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Cyanine3 (cy3)

Manufactured by Jackson ImmunoResearch
Sourced in United States, United Kingdom, Panama, Germany, Cameroon, China

Cy3 is a fluorescent dye that can be used as a labeling agent for various biomolecules such as proteins, nucleic acids, and other biological molecules. It exhibits an excitation maximum at 550 nm and an emission maximum at 570 nm, making it suitable for detection and visualization applications.

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406 protocols using cyanine3 (cy3)

1

Immunohistochemical Analysis of Cholinergic Neurons

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Adult mice were anesthetized with an overdose of pentobarbital and then transcardially perfused with 4% paraformaldehyde (PFA). Mouse brain was dissected and fixed in 4% PFA for 4 h. After cryoprotection in 30% sucrose, brain sections (35 μm) were cut on a cryostat microtome (Leica CM1950, Leica Biosystems, Wetzlar, Germany). After rinsing with PBS and 0.3% Triton-X in 0.1 M PBS (PBST), the brain sections were blocked with 2% (w/v) bovine serum (BSA) in PBST for 1 h. Then, the brain sections were incubated with primary antibodies at 4°C for 48 h and secondary antibodies at room temperature for 2 h. Images were collected using a Zeiss LSM510 Meta or Nikon A1 confocal microscope and analyzed using FIJI. The antibodies used were as follows: anti-choline acetyltransferase (1:200, goat, AB144P, MERCK, Kenilworth, NJ, United States), anti-NK1R (S8305, rabbit, 1:5,000, Sigma-Aldrich, St. Louis, MO, United States), goat anti-rabbit for NK1R (Cy3 and Alexa Fluor 488, Jackson ImmunoResearch Laboratories, Inc., West Grove, PA, United States), donkey anti-goat for choline acetyltransferase (Cy3 and Alexa Fluor 488, Jackson ImmunoResearch Laboratories, Inc., West Grove, PA, United States), and Cy3-streptavidin (1:500).
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2

Immunofluorescence Staining of WIPI2 and LC3B

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WIPI2 mouse mAb [2A2] (Abcam, ab105459, 1:2000), LC3B rabbit pAB (MBL, PM036, 1:500). Cy3, Cy5 and DyLight649-conjugated secondary antibodies were obtained from Jackson ImmunoResearch (Cy3: 715-165-151 and 711-165-152, Cy5: 711-175-152, DyLight649: 711-495-152, 1:500 for all).
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3

Immunohistochemical Analysis of Kidney Injury

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For injury marker detection, 10 µm slides from each swine in cREBOA and iREBOA groups were cut from the cortex of fresh frozen kidneys (stored in − 70 °C). Primary antibodies were diluted in 5% donkey serum and 95% primary buffer (0.01 M PBS + 0.1% NaN3 + 0.3% triton + 5% bovine serum albumin). NKCC2 antibody (1:2000, Everest Biotech, EB09143) was combined with either Osteopontin (1:400 Abcam 8448, Product ID: GR5225573-4), NGAL (1:1000, BioSite, Product ID: GTX60965) or Vimentin (1:100, BioGenex, Product ID: MU074-UC). Slides were rinsed for 10 min in PBS and incubated with primary antibodies overnight at 4 °C. Then, slides were rinsed and incubated with secondary antibodies for 1 h in room temperature, and all dilutes were 1:400 in 5% swine serum and secondary buffer (0.01 M PBS + 0.1% NaN3 + 0.3% triton). A mixture of Cy2 (Jackson ImmunoResearch, Product ID: 705225147) and of Cy3 (Jackson ImmunoResearch, Product ID: 715165151) was used for slides stained with Osteopontin or Vimentin. For slides stained with NGAL, a mixture of Cy2 (Jackson ImmunoResearch, Product ID: 705225147) and of Cy3 (Jackson ImmunoResearch, Product ID: 711165152) was used. Slides were then rinsed in 0.01 M PBS and mounted with Mowiol.
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4

