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4 protocols using pdia6

1

Cell line culture and protein extraction

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RPMI 1640 and fetal bovine serum (FBS) were obtained from HyClone Laboratories (HyClone Laboratories Inc.). Dimethyl-labeled agents, CH2O, CD2O, NaCNBH3 were obtained from Sigma-Aldrich Company (St. Louis, MO). The primary antibodies for Hsp90 alpha, ENO1, ALDOA, HSPA5, JUP, KRT6A, PDIA6, AKT, PCNA, FN1, β-actin and all the secondary antibodies were obtained from Proteintech Group (Proteintech Group, Inc., USA).
All other agents were purchased from Sigma Chemical Co. (St. Louis, MO) unless otherwise specified. The water used in the experiments was thrice-distilled; all other materials were of analytical reagent grade.
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2

Western Blot Analysis of Signaling Proteins

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Samples were harvested using SDS lysis buffer (62.5 mm Tris-HCl, pH 6.8, 2% SDS, and 10% glycerol) supplemented with protease and phosphatase inhibitors (Sigma-Aldrich) as previously described (Ferreira et al., 2018 (link)). Equal amounts of denatured proteins were separated via SDS–polyacrylamide gel electrophoresis followed by transfer and antibody inoculation as described previously (Tambe et al., 2019 (link)). Antibodies used were: Smad1(Cell signaling, D59D7), Smad5 (SCBT, sc-101151), PCSK9 (SCBT, sc-515082), IGFBP7 (SCBT, sc-365293), MMP13 (SCBT, sc-515284), VCAN (Invitrogen, MA5-27638), FN1 (Abclonal, A16678), DCN (R&D, MAB143), GAPDH (Invitrogen, A5-15738), PDIA6 (Proteintech, 18233-1), GRP78 (Proteintech, 11587-1), ATF4 (SCBT, sc-390063), ATF6 (SCTB, sc-166659), pSmad159 (Cell signaling, 13820), β-actin (Cell signaling, 4970), Goat Anti-Rabbit HRP (SeraCare, 54500010), and Goat Anti-Mouse HRP (Invitrogen, 31446) diluted according to manufacturer’s instruction.
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3

Chemical Synthesis and Biochemical Analysis

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Ipomoeassin F was chemically synthesized as described previously12 (link), 13 (link). PDI inhibitor CCF 642 (346640-08-2) was purchased from Tocris Bioscience (Shanghai, China). Thioflavin T (Th T) and Cycloheximide (CHX) were obtained from Sigma-Aldrich (USA). mRFP-GFP-MAP1LC3B plasmid was used as previously described14 (link). All antibody information is indicated as following: PDIA6 (#18233-1-AP, Proteintech), Calnexin (#10427-2-AP, Proteintech), GRP78/Bip (#11587-1-AP, Proteintech), ERp72 (PDIA4) (#2798, CST), eIF2α (#5324, CST), pho-eIF2α (#3597, CST), cleaved-caspase3 (#9664, CST), LC3B (#2775, CST), GAPDH (sc-3650620, Santa Cruz), α-Tubulin (sc-5286, Santa Cruz), anti-mouse linked with HRP (sc-2005, Santa Cruz), anti-rabbit IgG linked with HRP (sc-2004, Santa Cruz), Alexa Fluor 488 donkey anti-mouse antibody (#A21202, Thermo Fisher), and Alexa Fluor 594 donkey anti-rabbit antibody (#A21207, Thermo Fisher). Details for the use of antibodies can be found in Supplementary Table S2.
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4

Protein Expression Analysis in Cells

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Cells were seeded in 6-well plates and lysed in ice-cold RIPA buffer, which contained phosphatase and protease inhibitors cocktail (Basel, Roche). After centrifugation at 12000 rpm/min for 15 min at 4°C, the concentration of proteins in the supernatants was detected with BCA Protein Assay Kit (Beyotime, Shanghai, China). Equal amounst of proteins were separated by 10% sodium dodecyl sulfate polyacrylamide gels (SDS-PAGE), transferred onto nitrocellulose (NC) membranes and blocked with 5% non-fat milk in Tris buffered saline tween (TBST). Membranes were incubated overnight at 4°C with the following primary antibodies: PDIA6, Cyclin D1, Cyclin A1, Cyclin B1, Cyclin E1, c-myc, β-Catenin (ProteinTech, Wuhan, China), CK1α, GSK-3β, phosphor-GSK-3β (Ser9), β-TrCP (Abcam, Cambridge, MA, USA); phosphor-β-Catenin (Ser45), phosphor-β-Catenin (Ser33/Ser37/Thr41, Cell Signaling Technology, Danvers, MA, USA); β-actin (ZSGB-BIO, Beijing, China) and Histone H3 (Beyotime). After washing, the membranes were incubated with secondary antibodies (HRP-conjugated anti-rabbit IgG or anti-mouse IgG, ProteinTech) for 2 h at RT. Bands were visualized using ECL Plus Western Blot Detecting System (GE Healthcare, Beijing, China).
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