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7 protocols using anti goat minus

1

Immunofluorescence Visualization of EZH2 and PCNA

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Cells were prepared as described in the immunofluorescence section and incubated with anti-EZH2 (Goat) and anti-PCNA (mouse) primary antibodies following the manufacturer’s instructions (Sigma-Aldrich). Briefly, cells were incubated for 60 min at 37 °C with anti-mouse PLUS (Sigma-Aldrich, DUO92001) and anti-Goat MINUS (Sigma-Aldrich, DUO92006), washed twice with Buffer A (Sigma-Aldrich, DUO82047), and then incubated with the ligation solution (Sigma-Aldrich, DUO92014) for 30 min at 37 °C. After ligation, cells were washed twice with Buffer A and then incubated for 100 min at 37 °C with amplification reagents (Sigma-Aldrich, DUO92014). Finally, the cells were washed three times with Buffer B (Sigma-Aldrich, DUO82048), stained, and mounted with mounting medium (Sigma-Aldrich, DUO82040) to visualize the nuclei. Images were captured with a Nikon Eclipse 300 fluorescence microscope (CompixInc).
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2

GHSR and DRD1 Protein Interaction Detection

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Protein interactions between GHSR/DRD1 in mouse brain slices were detected using Duolink PLA detection kits (Sigma-Aldrich, DUO92008) following manufacturer’s instructions. The following primary antibodies were used: GHS-R1a (Santa Cruz Biotechnology, sc-10359, 1:100) and anti-DRD1 (Abcam, ab81296, 1:200). The specificity of antibodies to GHSR and DRD1 was validated as previously described (17 (link)). The following Duolink in Situ PLA Probes were used: anti–rabbit PLUS (Sigma-Aldrich, DUO92002) and anti–goat MINUS (Sigma-Aldrich, DUO92006). Images were collected on a Nikon Ti2 confocal microscope. The mean intensity of PLA+ signals was analyzed using Nikon-Elements Advanced Research software.
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3

Imaging CD47, CXCR4, TLR4, and RAGE in Cells

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2x104 MM cells were seeded on glass coverslips and the following day treated overnight with either BoxA (400 nM) or CXCL12 (10 nM) and PBS (control). Following treatment, cells were fixed with 4% paraformaldehyde in PHEM buffer for 10 min at RT, washed twice with 1% BSA in PBS for 5 min, and then blocked with 4% BSA and 10% goat serum in PBS. Cells were overlayed with the primary antibodies:
rabbit monoclonal anti‐CD47 (1:100, EPR21794, Abcam #AB218810); mouse monoclonal anti‐CD47 (1:50, B6H12, Santa Cruz #sc12730) either alone or in combination or goat polyclonal anti‐CXCR4 (1:100, Abcam #AB1670), or rabbit monoclonal anti‐TLR4 (1:50, Cell signaling #14358) and or rabbit polyclonal anti‐RAGE (1:100, Invitrogen #PA1‐075) for 1 h at room temperature. Following three washes with 0.2% BSA in PBS, the cells were incubated with secondary antibodies in 0.2% BSA/PBS + 10% goat serum and incubated for 45 min at RT. For nuclei staining, 1 µg/ml Hoechst 33358 was used. For cytosol detection, Phalloidin FITC (P5282, Sigma‐Aldrich) was used.
Secondary probes (Duolink, Sigma‐Aldrich) for PLA reaction were as follows: Anti‐Rabbit MINUS (#DUO92005), Anti‐Rabbit PLUS (#DUO92002), Anti‐Goat MINUS (#DUO92006), and Anti‐Goat PLUS (#DUO92003). When both primary antibodies were used, the PLA products were obtained by using the Anti‐Rabbit PLUS and Anti‐Goat MINUS probes.
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4

