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Alexa fluorophore conjugated secondary antibody

Manufactured by Thermo Fisher Scientific
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Alexa fluorophore-conjugated secondary antibodies are a type of lab equipment used in fluorescence-based applications. They consist of a secondary antibody that is chemically conjugated to an Alexa dye fluorophore, enabling the detection and visualization of target proteins or molecules in biological samples.

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60 protocols using alexa fluorophore conjugated secondary antibody

1

Immunostaining of Cerebellar and Spinal Cord Tissue

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Cerebellar slices were washed in PBS, permeabilized and blocked in 4% goat serum and 0.1% Triton X‐100 in PBS (blocking buffer) for 1 h and incubated overnight at 4°C with primary antibodies (Table 2). Slices were washed in PBS with 0.1% Triton X‐100 and incubated with Alexa fluorophore‐conjugated secondary antibodies (1:400; Invitrogen) in blocking buffer for 1 h at RT. Slides with cryostat spinal cord sections were air‐dried for 1 h, rehydrated in Tris buffer saline (TBS; 20 mM Tris and 1.4 M NaCl in dH2O; pH 7.6) and pre‐treated with absolute ethanol (Sharlab) for 15 min at −20°C. For APC and Olig2 immunostaining, antigen retrieval was performed by heating the sections in low‐pH retrieval buffer (Vector Laboratories) for 45 s using a microwave. After washing, samples were incubated in blocking buffer solution (1% BSA, 5% goat serum, and 0.1% Triton X‐100) for 30 min at RT, and then with the primary antibodies diluted in blocking buffer overnight at 4°C (Table 2). Sections were washed in TBS, and incubated with Alexa fluorophore‐conjugated secondary antibodies (1:500; Invitrogen) in blocking solution for 1 h at RT. Cell nuclei were counterstained with DAPI (4 μg/ml, Sigma‐Aldrich) and sections were mounted with Fluoromount‐G (SouthernBiotech).
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2

Immunofluorescence Staining of Pancreatic Cells

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Cells were trypsinyzed, spotted on slides using a Shandon Cytospin4 centrifuge (Thermo Scientific), and fixed for 15 min at RT in 4% paraformaldehyde (PFA). Samples were blocked for 30 min in PBS containing 1% BSA, 5% fetal goat serum (FGS), and 0.2% saponin (blocking buffer). Samples were incubated overnight at 4 °C with primary antibodies diluted in blocking buffer as follows: rat anti-human C-peptide (1:1000; BCBC); mouse anti-human PDX1 (1:500; R&D, Minneapolis, MN); mouse anti-NKX2.2 (1:1000; Hybridoma Bank, Iowa City, IA); mouse anti-NKX6.1 (1:1000; Hybridoma Bank); rabbit anti-eGFP (1:1000; Life Technologies, Carlsbad, CA); and mouse anti-Ki67 (1:200; Zymed, San Francisco, CA). Slides were washed in PBS with 0.1% Tween 20 (Sigma) and incubated with Alexa fluorophore-conjugated secondary antibodies (1:1000; Life Technologies). Nuclei were stained with DAPI. Images were obtained using a Leica SP5 confocal microscope.
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3

