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367 protocols using anti gfp

1

Comprehensive Antibody Protocols for Neuronal Analysis

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Primary antibodies: anti-CNK2 (guinea pig, Eurogentec, custom-made), anti-CNK2 (rabbit, Sigma/Atlas, HPA 001502), anti-Homer-1 (guinea pig, Synaptic Systems, 160004), anti-MAP2 (guinea pig, Synaptic Systems, 188004), anti-MAP2 (mouse, Millipore, 05–346), anti-Mortalin (mouse, Antibodies Inc.,75–127), anti-PSD-95 (mouse, Antibodies Inc., 75–028), anti-SYNAPSIN-1 (rabbit, Synaptic systems, 106 103), anti-TNIK (mouse, Santa Cruz, sc-136103), anti-FLAG-HRP (mouse, Sigma), anti-GFP (chicken, Abcam, ab13970), anti-GFP (mouse, Roche, 11814460001), anti-GFP (goat, Abcam, ab6673), normal mouse IgG (sc-2025, Santa Cruz), anti-V5 (mouse, Invitrogen, R960–25), anti-V5 (rabbit, Millipore, AB3792). Secondary antibodies: anti-mouse-HRP (Dianova, 115-035-003), anti-rabbit-HRP (Dianova, 111-035-003), anti-goat-HRP (Santa Cruz, sc-2020), anti-guinea pig Alexa Fluor 405 (Abcam, ab175678), anti-mouse Alexa Fluor 405 (Invitrogen, A-31553), anti-guinea pig Alexa Fluor 488 (ThermoFisher, A-11073), anti-chicken Alexa Fluor 488 (Jackson Immuno Research, 703-545-155), anti-rabbit Alexa Fluor 568 (Life Technologies, A-11036), anti-mouse Alexa Fluor 568 (Life Technologies, A-11031).
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2

Immunohistochemical Profiling of CNS Markers

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For immunohistochemical, immunocytochemical, and Western blot procedures please reference the Supplemental Experimental Procedures. Antibodies used for immunohistochemistry were anti-GFP (Abcam, 1:500), anti-Brdu (Accurate,1:200, 30 min 2N HCl followed by 15 min 0.1M Boric Acid brain section pre-treatment), anti-NG2 (Millipore, 1:500), anti-GFAP (Sigma, 1:500), anti-ET-1 (Abbiotec, 1:200), anti-CD31 (BD Biosciences, 1:500), anti-Jagged-1 (Iowa Hybridoma Bank, 1:200), anti-IBA1 (Wako, 1:500), anti-MAG (Santa Cruz, 1:200), anti-MBP (Covance (SMI-99p), 1:1000), anti-Hes1 (Millipore, 1:1000), anti-CD11b/MAC1 (ABD Serotec, 1:400), anti-Olig2 (Millipore, 1:500), and anti-APC (Ab-7) (CC-1) (Calbiochem, 1:500). Antibodies used for immunocytochemistry were anti-GFP (Abcam, 1:500), anti-O1 (R&D systems, 1:500), anti-GFAP (Sigma, 1:500), and anti-NG2 (Millipore, 1:500). Antibodies used for Western Blot analysis include anti-MBP (Covance (SMI-99p), 1:5000), anti-MAG (Santa Cruz (sc-15324), 1:200), anti-CNPase (Covance, 1:500), anti-Jagged1 (Santa Cruz (sc-135955), 1:200), anti-β-actin(C4) (Millipore, 1:5000), anti-GFAP (Sigma, 1:5000), and anti-NICD (Iowa Hybridoma Bank C17.9C6, 1:1000).
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Comprehensive Immunohistochemical Profiling

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The following primary antibodies were used: anti-Krt14 (polyclonal chicken, 1:10000, Biolegend), anti-GFP (polyclonal rabbit, 1:1000, Abcam, RRID:AB_305564), anti-Krt5 (polyclonal rabbit, 1:4000, LabNed), anti-GFP (polyclonal goat, 1:1000, Abcam, RRID AB_305643), anti-GFP (polyclonal chicken, 1:500, Invitrogen, RRID:AB_2534023) anti-p63 (rabbit monoclonal, 1:1000, Abcam, RRI-D:AB_10971840), anti-EpCam (rabbit polyclonal, 1:500, Abcam, RRID: AB_1603782), anti-EpCam (rat polyclonal, 1:500, Biolegend, RRID:AB_1089027), anti-Krt7 (rabbit monoclonal, 1:1000, Abcam), anti-Krt20 (rabbit polyclonal, 1:1000, LabNed), anti-Krt8 (rat monoclonal, 1:250, DSHB, RRID:AB_531826), anti-Sox9 (rabbit polyclonal, 1:10000, Merck, RRID:AB_2239761), anti-Cldn18 (rabbit monoclonal, 1:2000, abcam).
The following secondary antibodies were used: anti-rabbit, anti-rat, anti-chicken, conjugated to AlexaFluor488 (1:500, Jackson ImmunoResearch), to rhodamine Red-X (1:500, Jackson ImmunoResearch) or to Cy5 (1:1000, Jackson ImmunoResearch).
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Co-IP and Ubiquitination Assays in N. benthamiana

