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10 protocols using anti mouse plus

1

Detecting LC3B-ATG5 Binding in GBM Cells

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PLA was performed to detect LC3B-ATG5 binding in GBM cells. U87MG and LN229 cells (3 × 104) expressing EGFP-CD9 were seeded on fibronectin (FN, 10 μg/ml; Sigma-Aldrich, Cat. No. F0895, St. Louis, MO, USA)-coated coverslips in 48-well plates for 1 day. The cells were then fixed in 4% PFA for 15 min at RT. Cells were washed twice with 1 × PBS. The fixed cells were permeabilized using 0.05% saponin (Sigma-Aldrich, Cat. No. S7900) in PBS for 30 min. Samples were stained using primary antibodies for 3 h at RT followed by Duo-Link in situ PLA probes with anti-rabbit MINUS (Sigma-Aldrich, Cat. No. DUO92005), anti-mouse PLUS (Sigma-Aldrich, Cat. No. DUO92001), and Duo-Link in situ detection reagents Red (Sigma-Aldrich, Cat. No. DUO92008). Anti-LC3B antibody (rabbit polyclonal antibody, 1:100; Novus Biologicals, Cat. No. NB100-2220, Centennial, CO, USA, RRID:AB_10003146) and anti-ATG5 antibody (mouse monoclonal antibody, 1:100; Santa Cruz Biotechnology, Cat. No. sc-133158, Dallas, TX, USA, RRID:AB_2243288) were used as primary antibodies. Mounted samples were observed using confocal laser scanning microscopy (CLSM) (LSM700; Carl Zeiss, Jena, DEU, Plan-Apochromat × 63/1.40 Oil DIC M27).
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2

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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3

Proximity Ligation Assay for SL-13R-Protein Interaction

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To examine SL-13R-protein interaction, proximity link assay was performed. UCB CD34+ cells were cultured with biotin-conjugated SL-13R for 48 h. Cytospin, cell fixation and permeabilization are similar to previous mention in Immunocytochemistry. After overnight incubation with rabbit anti-AHNAK, ANXA2, and PLEC antibody (Table S4) and mouse anti-biotin antibody, Duolink In Situ PLA Probe anti-rabbit MINUS and anti-mouse PLUS were applied to samples (Sigma-Aldrich, Uppsala, Sweden). Proximally located antibody-binding probes were ligated with oligonucleotide by ligase at 37℃ for 30 min using Duolink In Situ Detection Reagent Green (Sigma-Aldrich, Uppsala, Sweden). Rolling Circle Amplification of probes was performed using DNA polymerase at 37℃ for 100 min. After wash with Buffer B, nuclei were stained with TOTO-3, and analysed using a FluoView 1000 Confocal Microscope.
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4

Proximity Ligation Assay for Rab7-RILP Interaction

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Duolink Proximity Ligation Assay38 was used to study interaction between Rab7 and RILP. Briefly the primary neurons from WT and Cln1−/− mice were grown in chamber slides and fixed with methanol for 15 to 20 min at −20°C. The cells were blocked with goat serum and incubated with Rab7 antibody (Abcam; Cat#ab50533; dilution 1:1000) and RILP antibody (Abcam; Cat#ab140188; dilution 1: 3000) overnight at 4°C. After three washes with PBS the cells were incubated with anti-rabbit-MINUS (Sigma–Aldrich; Cat#DUO92005 Anti-RILP) and anti-mouse–PLUS (Sigma–Aldrich; Cat#DUO92001-for Rab7 antibody) PLA probes and subjected to ligation and amplification reaction using Duolink® In Situ Detection Reagents Green (Sigma–Aldrich; DUO9201) according to manufacturer’s protocol. For controls, cells were similarly processed but without primary antibody or with one primary antibody only. When the primary antibodies were in close proximity (<40 nm apart) fluorescent signals were detected as green dots under the FITC channel. The cells were mounted with DAPI-Fluoromount G (Thermo Fisher, Cat#010020) and visualized using an LSM710 confocal microscope. High resolution z stack images were captured at 40X, the z stacks were merged by maximum intensity projection using Zen Desk software to include all the PLA signals and quantitated using Duolink image tool.
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5

In situ PLA and Immunofluorescence for WRN and MRE11

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The in situ PLA in combination with immunofluorescence microscopy was performed using the Duolink II Detection Kit with anti-Mouse PLUS and anti-Rabbit MINUS PLA Probes, according to the manufacturer's instructions (Sigma-Aldrich).
To detect proteins, we used rabbit anti-WRN (Abcam) and mouse anti-MRE11 (Abcam) antibodies. Detailed information on antibodies and their usage can be found in Supplementary Information Online.
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6

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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7

Proximity Ligation Assay for Protein-Protein Interactions

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Cells cultured in 8-well slide chamber were fixed and blocked in 5%
(vol/vol) donkey serum for 1 hour at room temperature and incubated overnight
with the respective target primary antibodies at 4°C. The cells were then
incubated for 1 hour at 37°C with the following Duolink proximity
ligation assayprobes: anti-rabbit MINUS (Sigma-Aldrich, DUO92005) and anti-mouse
PLUS (Sigma-Aldrich, DUO92003). Duolink in situ detection reagent kit
(Sigma-Aldrich, DUO92008) was used for ligation and amplification at 37°C
according to the manufacturer’s protocol. All images were acquired using
Leica WLL SP8 confocal laser scanning microscope with LASX image processing
interface.
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8

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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9

Duolink Proximity Ligation Assay

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Cells were prepared as described in the immunofluorescence section. The assay was developed following the manufacturer’s instructions (Duolink manual from Olink Biosciences). Briefly, cells were incubated with an anti-mouse PLUS (Sigma, DUO92001) and an anti-rabbit MINUS (Sigma, DUO92005) for 1 h at 37 °C, washed twice and then incubated with the ligase mix for 30 min at 37 °C (Sigma, DUO92014). After the ligase reaction, cells were washed twice and then incubated with the polymerase reaction containing a green intercalating dye for 100 min at 37 °C (Sigma, DUO92014). Finally, cells were washed twice and stained with 4',6-diamidino-2-phenylindole staining to visualize the nuclei (see immunofluorescence description). Pictures were taken using confocal microscopy (see immunofluorescence description). Cells were considered positive if at least three dots per cells were observed after merging all images of the Z-stack.
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10

Proximity Ligation Assay for Protein-Protein Interactions

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The in situ proximity ligation assay (PLA) in combination with immunofluorescence microscopy was performed using the Duolink II Detection Kit with anti-Mouse PLUS and anti-Rabbit MINUS PLA Probes, according to the manufacturer's instructions (Sigma-Aldrich) (24 (link)). To detect proteins we used rabbit anti-WRN (Abcam) and rabbit anti-MRE11 (Novus Biological) antibodies. IdU-substituted ssDNA was detected with the mouse anti-BrdU antibody (Becton Dickinson) used in the DNA fibre assay.
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