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4 protocols using tfe3 hpa023881

1

Quantitative Western Blot Analysis of B Cell Signaling

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B cells were lysed in radioimmunoprecipitation assay (RIPA) buffer (50 mM Tris (pH 7.4), 150 mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 0.1% sodium dodecyl sulfate (SDS)) supplemented with protease inhibitor cocktail and phosphatase inhibitor cocktail (Sigma-Aldrich). Protein concentration was detected by BCA assay (Thermo Fisher Scientific), and an equal amount of protein was resolved in 4–12% SDS-polyacrylamide gel electrophoresis (SDS-PAGE) (Bio-Rad). Proteins were transferred to polyvinylidene difluoride membranes (Millipore) and probed overnight with the following primary antibodies: : anti-p-S6K (108D2), anti-p-S6 (D57.2.2E), anti-LAMP1(C54H11), anti-p-4EBP1 (236B4), anti-Raptor (24C12), and anti-RagA (D8B5) all from Cell Signaling Technology), anti-AID (mAID-2, Thermo Fisher Scientific), anti-TFEB (A303–673A, Bethyl Laboratories), Lamin B (66095–1-Ig, Proteintech), tubulin (11224–1-AP, Proteintech), TFE3 (HPA023881, Sigma-Aldrich) and anti-β-actin (13E5, Sigma-Aldrich). The membrane was washed and incubated with indicated secondary antibody for the subsequently enhanced chemiluminescence (ECL, Thermo Fisher) exposure.
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2

Western Blot Analysis of Signaling Pathways

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B cells were lysed in radioimmunoprecipitation assay (RIPA) buffer (50 mM Tris (pH 7.4), 150 mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 0.1% sodium dodecyl sulfate (SDS)) supplemented with protease inhibitor cocktail and phosphatase inhibitor cocktail (Sigma-Aldrich). Protein concentration was detected by BCA assay (Thermo Fisher Scientific), and an equal amount of protein was resolved in 4–12% SDS-polyacrylamide gel electrophoresis (SDS-PAGE) (Bio-Rad). Proteins were transferred to polyvinylidene difluoride membranes (Millipore) and probed overnight with the following primary antibodies: anti-p-S6K (108D2), anti-p-S6 (D57.2.2E), anti-LAMP1(C54H11), anti-p-4EBP1 (236B4), anti-Raptor (24C12), and anti-RagA (D8B5) all from Cell Signaling Technology), anti-AID (mAID-2, Thermo Fisher Scientific), anti-TFEB (A303–673A, Bethyl Laboratories), Lamin B (66095–1-Ig, Proteintech), tubulin (11224–1-AP, Proteintech), TFE3 (HPA023881, Sigma-Aldrich) and anti-b-actin (13E5, Sigma-Aldrich). The membrane was washed and incubated with indicated secondary antibody for the subsequently enhanced chemiluminescence (ECL, Thermo Fisher) exposure.
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3

Immunoblot Analysis of Cellular Proteins

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The methods used for the preparation of cell lysates from in vitro and in vivo samples and for immunoblot analyses have been previously described [20 (link)]. The antibodies used included TFE3 (HPA023881, MilliporeSigma, Burlington, MA, USA), ATP6V1A (17115-1-AP, Proteintech, Rosemont, IL, USA), ATP6V1B1 (A-6427, Invitrogen, Waltham, MA, USA), Histone H3 (4499, Cell Signaling Technology, Danvers, MA, USA), LaminB1 (13435, Cell Signaling Technology), pTfeb (Ser142) (AF3845, Affinity Biosciences, Cincinnati, OH, USA), Atg7 (8558, Cell Signaling Technology), GAPDH (2118S, Cell Signaling Technology), αTubulin (T6199, Sigma-Aldrich, Burlington, MA, USA) and Tfeb (A303-673A, Bethyl Laboratories, Montgomery, TX, USA; sc-48784, Santa Cruz Biotechnology, Dallas, TX, USA).
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4

Antibody Panel for Autophagy Signaling

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Antibodies used in this study were as follows: ATG16L1 (8089, human), phospho-ATG14 S29 (92340), ATG14 (96752), phospho-Beclin S30 (54101), FIP200 (12436), FLCN (3697), GABARAPL1 (26632), GABARAPL2 (14256), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) [5174, 1:10,000 for WB (Western blot)], DYKDDDDK tag (14793), HA tag (3724), myc tag (2278), LC3A/B (12741), LC3B (3868), LAMTOR1 (8975), LAMP1 [15665, 1:1000 for immunofluorescence (IF)], NFAT1 (5861, 1:250 for IF), NPRL2 (37344), phospho-S6K (9234), S6K (2708), phospho-S6 S235/236 (4858, 1:3000 for WB), S6 (2217, 1:5000 for WB), TAX1BP1 (5105), TFEB (4240), TFEB (37785, 1:200 for IF), and phospho-ULK S757 (14202) were from Cell Signaling Technology. Mouse monoclonal anti–S. Typhimurium lipopolysaccharide (clone 1E6, ab8274) and FNIP1 (ab134969) were from Abcam. TFE3 (HPA023881) was from MilliporeSigma. p62 (GP62-C) was from Progen. Galectin-3 (sc-23938) was from Santa Cruz Biotechnology. TFEB (A303-673A, 1:200 for IF in murine cells) was from Bethyl Laboratories. All antibodies were used at a 1:1000 dilution for Western blotting unless otherwise noted.
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