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7 protocols using lamin b1 antibody

1

Quantitative Immunoblotting Analysis Techniques

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These protocols have been performed following standard techniques. Ring1B, Fak and p63 antibodies were purchased from Millipore (Billerica, MA, USA). pY861-Fak antibody was from Biosource International (Life Technologies, Paisley, UK). Anti-activated MAP kinase (diphosphorylated Erk 1/2) was from Sigma (St. Louis, MO, USA) and Erk 2 (C-14) antibody was purchased from Santa Cruz Biotechnology (Heidelberg, Germany). Lamin B1 antibody was from Abcam (Cambridge, MA, USA) and Vinculin and α-Tubulin antibodies from Sigma (St. Louis, MO, USA). Fluorescent secondary antibodies were obtained from Invitrogen (Life Technologies, Paisley, UK) and Jackson ImmunoResearch Laboratories (West Grove, PA, USA). Rhodamine-Phalloidin was from Sigma (St. Louis, MO, USA). For focal contact counting, the cells were labeled with anti-Vinculin antibody and the Vinculin-positive patches were manually counted.
Western blot quantification was performed using Image J densitometry software. The intensity of individual bands was normalized to Lamin B or α-Tubulin signal, as a measure of protein relative abundance in the different samples and referred to control conditions.
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2

Antibodies and Reagents for DNA Damage Response

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The anti‐α‐tubulin antibody, aphidicolin, and nocodazole were purchased from Sigma‐Aldrich. The anti‐p‐ATM (Ser1981), cGAS, and GFP antibody were from Santa Cruz. Antibodies against ATM, Flag, mouse cGAS, human cGAS, STING, MRE11, PARP1, H2A, H2A.X, γ‐H2A.X p‐IRF3, and IRF3 were from Cell Signaling Technology; Alexa 488‐anti‐Sca‐1 was from Invitrogen and PECY7‐anti‐cKit; V450‐Ly6G and FITC‐anti‐GR1 were from BD Pharmingen; 2′,3′‐cGAMP and immunostimulatory DNA (ISD) were from InvivoGen; and ATP was from New England Biology, while GTP, Rad51, and Lamin B1 antibody were from Abcam.
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3

Mapping Lamin B1 Localization by Dam-ID

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HT1080 cells expressing inducible Dam‐Lamin were plated both on coverslips and in a regular culture dish and Dam‐Lamin B1 expression was activated overnight with 500 nM Shield1 (Aobious #AOB1848). Cells grown in the culture dish were trypsinized and processed with the pA‐DamID protocol, but without pA‐Dam or Dam added. The cells were then fixed on poly‐L‐lysine‐coated coverslips as described above. As soon as the culture dish cells were permeabilized, the cells on coverslips were fixed with 2% formaldehyde/PBS for 10 min, permeabilized for 20 min with 0.5% NP‐40/PBS and blocked with 1% BSA/PBS for 1 h. Next, coverslips were incubated for 1 h at room temperature with 1:500 Lamin B1 antibody (Abcam ab16048, rabbit) and washed 3× with PBS. PBS with 1:500 m6A‐Tracer protein (1.15 mg/ml) and 1:500 secondary anti‐rabbit antibody (Jackson 711‐585‐152, donkey, Alexa 594) was added and incubated for 1 h, followed by washing with PBS (3×) and H2O (1×), and mounted with Vectashield + DAPI. For comparison, wild‐type HT1080 cells (not expressing Dam‐Lamin B1) were subjected to pA‐DamID using Lamin B2 antibody and processed as the HT1080 Dam‐Lamin B1 HTC75 cells.
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4

