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11 protocols using donkey anti mouse alexa 647

1

ABC-DLBCL Cell Line Culture and Screening

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ABC-DLBCL cell lines were maintained in RPMI 1640-GlutaMAX medium (Gibco 61870-044) supplemented with 15% fetal bovine serum (Biowest S181B-050) and 1% penicillin-streptomycin (Gibco 15140-122) at 37°C in a humidified atmosphere containing 5% CO2. Cell lines were obtained as previously described (21 (link)) and their identity was authenticated by short tandem repeat DNA profiling (IDEXX BioResearch, Ludwigsburg, Germany). Real Time Glo was from Promega (G9713). The Selleck Cambridge Cancer Compound library was obtained from and printed onto 384-well plates [384 well, PS, F-bottom, μclear, white, lid, sterile, Greiner Bio-One 781098 (82050-076)] by the High-Throughput Chemical Biology Screening Platform at the Center for Molecular Medicine Norway (NCMM). Antibodies used were: rabbit-anti-phospho-BRCA2(Ser3291) (AB9986 Millipore), rabbit-anti-Cleaved-PARP (Asp214) Alexa647-conjugate (#6987, Cell Signaling), rabbit-anti-phospho-histone 3-Ser10 (06-570, Millipore), Alexa488 anti-rabbit (A21206, Life Technologies), and Alexa647 donkey-anti-mouse (Jackson ImmunoResearch, UK). The DNA stain FxCycle™ Far Red (200 nM FxCycle and 0.1mg/ml RNase A) (Thermo Fisher Scientific) was used together with Pacific Blue (Thermo Fisher Scientific, P10163) staining, and Hoechst 33258 (Sigma-Aldrich) (1.5 μg/ml) in other experiments.
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2

Immunostaining of Muscle Cell Markers

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Immunostaining was performed with modifications from standard protocol previously described (Nielsen and Dymecki, 2010 (link)). Primary antibody dilutions: rat anti-CD13 (MCA2183GA) (1:500) (AbD Serotec); mouse anti-desmin (D33) (1:50) (DAKO/Agilent); mouse anti-N-cadherin (3B9) (1:300) (Invitrogen); rat anti-Pdgfrβ (CD140b) (1:50) (Invitrogen). Secondary antibodies: Cy3 donkey anti-rat; Alexa647 donkey anti-mouse; Alexa647 donkey anti-rat (all dilutions 1:500) (Jackson ImmunoResearch). For EdU incorporation assay, mice were injected intraperitoneally with 10 μg/gram of body weight with EdU at P5–7 or P8–10 or P12–14. On the day of harvest (P7 or P10 or P14), tissue was harvested 2 h post-injection. Detection of EdU used Click-iT™ Plus chemistry, with AlexaFluor® 647 component following manufacturer’s instructions (Invitrogen). Cell nuclei were counterstained with 4′,6′-diamidino-2-phenylindole (DAPI). Tissue sections were mounted with ProLong Gold™ (Invitrogen) and coverslipped for imaging.
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3

Drosophila Brain Immunostaining Protocol

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Primary antibodies used include mouse anti-Brp94 (link) (nc82, DSHB, RRID AB_2314866) at 1:50 v/v dilution, anti-Dlg95 (link) (4F3, DSHB, RRIDAB_528203) at 1:50 v/v dilution, and chicken anti-GFP (Ab13970 Abcam, RRID: AB_300798) at 1:2000 v/v dilution. Secondary antibodies used include Alexa 488 goat anti-chicken (A-11039 Thermo Fisher Scientific, RRID: AB_2534096) at 1:1000 v/v dilution and Alexa 647 donkey anti-mouse (715-605-151, Jackson ImmunoResearch, RRID: AB_2340863) at 1:500 dilution. Adult brains were dissected in cold PBS (0.1 mM PB) and fixed with 4% paraformaldehyde for 30 min as previously described13 . Briefly, fixed brains were washed three times in PBST (0.2% Triton-100, 85111 Thermo Fisher Scientific) and incubated in primary antibodies in PBST at 4 °C for 48 h, after which they were rinsed and incubated in secondary antibodies in PBST at 4 °C. Finally, the brains were washed three times in PBST for 15 min each and mounted on microscope slides in Vectashield Vibrance (H-1700 Vector Laboratories, Burlingame, CA) and covered with a coverslip. Slides containing mounted fly brains were viewed under a Leica TCS SP8 STED 3X or a Zeiss LSM700 upright microscope using a 20× objective. Maximum intensity projections were calculated using Leica Application Suite X software on the z-axis.
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4

