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7 protocols using β4 integrin

1

Antibody Staining Protocol for Stem Cell Markers

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The following antibodies were used for immunostaining: TCF3 (1:100; Fuchs laboratory18 (link)), TCF4 (1:200; Cell Signaling Technology, 2569), LEF1 (1:1,000; Cell Signaling Technology, 2230), TCF1 (1:200; Cell Signaling Technology, 2203), CD34 (1:100; eBiosciences, 13-0341), SOX9 (1:1,000; Fuchs laboratory56 (link)), β-catenin (1:500; BD, clone 14), GFP (1:5,000; Abcam, ab13970), Keratin 5 (1:200; Covance, PRB-160P), Keratin 10 (1:200; Covance, PRB-159P), Integrin β4 (1:100; BD, 553745), PPARγ (1:100; Santa Cruz Biotechnology, H-100, sc-7196). The following antibodies were used for immunoprecipitation and immunoblotting: TCF3 (for immunoprecipitation, Fuchs laboratory18 (link); for immunoblotting, 1:1,000; Santa Cruz Biotechnology, V-17, sc-12491), TCF4 (1:1,000; Santa Cruz Biotechnology, N-20, sc-8631), TLE (1:1,000; Santa Cruz Biotechnology, C-19, sc-13373), HDAC1 (1:1,000; Abcam, ab7028), β-catenin (1:2,000; Sigma, C7207), α-tubulin (1:2,000; Millipore, 05829). The following antibodies were used for FACS: integrin α6 (1:500; eBiosciences, PE-conjugated, 12-0495; PE-Cy7-conjugated, 25-0495), CD34 (1:100; eBiosciences, Alexa Fluor 660-conjugated, 50-0341), Sca1 (1:1,000; eBiosciences, PerCP-Cy5.5-conjugated, 45-5981).
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2

Antibody Panel for EMT Markers

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Antibodies against Vimentin, and αSMA were purchased from Sigma-Aldrich. N-cadherin, p44/42 MAPK, Phospho-p44/42 MAPK, EGFR antibodies were from Cell Signaling Technology (Danvers, MA); α-tubulin and ROBO1 from Abcam (Cambridge, MA). Fibronectin, Integrin αV, Integrin α2, Integrin α5, Integrin β1, Integrin β4 (BD Biosciences); MMP14 (Epitomics, Burlingam, CA); Ki67 Vector Laboratories (Burlingame, CA).
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3

Immunofluorescence Staining of Proteins

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Primary antibodies against the following proteins were purchased and used as follows: GFP (Abcam, ab13970, 1:3000), keratin 14 (K14) (BioLegend, PRB-155P, 1:1000), keratin 10 (K10) (BioLegend, PRB-159P, 1:1000), loricrin (BioLegend, Poly19051, 1:1000), nidogen (Santa Cruz Biotechnology, sc-33706, 1:2000), integrin β4 (BD Biosciences, clone 346-11A, 1:400), Ki67 (Abcam, ab15580, 1:500), BrdU (Abcam, ab6326, 1:500), CELSR1 (a gift from Elaine Fuchs, Rockefeller University, New York, NY, USA, 1:2000), Par3 (Millipore, 07-330, 1:500), pericentrin (BioLegend, PRB-432C, 1:500), E-cadherin (Cell Signaling Technology, 3195, 1:500), α-catenin (Sigma-Aldrich, C8114, 1:500), occludin (Abcam, ab31721, 1:100), vinculin (Millipore, clone 7F9, 1:200), γ-actin (Millipore, clone 2A3, 1:2000), G-actin (Millipore, clone JLA 20, 1:200), β-actin (Sigma-Aldrich, clone Ac15, 1:5000), and TMSB4X antibody (AB6019, Millipore; 1:500). Secondary antibodies were of the appropriate species/isotype reactivity conjugated to Alexa Fluor 488 or 647 or Rhodamine Red-X (Jackson ImmunoResearch, 703-545-155, 711-295-152, 712-605-153, 715-295-150, 1:500). F-actin was labelled with Phalloidin-iFluor 647 (Abcam, ab176759, 1:500). Nuclei were labelled with 4′,6-diamidino-2-phenylindole (DAPI; Sigma-Aldrich).
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4