Characterization of Neisseria gonorrhoeae antibodies

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The purified chicken IgY anti-Neisseria gonorrhoeae antibody was raised against formalin-killed FA1090 gonococci by Cocalico Biologicals and it cross-reacts with the MS-11, FA19 and F62 strains. The rabbit anti-N.g polyclonal antibody (cat# 20-NR08) was purchased from Fitzgerald Industries. Rabbit monoclonal antibodies against the following antigens were purchased from Cell Signaling—Rab5 (C8B1), Rab7 (D95F2), EEA1 (C45B10), GM130 (D6B1), Ezrin (#3145), LC3A/B (D3U4C), V5-Tag (E9H80), CEACAM1 (D3R80) and ACTR2 (#3128S). Mouse antibodies against the following antigens were purchased from Santa Cruz–Actin (sc8432), FMNL1 (sc390466), FMNL2 (sc390298), FHOD1 (sc365473), DAAM1 (sc100942). Mouse anti-Cas9 (7A9-3A3) was purchased from Cell Signaling. Anti-FMNL3 (ab57963) and anti-Galectin 3 (ab2785) mouse monoclonal antibodies were purchased from Abcam. Anti-human LAMP-2 (H4B4) was purchased from BioLegend. Anti-DIAPH2 (A300-079A-T) was purchased from Bethyl Labs. Highly cross-absorbed Alexa fluorophore conjugated secondary antibodies were purchased from Life Technologies.
Inhibitors used in this study were purchased from: (1) Cayman Chemicals—cytochalasin D (5μM), CK869 (10μM), Dynasore (30μM), GSK269962 (1μM), Nocodazole (3μM), ML-141 (5μM), EHT 1864 (5μM), BMS-5 (1μM) and (-) blebbistatin (5μM); (2) Cell Signaling—LY294002 (10μM); (3) Abcam—SMIFH2 (12.5μM to 100μM).
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4

Immunofluorescence Staining Protocol

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Cells were fixed in 4% PFA for 10 min at room temperature. When indicated, pre-extraction with CSK buffer (10 mM PIPES pH 7.4, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl2) containing 0.2% Triton-X was performed for 5 min on ice prior to fixation. Cells were incubated overnight with primary antibody at 4°C. Subsequently, cells were incubated with Alexa-fluorophore-conjugated secondary antibodies (Life Technologies). The mounting was carried out in Vectashield with DAPI (Vector Laboratories). CPD staining (TDM-2 CosmoBio) was performed according to the manufacturer's protocol, prior to incubation with primary antibodies.
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5

Immunofluorescence Imaging of DNA Repair Processes

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Cells were fixed in 4%PFA for 10 min at room temperature. Pre-extraction with CSK buffer (10mM PIPES pH- 7.4, 100mM NaCl, 300mM sucrose, 3mM MgCl2) containing 0.2% Triton-X, for 5 min on ice, was performed prior to fixation when indicated. Cells were incubated overnight with primary antibody at 4 °C. Subsequently cells were incubated with Alexa-fluorophore-conjugated secondary antibodies (Life Technologies). The mounting was carried out in Vectashield with DAPI (Vector Laboratories).
Micropore irradiation experiments were performed on MRC5 fibroblasts. Cells were exposed to localized UV damage (100 J/m2) using a micropore membrane with 5-μm pore size as described previously (Katsumi et al., 2001).
PARP inhibitor treatment was performed as described in (Luijsterburg et al. 2012b). Briefly, 5mM IPTG was added to the cells before and during transfection with the mCherry-LacR-fusion plasmid. IPTG was washed out 24 hours post transfection, and replaced with medium containing 1 μM PARP inhibitor (KU-0058948). Cells were incubated with inhibitor for 16 hours, followed by fixation and staining.
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6

Immunofluorescence Staining of Pancreatic Cells

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Cells were trypsinyzed, spotted on slides using a Shandon Cytospin4 centrifuge (Thermo Scientific), and fixed for 15 min at RT in 4% paraformaldehyde (PFA). Slides were blocked for 30 min in PBS containing 1% BSA, 5% fetal goat serum and 0.2% saponin (blocking buffer). Slides were incubated overnight at 4°C with primary antibodies diluted in blocking buffer as follows: rat anti-human C-peptide (1:1000; BCBC); mouse anti-human PDX1 (1:500; R&D); rabbit anti-eGFP (1:1000; Life Technologies); mouse anti-β-catenin (1:200; Cell Signaling); and mouse anti-Ki67 (1:200; Zymed). Slides were washed in PBS with 0.1% Tween 20 (Sigma) and incubated with Alexa fluorophore-conjugated secondary antibodies (1:1000; Life Technologies). Nuclei were stained with DAPI (Abcam). Images were taken using a Leica SP5 confocal microscope.
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7

