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9 protocols using cell culture supplements

1

Angiogenesis Signaling Pathway Protocol

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All cell culture serum and media were purchased from Thermo Fisher Scientific, while cell culture supplements were purchased from Sigma. Rat anti-CD31 (553369) was purchased from Pharmingen while antibodies against alpha SMA (ab7817), phosphor-ErK (ab50011) and ErK1/2 (ab17942) were from Abcam. The antibodies against phospho-Akt (sc-7985R), Akt1 (sc-1619) and GAPDH (sc-25778) were from Santa CruZ Biotech. The antibody against VEGF (SAB1402390) was from Sigma. All secondary antibodies were from Dakocytomation. All microRNA reagents were purchased from Thermo Fisher Scientific. PDGF, insulin, holo-transferrin, SU5416, LY294002, DMSO, DAPI and Giemsa were purchased from Sigma.
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2

Epigenetic Regulation in Cell Culture

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DMEM medium and cell culture supplements were purchased from Sigma (Steinheim, Germany). Cell culture plastics, phosphate-buffered saline (PBS), and fetal calf serum (FCS) were purchased from PAA Laboratories GmbH (Pasching, Austria). DNase I (RNase-free) and First Strand cDNA Synthesis Kit were purchased from Fermentas (Ontario, Canada). 5-AZA and L-ascorbic acid 2-phosphate were obtained from Sigma-Aldrich (Steinheim, Germany). All other chemical compounds were purchased from Carl Roth (Karlsruhe, Germany). 5-hmC (39769) mouse mAB was purchased from Active Motif (Carlsbad, CA, USA). Proliferating cell nuclear antigen (PCNA) (ab92552) rabbit mAB was obtained from Abcam (Cambridge, UK). Corresponding secondary antibodies goat anti-rabbit Alexa 555 and goat anti-mouse 488 were acquired from Invitrogen (Carlsbad, CA, USA). Anti TET2 (SAB3500711), anti TET3 (SAB2700682), and anti glyceraldehyde 3-phosphate dehydrogenase (GAPDH) (G9545) antibodies were used from Sigma (Munich, Germany). GADD45B (SC33172) rabbit mAB was from Santa Cruz, and Snail (3879) rabbit mAB, E-cadherin (14472) mouse mAB, p21 (2947) rabbit mAB, cyclin-B1 (4138) rabbit mAB, and HRP-linked anti-mouse and anti-rabbit IgG secondary antibody were purchased from Cell Signaling (Beverly, MA, USA).
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3

Characterization of B-cell and Cancer Cell Lines

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This study utilized the extensively characterized WEHI-231 (IgM+) and A20.2J (IgG+), B cell lymphoma lines 12 (link)–14 (link). Some experiments utilized Daudi and Ramos, human IgM+ cell lines 15 (link), and K-562 and Jurkat (human CML and T-cell leukemia models 16 (link).) These cells were kindly provided by Dr. David W. Scott, USUHS, Bethesda, MD. Additional experiments utilized human DU-145 and LNCAP prostate cancer lines 17 (link) (obtained from Dr. Vincent Njar, University of Maryland, Baltimore). Suspension cells were grown in supplemented RPMI 1640 culture medium as previously described 8 (link), 12 (link), 18 (link) or in DMEM as described in the references above. Cell culture supplements were obtained from Sigma-Aldrich (St. Louis, MO), Cellgro (Manassas, VA), Bio-Whittaker (Walkersville, MD), Invitrogen (Carlsbad, CA), Atlanta Biologicals (Lawrenceville, GA) and Gemini Bioproducts (West Sacramento, CA).
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4

Mitochondrial and Glycolytic Stress Assays

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Cell culture supplements were from Sigma-Aldrich, India. TUNEL assay kit was from Invitrogen (#C10617), mitotracker from Invitrogen (#M7514), and Seahorse XF Cell Mito Stress Test Kit and Seahorse XF Glycolysis Stress Test Kit from Agilent Technologies.
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5