Mapping Serotonin and Retrogradely-Transported Projections in the NI Region

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The relative localization of in the NI region of RLN3, serotonin and retrogradely-transported BDA in the NI region after MS injection was assessed by immunofluorescent detection of BDA – 5HT – RLN3. Briefly, free-floating brain sections were rinsed and incubated in blocking solution for 1 h and then transferred to primary antibody solution containing 1:2000 polyclonal rabbit anti-serotonin (S5545, Merck (Sigma-Aldrich); Madrid, Spain) and 1:5 mouse anti-RLN3 overnight at room temperature. For BDA – 5HT – RLN3 visualization, brain samples were incubated with 1:200 Alexa 488 donkey anti rabbit (#711–545-152, Jackson ImmunoResearch; Cambridge, United Kingdom), 1:200 Alexa 647 donkey anti-mouse (#715–605-150, Jackson ImmunoResearch; Cambridge, United Kingdom) and 1:200 Cy3 streptavidin (#016–160-084, Jackson ImmunoResearch; Cambridge, United Kingdom) for 2 h at room temperature. Finally, sections were mounted on clean slides and coverslipped using Fluorsave™.
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5

Immunostaining Procedure for Zebrafish Embryos

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Immunostaining was performed as previously described (Lewellis et al., 2013 (link)). Briefly, embryos were fixed in 4% PFA for two hours at room temperature. Following fixation, they were permeabilized in methanol at −20°C, rehydrated, permeabilized with 10 μg/ml proteinase K in PBST for 8 minutes at room temperature, and post-fixed in 4% PFA for 20 minutes at room temperature. Embryos were blocked in 2% BSA in PBST for 1 hour and incubated in primary antibody at 4 degree C overnight. Following PBST washes, they were incubated in secondary antibody overnight at 4 degree C. Rabbit anti-GFP (1:1000, Invitrogen), affinity-purified goat anti-GFP (1:100, (Venkiteswaran et al., 2013 (link))), affinity-purified sheep anti-mCherry (1:1000, custom-made antibody generated against bacterially-produced, recombinant full-length mCherry protein by Covance), zns-2 (1:50, Developmental Studies Hybridoma Bank) and mouse anti-ZO-1 (1:500, ThermoFisher) were detected with goat anti-rabbit-Alexa488 (1:1000, Invitrogen), donkey anti-rabbit- Cy3 (1:1000, Jackson ImmunoResearch), donkey anti-goat-Alexa488 (1:1000, Invitrogen), donkey anti-goat-Cy3 (1:1000, Jackson ImmunoResearch), donkey anti-sheep-Alexa647 (1:1000, Jackson ImmunoResearch), donkey anti-mouse-Cy3 (1:1000, Jackson ImmunoResearch) and donkey anti-mouse Alexa647 (1:1000, Jackson ImmunoResearch) secondary antibodies.
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6

Immunocytochemistry for Cellular Components

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IF experiments were performed as previously described (Welshhans and Bassell, 2011 (link)), and the following primary antibodies were used: mouse anti-paxillin antibody (1:500), mouse anti-vinculin antibody (1:500), rabbit anti-RACK1 antibody (1:500; Santa Cruz Biotechnology), mouse anti-RACK1 antibody (1:500; Santa Cruz Biotechnology), rabbit anti-ribosomal protein S6 antibody (1:100; Santa Cruz Biotechnology), mouse anti-ribosomal protein S6 antibody (1:100; Santa Cruz Biotechnology), and mouse anti-ribosomal RNA 5.8s Y10b antibody (1:100, Abcam). The following secondary antibodies were used: goat anti-mouse Alexa 488, goat anti-rabbit Alexa 488, goat anti-mouse Cy3 and donkey anti-mouse Alexa 647 (all from Jackson ImmunoResearch). Rhodamine phalloidin or Alexa Fluor 350 phalloidin (Life Technologies) was also added in experiments during the secondary antibody incubation to stain F-actin for visualization of growth cone area.
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7