Drosophila Ovary Immunohistochemistry

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The following primary antibodies were used: guinea-pig anti-Tj (G5 or GP6, 1:5000) [57 (link)], rat anti-Bab2 (R10, 1:3000; or R7, 1:2000) [20 (link)], rabbit anti-Vasa (1:2000) [80 (link)], rabbit anti-Vasa (d-260, 1:500; Santa Cruz Biotechnology), chicken anti-Vasa (1:5000; gift from K. Howard and M. Van Doren), rabbit anti-α-spectrin (#254, 1:1000; gift from D. Branton), mouse anti-LamC (LC28.26, 1:50), mouse anti-Hts (1B1, 1:5), mouse anti-N (C17.9C6, 1:5; C458.2H, 1:5), mouse anti-Dl (C594.9B, 1:5), mouse anti-Engrailed (4D9, 1:5), and mouse anti-ßPS integrin (CF.6G11, 1:10) (Developmental Studies Hybridoma Bank), rabbit anti-pMad (PS1, 1:250; gift from T. Tabata) [81 (link)], rabbit anti-pMad (pSmad1/5, 41D10, 1:100; Cell Signalling), rabbit anti-ß-galactosidase (1:1500; MP Biomedicals), and rabbit anti-GFP (1:100; BD Biosciences). Secondary antibodies (1:400) were conjugated either to Cy3, Cy5 (Jackson Immuno Research Laboratories), Alexa-405, Alexa-555, Alexa-488, or Alexa-647 (Molecular Probes, Life Technologies). Ovaries were mounted in Vectashield (Vector Laboratories).
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5

Immunofluorescence Staining and 3D Reconstruction of Extracellular Matrix and Neural Markers

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For in vitro study, samples were immunofluorescently stained for FN (Polyclonal IgG from Rabbit, EMD Millipore), Laminin (LN, Boster, Wuhan, China), Vitronectin (VN, Boster), and NG2 (a chondroitin sulfate proteoglycan, EMD Millipore) Neurofilament‐150 (NF, Sigma), Intergrin‐β1 (EMD Millipore), β‐III tubulin (Sigma). For in vivo study, rats were perfused with 4% paraformaldehyde and their spinal cord were dissected, embedded in OTC and horizontally sectioned into 30‐μm‐thick slices. Primary antibodies including those targeting against FN (Polyclonal IgG from Rabbit, EMD millipore), NF (Sigma) and growth associated protein‐43 (GAP‐43, Sigma) were used for in vivo study. After blocking with 10% goat serum, the respective primary antibodies were used along with Cy3, DyLightTM405‐tagged goat IgG or DyLightTM649‐tagged goat IgG as the secondary antibody (Jackson ImmunoResearch). Hoechst33342 was used for counterstaining of nucleus as necessary. The sections were observed and imaged under the confocal microscope (Carl Zeiss, Germany). For 3D reconstruction, Z stack scanning was first performed, followed by image processing with Zen 2012 software (Carl Zeiss).
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6

Immunostaining of TDP-43, TFIIS, and MAP2

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Following primary antibodies were used for immunostaining, α-TDP-43 (10782-2-AP) from ProteinTech (used at 1:500); α-TFIIS (611204) from BD Transduction Laboratories (used at 1:275); α-MAP2 (M4403) from Sigma-Aldrich (used at 1:1000). Secondary antibodies were conjugated to Cy-3 or Cy-5 (1:500, Jackson ImmunoResearch Laboratories). Coverslips containing transfected neurons were fixed as described above followed by 3 washes with 1X PBS. The coverslips were then incubated with primary antibodies) diluted in gelatin blocking buffer at 4 °C overnight in a humidified chamber (30 minutes at room temperature for MAP2). Coverslips were then washed 3 times with 1X PBS and incubated with secondary antibodies at room temperature for 2 hours. Coverslips were then washed 3 times with 1X PBS, submerged in MilliQ water and then mounted on glass microscope slides with Aquamount (Lerner Laboratories). Neurons were imaged using an Ni-E inverted microscope equipped with a Nikon C2 confocal head and a 60X oil (NA 1.4) objective, using similar acquisition settings for laser power, offset and detector gain across conditions in a blinded manner.
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7