Quantifying Nuclear NFκB Levels

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For total expression of NFκB measurement, left ventricle tissue homogenate was analyzed by Western blot using anti-NFκB p65 antibody from Abcam (Cat. No. AB32536). To detect the nuclear fraction of NFκB p65, left ventricle tissue was homogenized and the nuclear and cytoplasmic isolation was performed using a commercial extraction kit (Fisher Thermo, Cat. No. 78835). Western blot was then used to analyze the levels of NFκB p65 in nuclear and cytosol fractions. Lamin B1 was used as a marker and loading control for the nuclear fraction. The Lamin B1 antibody was purchased from Abcam (Cat No: AB16048). The nuclear/cytosol ratio of NFκB was calculated after correction by Lamin B1 and GAPDH, respectively.
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5

Western Blot Analysis of Differentiating EBs

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Western blot analysis was performed as described previously49 (link). Briefly, differentiating EBs following –Dox and + Dox treatment were lysed in ice-cold lysis buffer for 30 minutes and centrifuged at 10000 rpm for 10 min at 4 °C. Equal amounts of protein was loaded on 10% SDS-polyacrylamide gels. The PVDF membrane was blocked with 5% (w/v) milk protein and incubated with a goat-PCNA antibody [Santa Cruz, 1:1000] and LaminB1 antibody (Abcam; 1:1000) for an overnight period at 4 °C. The membrane was subsequently incubated with anti-goat HRP-conjugated secondary antibody and was visualized using SuperSignal West Femto Maximum Sensitivity Substrate kit (Thermo Scientific, USA) according to the manufacturer’s instructions. The protein bands were visualized and imaged using ImageLab 6.0.1 software.
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6

Detecting NRF2-Keap1 Interaction via Immunoprecipitation

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Cells were lysed and immunoprecipitated with anti-NRF2 antibody (Cell Signaling Technology). 30 µL protein A/G agarose beads (GE Healthcare, Pittsburgh, PA, USA) were used for 4 h to detect the association between NRF2 and Keap1.Isolated protein was subjected to sodium dodecyl sulfate polyacrylamide gel electrophoresis and transferred to polyvinylidene-fluoride membranes (Millipore, Billerica, MA, USA). The primary antibodies included HO1 (Abcam, 1/1,000, ab68477), NQO1 (Abcam, 1/1,000, ab28947), NRF2 (Novus, 1/1,000, NBP1-32822), FPRL1 (Novus, 1/1,000, NLS1878) and Keap1 (Santa Cruz Biotechnology, 1/200, sc-514914). Secondary antibodies (ZSGB-BIO, 1/3,000, ZB-2301 and ZSGB-BIO, 1/3,000, ZB-2305) were also employed. Equal protein loading among the samples was confirmed by the β-actin antibody (Sigma-Aldrich, St. Louis, MO, USA) and the Lamin B1 antibody (Abcam, Cambridge, MA, USA). An enhanced chemiluminescence system (West Pico Kit, Pierce, Loughborough, UK) was employed to detect the membrane signals. The relative intensities were analyzed with Image J software.
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7

Immunoprecipitation and Immunoblotting of IKKα

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These protocols were performed following standard techniques. Polycomb antibodies were the same as those for immunohistochemistry. Antibodies to detect NF-κB proteins and NIK were from Cell Signaling. Lamin B1 antibody was from Abcam, Actin and α-Tubulin antibodies from Sigma-Aldrich and HRP-conjugated antibodies from Dako (Agilent Technologies). For immunoprecipitation experiments cells were lysed 30 min at 4°C in 300 µl PBS plus 0.5% Triton X-100, 1mM EDTA, 100 mM Sodium Orthovanadate, 0.25 mM PMSF and complete protease inhibitor cocktail (Roche, Spain). Supernatants were precleared 2 hours with 1% of BSA, 1 µg IgGs and 50 µl Protein G Agarose beads (Sigma-Aldrich) and then incubated O/N at 4°C with Protein G Agarose beads together with anti-IKKα (clone 881H3, Millipore, Sigma-Aldrich) antibody. The beads were washed three times with lysis buffer and directly resuspended in sample buffer, separated by SDS-PAGE, transferred to a Nitrocellulose membrane and analyzed by immunoblotting. The antibody used to detect IKK phosphorylated at Ser176 was from MyBioSource.
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