer Cells

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MDA-MB-231 and HCC70 cells (200.000) treated or not with TNF-α (50 ng/mL) for 18 h were collected and washed with phosphate buffered saline solution (PBS). Cells were incubated with cAbVCAM1-5 (10 μg/mL) and then with an anti-poly histidine antibody (anti-6x His tag antibody, ab9108 Abcam), followed by a AlexaFluor®488-anti-Rabbit-IgG (Goat anti-Rabbit IgG H&L, AlexaFluor® 488, ab150077 Abcam). Binding was measured on a FACS Accuri C6 analyzer (BD Biosciences, San Jose, CA, USA). Background fluorescence was determined by measuring the fluorescent signal from cells stained with the irrelevant control sdAb.
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3

Western Blot Antibody Validation Protocol

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Western blot was performed as previously described [19 (link)]. The following antibodies were used for western blotting: rabbit polyclonal anti-6×His tag antibody (1:1000, Abcam, ab9108), rabbit monoclonal RPE65 antibody (1:1000, Abcam, ab231782), rabbit polyclonal anti-HTRA1 antibody (1:1000, Proteintech, 55011-1-AP), rabbit monoclonal anti-HIF1α antibody (1:1000, CST, #36,169), rabbit polyclonal anti-GAPDH antibody (1:1000, Abclonal, AC001), mouse polyclonal β-actin antibody (1:1000, Abclonal, AC004), Histone-H3 antibody (1:1000, Proteintech, 17168-1-AP) and secondary antibodies: horseradish peroxidase linked anti-rabbit/mouse IgG (1:5000, CST, #7074/7076). Blots were visualized using secondary antibodies conjugated with horseradish peroxidase by Chemiluminescence Imaging System (UVITEC).
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4

SARS-CoV-2 Spike Protein Binding Assay

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His Tag antibody plates were coated with a 0.5 µg/mL solution of spike protein antigens diluted in PBS at 4 °C for 12 h then washed with 1X TBST. To test blocking of ACE2 binding, 100 µL of precipitated phage (1013 titer) or 10 µg/mL of converted antibody was applied to each well and incubated for 1 h at 4 °C. After vigorous washing, the wells were then incubated with 100 µL of recombinant ACE2-His protein (RayBiotech Life, Inc, Peachtree Corners, GA) for 1 h at 4 °C. After 6X washing, 100 µL of rabbit anti-6X His tag polyclonal antibody (Abcam, ab9108) diluted 1:1,000 in PBS was added and incubated for 1 h at 4 °C. Following 6 washes with 1X TBST, wells were then incubated with 100 µL of goat anti-rabbit IgG (H + L) antibody HRP diluted 1:10,000 in 1X TBST for 1 h at 4 °C. Competitive ELISAs were developed and measured identical to binding ELISAs described above. A negative control antibody, SARS-CoV-2 spike mouse mAb (40591-MM42) (Sino Biological, Wayne, PA) that binds to the SARS-CoV-2 spike protein but does not neutralize, and a positive control antibody, SARS-CoV-2 spike mouse mAb (40592-MM57) (Sino Biological) that blocks interaction with ACE2 were used at 10 µg/mL. An ACE2-His alone condition without phage or antibody served as the baseline signal for spike-ACE2 binding. Blocking potential was measured as a decrease in signal from ACE2-His alone.
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5

Protein-Protein Interaction Assay

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The coding region of Ghd8 was cloned into the pET-32a vector (Novagen) and pGEX-6P-1 vector (GE Healthcare) with EcoRI and XhoI sites, respectively. To obtain the OsHAP5b protein, we used the same method for GHD8. The recombinant expression vector was expressed in Escherichia coli Transetta (DE3) cells (Transgen). The pull-down experiment was performed as described previously [50 (link)]. In brief, supernatants with equal amounts of Glutathione S-transferase (GST) or OsHAP5b-GST with GHD8-His recombinant proteins were incubated for 6 h at 4 °C in a total volume of 2 ml of pull-down buffer (20 mmol Tris-HCl, pH 8.0, 200 mmol NaCl, 1 mmol EDTA, 0.5% Lgepal CA-630 and protease inhibitor), after which 200 μl of GST resin was added (GE Healthcare; 17–5132-01) and the mixture incubated for 2 h at 4 °C. The binding reaction was then washed 5 times (10 min each time at 4 °C) using the pull-down buffer. After extensive washing, the pulled-down proteins were eluted by boiling at 95 °C for 10 min, separated on 12% SDS-PAGE and detected by immunoblots using an anti-GST antibody (Abcam; ab19256) and anti-His antibody (Abcam; ab9108), respectively.
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6