Immunofluorescence Protocol for Cell Fixation

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Cells were fixed in 4% PFA for 10 min at room temperature. When indicated, preextraction with CSK buffer (10 mM Pipes, pH 7.4, 100 mM NaCl, 300 mM sucrose, and 3 mM MgCl2) containing 0.2% Triton X-100 was performed for 5 min on ice before fixation. Cells were incubated overnight with primary antibody at 4°C. Subsequently cells were incubated with Alexa fluorophore–conjugated secondary antibodies (Life Technologies). The mounting was performed in Vectashield with DAPI (Vector Laboratories).
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8

Antibodies and Inhibitors for Gonococcal Trafficking

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The purified chicken IgY anti-Neisseria gonorrhoeae antibody was raised against formalin-killed FA1090 gonococci by Cocalico Biologicals and it cross-reacts with the MS-11, FA19 and F62 strains. The rabbit anti-N.g polyclonal antibody (cat# 20-NR08) was purchased from Fitzgerald Industries. Rabbit monoclonal antibodies against the following antigens were purchased from Cell Signaling -Rab5 (C8B1), Rab7 (D95F2), EEA1 (C45B10), GM130 (D6B1), Ezrin (#3145), LC3A/B (D3U4C), V5-Tag (E9H80), CEACAM1 (D3R80) and ACTR2 (#3128S).
Mouse antibodies against the following antigens were purchased from Santa Cruz -Actin (sc8432), FMNL1 (sc390466), FMNL2 (sc390298), FHOD1 (sc365473), DAAM1 (sc100942).
Mouse anti-Cas9 (7A9-3A3) was purchased from Cell Signaling. Anti-FMNL3 (ab57963) and anti-Galectin 3 (ab2785) mouse monoclonal antibodies were purchased from Abcam. Anti-human LAMP-2 (H4B4) was purchased from BioLegend. Anti-DIAPH2 (A300-079A-T) was purchased from Bethyl Labs. Highly cross-absorbed Alexa fluorophore conjugated secondary antibodies were purchased from Life Technologies.
Inhibitors used in this study were purchased from: (1) Cayman Chemicals -cytochalasin D (5µM), CK869 (10µM), Dynasore (30µM), GSK269962 (1µM), Nocodazole (3µM), ML-141 (5µM), EHT 1864 (5µM), BMS-5 (1µM) and (-) blebbistatin (5µM); (2) Cell Signaling -LY294002 (10µM); (3) Abcam -SMIFH2 (25µM).
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9

Immunocytochemical Staining Protocol

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For immunocytochemical staining, cells were washed twice in PBS, fixed in 4% paraformaldehyde for 5 min and then covered with 70% ethanol for storage at −20°C. When immunostained, cells were rehydrated in PBS and then stained with antibodies as described previously [11 (link)]. Primary antibodies were used at a dilution of 1:500, except for Mago (1:250) and eIF4A3 (antibodies a and b at 1:250 and 1:2000 respectively). Alexa fluorophore-conjugated secondary antibodies (Thermo-Scientific, Life Technology) were used at a dilution of 1:500. Fluorescently labelled cells were viewed using Zeiss Axioscope fluorescence microscope (Zeiss, Cambridge, U.K.), and images were captured using an Axiocam digital camera system (Zeiss) and Axiovision image analysis software (version 4.7, Zeiss). Images from immunocytochemistry were analysed on ImageJ and ratio of cytosolic over nuclear fluorescence was obtained by subtracting the background fluorescence measured in several points next to each cell. The corrected total cell fluorescence (CTCF) intensity is measured according to the formula: CTCF = integrated intensity – (area of selected cell × mean fluorescence of background readings).
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10

Histological and Immunofluorescence Staining

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For histology, brain sections were stained with hematoxylin and eosin. For immunofluorescence, frozen sections or confluent bEnd.3 cells were stained with primary antibodies followed by incubation with corresponding Alexa fluorophore-conjugated secondary antibodies (Thermo-Fisher Scientific). Immunofluorescence images were analyzed via corrected total fluorescence on ImageJ (NIH; see Supplementary Materials).
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