Immunostaining Antibody Usage Protocol

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The following antibodies and dilutions were used: SOX9 (rabbit, 1:1000, Millipore), NFIB (rabbit, 1:1000, Active Motif), LHX2 (rabbit, 1:2000, Fuchs lab), K6 (guinea pig, 1:5000, Fuchs Lab), K24 (rabbit, 1:5000, Fuchs lab), CD34 (rat, 1:100, BD-Pharmingen), LEF1 (rabbit, 1:100, Fuchs lab), NFATc1 (mouse, 1:100, Santa Cruz), TCF3 (guinea pig, 1:200; Fuchs laboratory), TCF4 (rabbit, 1:300; Cell Signaling Technology), FHL2 (rabbit, 1:100, abcam), PRRG4 (rabbit, 1:100, abcam), CUX1 (rabbit, 1:200, Santa Cruz), β4-Integrin (rat, 1:100, BD-Pharmingen), GFP (chicken, 1:2000, Abcam), RFP (rabbit, 1:5000, MBL; or guinea pig, 1:3000, Fuchs lab). Secondary Abs coupled to Alexa488, RRX, or Alexa647 were from Life Technologies. Nuclei were stained using 4’6’-diamidino-2-phenylindole (DAPI).
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5

Immunostaining Antibody Usage Protocol

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The following antibodies and dilutions were used: SOX9 (rabbit, 1:1000, Millipore), NFIB (rabbit, 1:1000, Active Motif), LHX2 (rabbit, 1:2000, Fuchs lab), K6 (guinea pig, 1:5000, Fuchs Lab), K24 (rabbit, 1:5000, Fuchs lab), CD34 (rat, 1:100, BD-Pharmingen), LEF1 (rabbit, 1:100, Fuchs lab), NFATc1 (mouse, 1:100, Santa Cruz), TCF3 (guinea pig, 1:200; Fuchs laboratory), TCF4 (rabbit, 1:300; Cell Signaling Technology), FHL2 (rabbit, 1:100, abcam), PRRG4 (rabbit, 1:100, abcam), CUX1 (rabbit, 1:200, Santa Cruz), β4-Integrin (rat, 1:100, BD-Pharmingen), GFP (chicken, 1:2000, Abcam), RFP (rabbit, 1:5000, MBL; or guinea pig, 1:3000, Fuchs lab). Secondary Abs coupled to Alexa488, RRX, or Alexa647 were from Life Technologies. Nuclei were stained using 4’6’-diamidino-2-phenylindole (DAPI).
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6

Integrin and TGF-β Signaling Assay

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Antibodies included: β1 integrin (#610167), β4 integrin (#553745), α6 integrin (#555734) (all from BD Biosciences); Smad2 (#3103), phospho-Smad2 (S465/467, #3101), NF-κB p65 (#4764), phospho-NF-κB p65 (S536, #3033), E-cadherin (#4065), β-actin (#4967), Caspase-3 (#9662), Cleaved Caspase-3 (#9661), Cleaved Caspase-9 (#9509), cleaved PARP (#9544) (all from Cell Signaling), α-tubulin (#T5168, Sigma-Aldrich), ZO-1 (#sc-33725, Santa Cruz), and Alexa-Fluor®-conjugated secondary antibodies (Molecular Probes®, Life Technologies). Growth factors/hormones included: rhTGFβ1 (Invitrogen) and insulin (Sigma-Aldrich). The TβRI inhibitor SB-431542 was from InvivoGen.
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7

Immunohistochemical Staining Protocol

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For immunohistochemical and immunofluorescence stainings cryosections from Optimal Cutting Temperature compound (OCT, Tissue Tek) embedded tissues were fixed (4% PFA or in methanol), blocked (10% normal goat serum in PBS) and incubated with primary antibodies (diluted in blocking buffer) over night at 4 °C (ref. 60 (link)). Bound primary antibody was detected by incubation with peroxidase-conjugated (EnVision System, Dako) secondary antibody, followed by incubation with peroxidase substrate (Sigma), or Alexa-Fluor 488- or Alexa Fluor 594-conjugated antibodies (Invitrogen). Nuclei were counterstained with hematoxylin or 4′,6-diamidino-2-phenylindole (DAPI, Invitrogen). After washing slides were mounted in mounting medium. Images were taken with a Zeiss Meta 710 Confocal Microscope. Used primary antibodies and their dilutions (Supplementary Table 1): mTOR (Cell Signaling Technology, CST), S6-pS240/244 (CST); Akt-pS473 (CST); K14 (PROGEN Biotechnik); K10 (Covance); K14 (Covance); K15 (Covance); loricrin (Covance); filaggrin (Covance); p63 (Santa Cruz Biotech); P-cadherin (Zymed); active Caspase3 (CST); Survivin (CST), K8/18 (PROGEN Biotechnik); Par3 (EMD Millipore); LGN (EMD Millipore) and β4-integrin (BD Biosciences).
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