Quantifying Cell Surface Protein Binding

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HUVECs at a cell density of 1 × 104 cells/well in a 96-well plate were fixed with 4% PFA at room temperature for 10 min. Non-permeabilized cells were blocked with 3% BSA/PBS at room temperature for 2 h before they were treated with various concentrations of TS5-p45 at room temperature for 2 h. Following the treatment, cells were washed with PBST thrice at room temperature for 5 min each and incubated with anti-His (Abcam, ab9108) and isotype control anti-IgG antibody (Santa Cruz, sc2027) incubations at 4 °C overnight. The next day, cells were washed as described and incubated with goat anti-rabbit IgG, Alexa Fluor 488 (Invitrogen, A-11034) at room temperature for 2 h, before fluorescence intensity was measured with Hidex Sense Microplate Reader (Hidex, Finland). Next, cells were counter-stained with 1 µg/ml DAPI (Calbiochem, Sigma-Aldrich, 268298) in PBS at room temperature for 10 min, followed by washing as described. Fluorescence intensity measurements for DAPI were used to normalize TS5-p45 fluorescence intensity across all conditions.
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7

Quantifying NCL-TS5-p45 Binding Affinity

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Anti-FLAG antibody-coated plate (GenScript, L00455C), recombinant His-tagged TS5-p45, and FLAG-tagged NCL-FL and Ctrl overexpression WCL were used in this experiment. Specific FLAG-tagged NCL-FL capture was first verified by titrating the Anti-FLAG antibody-coated plate with increasing doses of NCL-FL lysate. Anti-NCL primary antibody (Abcam, ab22758) and Alexa Fluor 488 conjugated anti-rabbit IgG (Invitrogen, A-11034) were used for detection. The same protocol was applied to Ctrl lysates as a negative control. Saturation binding experiment was then performed by titrating TS5-p45 over FLAG-tagged NCL-FL- and Ctrl-captured wells at 4 °C for overnight incubation. The following day, treated wells were incubated with anti-His (Abcam, ab9108) at room temperature for 2 h and Alexa Fluor 488 conjugated anti-rabbit IgG (Invitrogen, A-11034) at room temperature for 1 h. Finally, fluorescence intensity was measured with Hidex Sense Microplate Reader (Hidex, Finland). Binding affinity was calculated with GraphPad Prism 8.
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8

Western Blot Protein Detection

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Proteins were transferred to a nitrocellulose membrane using iBLOT system (Life Technologies). A rabbit anti-Histag (ab9108, Abcam,UK) or anti-acfC antibody were used as primary antibodies and a fluorescently labelled goat anti-rabbit IR Dye 680RD secondary antibody (Li-cor) was used as secondary antibody. The membrane was visualized using an Odyssey fluorescent imager (LI-COR). The un-cropped image of Fig. 1b is in Supplementary Figure 1.
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9

Chromatin Immunoprecipitation (ChIP) Assay Protocol

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ChIP assays were performed as previously described (Bowler et al., 2004 (link); Perrella et al., 2018 (link); van der Woude et al., 2019 (link)). DNA was sheared using an ultrasonic bath (FALC instruments LABSONIC LBS2.10), cooled at 4°C using the maximum kHz frequency of 20 cycles 45 s ON, 15 s OFF. Anti-6XHis tag (Abcam ab9108) was used to IP the chromatin according to the manufacturer's instructions. ChIP-qPCR was performed using the following cycles: 95°C × 2 min, 95°C × 3 s, 59.5°C × 30 s for 50 cycles, 95°C × 1 min, and 60°C × 30 s to estimate the melting curve. Oligonucleotides for YUCCA8 and PIF4 DNA genomic regions were designed based on Lee et al. (2014) (link) and Zhu et al. (2016) (link). Relative ChIP DNA abundance was calculated as previously described (Kaiserli et al., 2015 (link)). In detail, MED25 enrichment over loci was determined by normalizing immuno-precipitated DNA against genomic DNA for the indicated regions and temperature conditions and indicated as a percentage of nuclear DNA (%Input). DNA was also immunoprecipitated from Col-0 wild-type plants and used as a negative control for ChIP-qPCR amplifications.
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10

Antibody Detection of JCPyV VP1 and 5-HT2 Receptors

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A mouse monoclonal antibody obtained from the supernatant of a hybridoma was used to detect JCPyV VP1 (PAB597). Rabbit polyclonal primary antibodies were used to recognize the 5-HT2Rs and TFR in the proximity ligation assay. Anti-5-HT2AR and anti 5HT2CR were obtained from LS Biosciences, Inc cat# LS-A1106 and LS-A1119 respectively. Anti-5-HT2AR recognizes the N terminus while anti-5-HT2CR the C terminus. Anti-5-HT2BR was obtained from Novus Biologicals cat# NLS1111 and recognizes the second extracellular loop. Anti-TFR was purchased from Novus Biologicals cat# NB100–92243. For Western Blot analysis a rabbit monoclonal anti-β-arrestin½ was purchased from Cell Signaling Technologies (#4674) and a mouse monoclonal anti-GAPDH was purchased from Sigma-Aldrich (G8795). A Mouse monoclonal anti-pan Cadherin antibody was used as cell surface marker (abcam, ab6528) and Rabbit polyclonal anti-6X His tag was used to stain for truncated receptors (abcam, ab9108).
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