Immunolabeling of GluR2/3 and Calretinin

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Perfusion and tissue slicing were performed exactly as previously described [19 (link)]. Free-floating sections were permeabilized and blocked in 0.3% Triton X-100 and 3% normal donkey serum (Jackson ImmunoResearch, West Grove, PA) in PBS for 2 h at room temperature. Sections were incubated in rabbit anti-GluR2/3 (AB1506, Millipore Sigma, Burlington, MA, 1:200) and mouse anti-calretinin (MAB1568, Millipore Sigma, 1:1000) overnight at 4 °C. Sections were washed three times in PBS for 10 min each and then incubated in donkey anti-rabbit Alexa 488 and donkey anti-mouse Alexa 647 (Jackson ImmunoResearch, 1:1000) for 2 h at room temperature. Slices were washed in PBS, incubated with 4′,6-diamidino-2-phenylindol (DAPI, Millipore, 1:5000) for 5 min, washed again in PBS and mounted using Fluoromount-G (Electron Microscopy Sciences, Hatfield, PA).
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8

Immunofluorescent Staining of Neuronal Markers

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The following primary antibodies were used for cell culture and/or whole mount stainings: B-III tubulin (chicken, abcam® ab107216) (1:1000), NeuN (rabbit, Merck Millipore #ABN78) (1:1000), GFP (mouse, Life Technologies A11121) (1:200), c-myc (mouse, Developmental Studies Hybridoma Bank 9E 10) (1:200), and MECP2 (mouse, abcam® ab50005) (1:1,000). Cy3-streptavidin (Jackson ImmunoResearch 016-160-084) (1:400) was used to visualize neurobiotin filled neurons. Additional secondary antibodies, including goat anti-mouse Alexa 488 (Life Technologies A-11001), donkey anti-mouse Alexa 647 (Jackson Immuno Research 715-605-150), anti-rabbit Cy3 (Life Technologies A10042), and donkey anti-chicken Cy5 (Jackson ImmunoResearch 703-175-155) were applied at a concentration of 1:400.
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9

Tissue Preparation and Immunofluorescence Staining

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Spleens, thymuses and Intestines were harvested fresh, directly embedded and frozen in OCT compound (Sakura, Torrance, CA), and 10 μm sections were cut at −20°C (Leica CM 3050 S). Frozen sections were left at RT to air dry for 5 min, fixed with cold acetone for 10 min (spleen) or incubated with 0.1 M PBS followed by 15 min postfixation in 4% paraformaldehyde in 0.1 M PBS (intestine), and subsequently washed 3 times with PBS for 10 min. Sections were incubated in blocking buffer (5% normal donkey serum and 0.8% Triton X-100) for 1 h at RT. Primary antibodies were diluted in blocking buffer and incubated overnight at 4°C, washed 3 times with PBS for 10 min and then incubated with secondary antibodies diluted in blocking buffer as needed for 1 h at RT. Slides were washed 3 times with PBS 10 min each, air-dried and cover-slipped with ProLong Gold (Thermo Fisher Scientific, Carlsbad, CA), and imaged on a confocal microscope (Zeiss LSM-710). Anti-CD3 Alexa 488, Phalloidin Green 488, and anti-Podoplanin Alexa 488 were from Biolegend (San Diego, CA). Anti-B220 eFluor570 and donkey anti-goat Alexa 568 were from Thermo Fisher Scientific (Carlsbad, CA). Anti-pan neurofilament, anti-NF200, and anti-Contactin were from Neuromics (Edina, MN). Donkey anti-mouse Alexa 647 was from Jackson Immunoresearch (West Grove, PA).
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10

Immunolabeling of Drosophila Brain Tissues

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In brief, immunostaining was performed as previously described129 (link),131 (link). Tissues were dissected in PBS and fixed in 4% paraformaldehyde (PFA) in PBS at 4°C on a nutating platform, then transferred to 0.2% Triton X-100 in PBS (0.2% PBST) at 4°C on a nutating platform for overnight incubation. For immunostaining, the samples were blocked in 5% BSA/2% PBST and incubated with the primary antibodies: Rat anti-Elav (1:500, 7E8A10, DSHB132 (link)), Mouse anti-Repo (1:50, 8D12, DSHB,) and Mouse anti-S1P (1:100, Z-P300. Echelon Biosciences) diluted in 5% BSA/0.2% PBST at 4°C for 48 hrs with nutation, then washed 3x with 0.2% PBST for 5 min. The secondary antibodies Donkey anti-rabbit (Cy3) and Donkey anti-mouse (Alexa-647) (Jackson ImmunoResearch) were diluted 1:250 in 5% BSA/0.2% PBST and incubated with the samples at 4°C for 48 hrs on a rotating platform. Samples were cleared and mounted in RapiClear (SunJin Lab Co.) and imaged with a Leica SP8 Confocal Microscope under a 20x objective lens and analyzed using Fiji133 (link). Pupal brain staining was performed as described in86 (link).
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