Immunostaining of E7.5 Mouse Embryos

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E7.5 mouse embryos were dissected in 1× PBS and fixed in 4% paraformaldehyde in 1× PBS (PFA) for 30 min. After washing and permeabilization in PBS including 0.1 Triton X‐100 (PBTx), embryos were blocked in 1× PBTx/1% BSA. Embryos were labelled using rabbit anti‐LMBD1 antibody (1:500, HPA019547; Sigma‐Aldrich, Taufkirchen, Germany) over night at 4°C, followed by incubation with anti‐rabbit Cy3 (1:5000, 111‐166‐045; Jackson ImmunoResearch Laboratories, West Grove, PA, USA) conjugated secondary antibody. The embryos were mounted in fluorescence mounting medium (Dako, Hamburg, Germany), examined with a Zeiss Apotome Axiovert 200 (Munich, Germany) and processed with AxioVision v.4.8 and Adobe Creative Suite 4 (Zeiss, Munich, Germany).
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8

Immunostaining with Antibody Panel

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The following primary antibodies were used for immunostaining: goat anti-EphB2 (1:200–1:500, R&D), mouse anti-EphB2 (1:200–1:500, Invitrogen), mouse anti-HA (1:1000, BioLegend), mouse anti-FLAG (1:2000,Sigma), rabbit anti-actin (1:1000, Sigma), goat anti-ephrin-B1 (1:200, R&D systems), guinea pig anti-VGLUT1 (1:5000, Millipore). Secondary antibodies Atto 425, Dylight 488 or Cy2, Dylight 647 or Cy5, and Cy3 from Jackson ImmunoResearch, Rockland or Abcam were used from 1:200 to 1:500.
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9

NLRP3 Inflammasome Activation Assay

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LPS (L4391 for cell culture, L3012 for mice), ATP, MCC950, tamoxifen, and 4-hydroxytamoxifen were purchased from Sigma-Aldrich (St. Louis, MO, USA). Anti-F4/80 antibody (Cat# ab6640, RRID:AB_1140040) was obtained from Abcam (Cambridge, United Kingdom). Cy3- (Cat# 712-165-050, RRID:AB_2340666) and Alexa Fluor 488-conjugated (Cat# 712-545-150, RRID:AB_2340683) anti-rat IgG antibodies were purchased from Jackson ImmunoResearch (West Grove, PA, USA). FITC-dextran (46944) and TRITC-dextran (T1037) were obtained from Sigma-Aldrich. The IL-1 receptor antagonist (Cat# CYT-203) was purchased from ProSpec (Rehovot, Israel). Anti-mouse caspase-1 (Cat# AG-20B-0042, RRID:AB_2490248) and anti-NLRP3 (Cat# AG-20B-0014, RRID:AB_2490202) antibodies were obtained from AdipoGen Life Sciences (San Diego, CA, USA). Anti-mouse IL-1β antibody (Cat# AF-401-NA, RRID:AB_416684) was obtained from R&D Systems (Minneapolis, MN, USA), and anti-ASC antibody (Cat# SC-22514-R, RRID:AB_2174874) was purchased from Santa Cruz Biotechnology (Dallas, TX, USA). Anti-GFP antibody (Cat# NB600-308, RRID:AB _10003058) was obtained from NOVUS Biologicals.
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10

Dual Immunostaining of Adherent Cells

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Cells were planted on 24-well plates chamber slides and grew overnight to adhere. Dual immunostaining was performed sequentially. First, the cells were fixed with cooled 4% paraformaldehyde for 30 min and permeabilized with 0.25% Triton X-100 for 1 h. After being blocked with 5% BSA for 1 h, the cells were incubated in 5% BSA at 4 °C overnight with the primary antibody. Next, the cells were washed with PBS twice and incubated in 5% BSA for 1 h at room temperature with secondary antibodies Alexa Fluor 488 (Lot:12194) and Cy3(Lot:125099) from Jackson ImmunoResearch (USA). Nuclei were stained with Hoechst (Beyotime, 33342, Shanghai, China). Photographs were taken using a confocal microscope (Carl Zeiss Microscopy GmbH, Germany).
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