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Co-IP and ubiquitination assays were also performed in N. benthamiana leaves as described earlier (Shan et al. 2020) (link). MaMYB60-GFP and MaBAH1-His were transiently expressed in N. benthamiana leaves by Agrobacterium-mediated transformation. For proteasome inhibition, leaves were infiltrated with 10 μM MG132 solution for 12 h and proteins were then extracted using the method described above in the IP-MS assay. The protein complexes were immunoprecipitated with an anti-GFP antibody and subjected to immunoblotting using anti-His (Abcam, cat. no. ab9108) and anti-GFP (Abcam, cat. no. ab290) antibodies for the Co-IP assay, and an anti-ubiquitin antibody for the ubiquitination assay.
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Immunofluorescence Staining of Organoids and Intestines

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IF staining of organoids was performed as previously described19 (link). Anti-Ki67 (Abcam, 1:250), anti-GFP (Abcam, 1:1000) or FITC-anti-UEA-1 (Sigma, 1:1000) antibodies were used for staining. For IF staining of mouse intestine tissues, tissue sections were deparaffinized in xylene and rehydrated with ethanol. After pre-incubation with 2% BSA and 2% goat serum, tissue sections were incubated with the anti-LIF (Novus, 1:500), anti-lysozyme (Abcam, 1:5000), anti-Olfm4 (Cell signaling, 1:1000) or anti-GFP (Abcam, 1:1000) antibodies overnight at 4° C. Slides were then incubated with Alexa Fluor® 555 Goat Anti-Rabbit IgG (H + L) or Alexa Fluor® 488 Goat Anti-mouse IgG (H + L) (1:200). Nuclei were stained with 4’, 6-diamidino-2-phenylindole (DAPI; Vector labs).
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Ionizing Radiation Induced DNA-PKcs Signaling

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SW480 cells were transfected with survivin/PI3K expression vectors for 48 hours and cell lysates were prepared at 1 hour after a 4 Gy irradiation. Equal amounts of lysates were added to coupled Dynabeads Protein G (Thermo Fisher Scientific) and antibody complexes: Anti-GFP (#ab290; Abcam, RRID:AB_303395), anti-Flag (#2368S; Cell Signaling Technology), anti-DNA-PKcs (#MS-369-P1; Thermo Fisher Scientific) or IgG (Mouse #SC-2025, Rabbit #SC-2027; Santa Cruz Biotechnology) and incubated in a rotating mixer at 5 rpm overnight at 4 C. Next, beads were washed with PBS and proteins were eluted by boiling, subjected to Western immunoblotting and detected with primary antibodies: anti-survivin (AF886; R&D Systems), Anti-GFP (ab290; Abcam), anti-DNA-PKcs (#MS-369-P1; Thermo Fisher Scientific), anti-Flag-HRP (#ab49763; Abcam), anti-b-actin (A5441-.2ML; Sigma-Aldrich), anti-Foxo3 (#2497S), or anti-Foxo3 pS253 (#9466S; Cell Signaling Technology). For detection, horseradish peroxidase-conjugated goat anti-rabbit and goat anti-mouse secondary antibodies (Santa Cruz Biotechnology) and LI-COR WesternSure Premium Chemiluminescent Substrate (LI-COR) were used.
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Antibody Staining for Cell Imaging

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The following primary antibodies were used: anti-GFP (chicken polyclonal antibody; Abcam, Cambridge, UK), anti-GFP (rabbit monoclonal antibody; Abcam), anti-bromodeoxyuridine (rat monoclonal antibody, clone ICR1, cross-reacts with CldU but not with IdU; Abcam), anti-IdU (mouse monoclonal antibody, clone 32D8.D9; Abcam), anti-von Willebrand factor (anti-vWF) (rabbit polyclonal antibody; Dako, Ely, UK), anti-platelet-derived growth factor receptor α (anti-Pdgfrα) (rabbit polyclonal antibody; Abcam) and anti-CD16/CD32 (goat monoclonal antibody; R&D Systems, Minneapolis, MN, USA).
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Immunohistochemical Analysis of Retinal Tissue