Proximity Ligation Assay for Protein-Protein Interactions

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PLA was conducted according to manufacturer’s protocol (Sigma-Aldrich). Briefly, after fixation, permeabilization with 0.1% Triton X-100, and 40 min blocking, cells were incubated at room temperature for 2.5 h with primary antibodies: goat anti-FUS (1:300; Sigma-Aldrich) and rabbit anti-RALY (1:300; Bethyl). As negative controls, either no primary antibodies or goat anti-DYNACTIN1 (1:100; Novus Biologicals) and rabbit anti-RALY were incubated. After two 10-min washings with PBS, cells were incubated with Duolink In Situ PLA Probe anti-Rabbit PLUS and anti-Goat MINUS (Sigma-Aldrich), diluted 1:5 in blocking solution for 1 h at 37°C. After two 5-min washings in Wash Buffer A (Sigma-Aldrich), cells were incubated with ligase for 30 min at 37°C. After two 5-min washings in Wash Buffer A, cells were incubated with polymerase and amplification solution for 100 min at 37°C, washed twice for 10 min in Wash Buffer B (Sigma-Aldrich), once in 0.01% in Wash Buffer B, dried at room temperature in the dark, and mounted with Mounting Media with DAPI (Sigma-Aldrich). For MNs, after washings in Wash Buffer B, cells were incubated with mouse anti-SMI32 antibody (1:500, Abcam) and hence with Alexa Fluor 488–conjugated goat anti-mouse.
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5

Mitochondrial TFAM-TFSB2B Interaction

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To quantify the mitochondrial protein interactions of TFAM with the Transcription Factor 2B a Proximity Ligation Assay (PLA) was performed24 (link). Primary antibodies against TFAM (1:50, sc-376672, Santa Cruz Biotechnology) and mitochondrial Transcription Factor 2B (1:50, 13676, Abcam,) were incubated for 1 h at room temperature. Proximity probes (anti-Mouse Plus; DUO92001 and anti-Goat Minus; DUO92006, both Sigma-Aldrich, each 1:5) were incubated for 1 h at room temperature, S3 splint and S3 backbone oligonucleotides (Biomers.net; Ulm, Germany) were hybridized, ligated and amplified (Supplementary Figure 5). The rolling circle products were visualized with a detection oligonucleotide44 (link). Images were submitted to a Cell Profiler pipeline quantifying the proximity ligation assay signals with single cell resolution.
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6

Quantifying GPCR-Protein Interactions in Brain

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Protein interactions between GHSR/DRD1 and GHSR/β-arrestin 2 in mouse brain slices and hippocampal neuron cultures were detected using Duolink Proximity Ligation Assay (PLA) detection kits (Sigma-Aldrich, #DUO92008) following manufacturer’s instructions. The following primary antibodies were used in proper combinations: goat-anti-GHSR (Santa Cruz Biotechnology, #sc-10359, 1 : 100), rabbit-anti-DRD1 (Abcam, #ab81296, 1 : 200), mouse-anti -arrestin 2 (Santa Cruz, #sc-13140). The specificity of antibodies to GHSR and DRD1 was validated as previously described [3 (link)]. The following Duolink in Situ PLA Probes were used: anti-Rabbit PLUS (Sigma-Aldrich, #DUO92002), anti-Goat MINUS (Sigma-Aldrich, #DUO92006), anti-Mouse PLUS (Sigma-Aldrich, #DUO92001). Images were collected on a Nikon confocal microscope. PLA-positive dot number was counted using Nikon-Elements Advanced Research software.
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7

In Situ Protein Interaction Analysis

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Archived rectosigmoid biopsy samples were from the SCOPE cohort at the University of California, San Francisco (UCSF). The SCOPE cohort is an ongoing longitudinal study of over 1,500 HIV-infected and uninfected adults followed for research purposes. The UCSF Committee on Human Research reviewed and approved the SCOPE study (IRB# 10–01218), and all participants provided written informed consent. PLA starter Duolink® In Situ Orange Starter Kit Mouse/Goat was obtained from Sigma Aldrich containing the PLA probes anti-goat MINUS and anti-mouse PLUS with the detection reagent DuoLink® Orange. Fluorescence for proximity ligation was observed under a Cy3 filter on a Leica Inverted Microscope DMi8 S Platform Formalin fixed paraffin embedded (FFPE) tissues were stained with primary antibodies for anti-LINGO2 Ab was raised against Goat (R&D Systems; AF3679) and anti-TFF3 raised against mouse (eBioscience; 5uclnt3) were used to detect the LINGO2 and TFF3 interactions in situ and for PLAs that followed the manufacturers instruction (Sigma). Technical controls omitting either one of the antibodies served as a negative control as no circular DNA oligonucleotides were able to be amplified.
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