Comprehensive Cellular Signaling Pathway Analysis

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All cell culture medium and serum were purchased from Invitrogen, whereas cell culture supplements were purchased from Sigma. Antibodies against XBP1 (sc-7160), HDAC3 (sc-136290) phospho-Akt (sc-7985R), Akt1 (sc-1619), Nrf2 (sc-722), mTOR (sc-1549), histone H3 (sc-10809), IRE1α (sc-20790), and GAPDH (sc-25778) were purchased from Santa Cruz Biotechnology; antibodies against FLAG (F2426, F1804, and F7425), HA (H6908) and tubulin (T8203) were from Sigma; antibody against HO-1 (ab13248) was purchased from Abcam. Antibodies against XBP1u and XBP1s were raised in rabbits with peptides CRSSQRSTQKDPVPY and DSGGIDSSDSESDIC, respectively, by GenScript Corp. All secondary antibodies were from DakoCytomation. Inhibitors LY294002, PD98059, SU5416, actinomycin D, cycloheximide, and Tin protoporphyrin IX were purchased from Sigma. AZD2014 was purchased from Selleckchem. All inhibitors were dissolved in DMSO. All other chemicals were also from Sigma.
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6

Epigenetic Regulation Analysis Protocol

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Cell culture medium, DMEM medium, William’s medium E, and cell culture supplements were purchased from Sigma-Aldrich (Steinheim, Germany). Cell culture plastics, phosphate buffered saline (PBS), and fetal calf serum (FCS) were purchased from PAA Laboratories GmbH (Pasching, Austria). DNaseI (RNase—free) and first strand cDNA Synthesis Kit were purchased from Fermantas (Ontario, Canada). 5-Azacytidine (SLBH7350V) was obtained from Sigma-Aldrich (Steinheim, Germany). All other chemical compounds were purchased from Carl Roth (Karlsruhe, Germany). 5hmC (39769) rabbit pAB and 5mC (39649) mouse mAB were purchased from Active Motif (Carlsbad, CA, USA). Proliferating cell nuclear antigen (PCNA) (ab92552) rabbit mAB was obtained from Abcam (Cambridge, UK). Corresponding secondary antibodies goat anti-rabbit Alexa 555 and goat anti-mouse 488 were acquired from Invitrogen (Carlsbad, CA, USA). Anti-TET2, anti-TET3, and anti-glyceraldehyde 3-phosphate dehydrogenase (GAPDH) antibodies were used from Sigma-Aldrich (Munich, Germany). The HRP-linked anti-rabbit IgG secondary antibody was purchased from Cell Signaling (Beverly, MA, USA).
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7

Reverse Transcriptase and PCR Assay

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Avian moloney leukemic virus (AMLV) reverse transcriptase (RT) and taq polymerase (dNTP) were purchased from Thermo Scientific, USA. Insulin, rosiglitazone, TRI reagent, cell culture supplements, and reagents used were of molecular biology grade and purchased from Sigma-Aldrich, St. Louis, USA.
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8

Protein Expression Analysis of Cellular Markers

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All cell culture media and sera were purchased from Thermo Fisher Scientific, whereas cell culture supplements, growth factors, and inhibitors were purchased from Sigma. The XBP1u and XBP1s antibodies were raised by GenScript using peptide CRSSQRTQKDPVPY (XBP1u) and DSGGIDSSDSESDIC (XBP1s). The antibodies against Sca-1 (ab51317), IRE1α (ab37073), COL4A1 (ab6586), Col15A1 (ab58717), and Col18A1 (ab52022) were purchased from Abcam; antibody for GAPDH (sc-25778) was from Santa Cruz Biotechnology; antibody for FLAG (A4596 and F1804), alpha SMA (A5228), and all other chemicals from Sigma; all secondary antibodies were purchased from Dakocytomation.
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9

Signaling Pathway Modulation Protocol

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All cell culture serum and media were purchased from Gibico,while cell culture supplements were purchased from Sigma. Theantibody against Flag (ab190059) wasfrom Abcam. The antibodies against XBP1 (M-186,sc-7160), IRE1α (sc-20790),eNOS(sc-376542), Akt1/2/3 (sc-81434) and GAPDH (sc-25778) were fromSanta CruZ Biotech. All secondary antibodies werefrom Dakocytomation. All microRNA reagents were purchased from Thermo Fisher Scientific. SU1498, L-NAME, LY294002, KT-5823, DMSO, DAPI, crystal violet and Nitrite/Nitrate Assay Kit (23479)were purchased from Sigma.
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