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Eyes were harvested and fixed for 1 h in 4% PFA. Following cryopreservation in 10%, 20%, and 30% sucrose at 4°C for 30 min, 2 h and overnight, respectively, eyes were embedded in Tissue-Tek OCT compound (Electron Microscopy Sciences) and sectioned at 10 μm using a cryostat. The following primary antibodies were incubated with tissue sections overnight at 4°C: anti-Iba1 (1:200, Abcam), anti-CD68 (1:250, Bio-Rad), anti-GFAP (1:500, Abcam), anti-DLK (1:100, Genetex), anti-Atf3 (1:200, Novus Biologicals), anti-GFP (1:500, Abcam), anti-Il22Ra1 (1:200, Bioss), anti-Rbpms (1:100; PhosphoSolutions), anti-βIII-tubulin antibody (1:500, Promega). Following primary antibody application and washing, tissue was subsequently incubated in AF594, AF546, AF647, or AF488 secondary antibodies (1:400; Invitrogen, Thermo Fisher) for 1 h. DAPI (1:1000; Invitrogen) was used to label nuclei. Images were captured using an Axio Imager M2 (Zeiss), a LSM 880 confocal (Zeiss), or a TCS SP8 confocal (Leica). To visualize AAV infection in wholemount retinas, tissue was stained with an anti-GFP (1:500, Abcam) antibody for 3 d at 4°C. Retinas were subsequently washed in PBS, incubated with an AF488 secondary antibody (1:400; Invitrogen) for 2 h at room temperature, and washed in PBS.
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9

Immunohistochemical Analysis of Retinal Tissue

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Eyes were harvested and fixed for 1 h in 4% PFA. Following cryopreservation in 10%, 20%, and 30% sucrose at 4°C for 30 min, 2 h and overnight, respectively, eyes were embedded in Tissue-Tek OCT compound (Electron Microscopy Sciences) and sectioned at 10 μm using a cryostat. The following primary antibodies were incubated with tissue sections overnight at 4°C: anti-Iba1 (1:200, Abcam), anti-CD68 (1:250, Bio-Rad), anti-GFAP (1:500, Abcam), anti-DLK (1:100, Genetex), anti-Atf3 (1:200, Novus Biologicals), anti-GFP (1:500, Abcam), anti-Il22Ra1 (1:200, Bioss), anti-Rbpms (1:100; PhosphoSolutions), anti-βIII-tubulin antibody (1:500, Promega). Following primary antibody application and washing, tissue was subsequently incubated in AF594, AF546, AF647, or AF488 secondary antibodies (1:400; Invitrogen, Thermo Fisher) for 1 h. DAPI (1:1000; Invitrogen) was used to label nuclei. Images were captured using an Axio Imager M2 (Zeiss), a LSM 880 confocal (Zeiss), or a TCS SP8 confocal (Leica). To visualize AAV infection in wholemount retinas, tissue was stained with an anti-GFP (1:500, Abcam) antibody for 3 d at 4°C. Retinas were subsequently washed in PBS, incubated with an AF488 secondary antibody (1:400; Invitrogen) for 2 h at room temperature, and washed in PBS.
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Immunostaining of Stem Cell Markers

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The following primary antibodies were used: anti-Krt14 (polyclonal chicken; 1:10,000; BioLegend), anti-GFP (green fluorescent protein; polyclonal rabbit; 1:1000; Abcam, RRID:AB_305564), anti-GFP (polyclonal goat; 1:1000; Abcam, RRID AB_305643), anti-GFP (polyclonal chicken; 1:500; Invitrogen, RRID:AB_2534023), anti-p63 (rabbit monoclonal; 1:1000; Abcam, RRID:AB_10971840), anti-Krt8 (rat monoclonal; 1:250; DSHB, RRID:AB_531826), anti-Entpd2 (rabbit; 1:4000; http://ectonucleotidases-ab.com, mN2-36Li6), anti-Gnat3 (goat polyclonal; 1:500; Novus Biologicals, NBP1-20926), anti-Snap25 (rabbit polyclonal; 1:500; Sigma-Aldrich, S9684), anti-Tas1r2 (rabbit; 1:500; Invitrogen, PA5-99935), anti-Lef1 (rabbit monoclonal; 1:100; Thermo Fisher Scientific, MA5-14966), anti-Sox2 (rabbit monoclonal; 1:200; Abcam ab92494).
The following secondary antibodies were used: anti-rabbit, anti-rat, anti-chicken, anti-goat conjugated to Alexa Fluor 488 (1:500; Jackson ImmunoResearch), to rhodamine Red-X (1:500; Jackson ImmunoResearch), or to Cy5 (1:1000; Jackson ImmunoResearch).
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