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17 protocols using cm4000

1

SILAC Labeling of Primary Human Cells

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Primary human hepatocytes purchased from KaLy-Cell, kept in Williams E medium (ThermoFisher, 22551022) supplemented with 10% dialyzed FBS and with primary hepatocyte maintenance supplement (ThermoFisher, CM4000), as well as human monocytes, B-cells, and NK cells, isolated from peripheral blood mononuclear cells, derived from buffy coats (German Red Cross, Mannheim) by magnetic-bead based negative selection (STEMCELL Technologies), and resuspended in RPMI-1640 medium (ThermoFisher, 21875-034) supplemented with 10% dialyzed FBS, were cultured in the presence of light (L) SILAC amino acids lysine and arginine overnight at 37 °C. The cells were then pulse-labeled with corresponding media containing heavy (H) isotope-labeled amino acids (lysine, (13C615N2, Sigma-Aldrich, 608041) and arginine (13C615N4, ThermoFisher, 88434)) for the indicated time periods (Supplementary Data 1), washed, pelleted, and snap-frozen in liquid N2. The cell pellets were lysed in buffer containing 4% SDS and digested with benzonase.
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2

Evaluating CYP3A Activity in iPS-hep

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CYP3A activity in iPS-hep on day 30 of differentiation was evaluated. PHH plated for 4 h or 48 h were used as references. iPS-hep or PHH cultures were washed with warm William’s E media supplemented with PS, L-Gln, and Primary Hepatocyte Maintenance Supplements (CM4000, ThermoFisher). Assays were started by adding media containing 5 μM midazolam (Wako). The volume of media added was 500 μL to the PHH, 300 μL to the upper, and 600 μL to the lower chamber. 0.5, 1, and 2 h, 60 μL of supernatants were collected from the upper and lower chamber and kept at −80℃ until LC–MS/MS analysis of the metabolite, 1’-OH midazolam. For iPS-hep, midazolam was added to both the upper and lower chambers. Supernatants from both the upper and lower chambers were collected and combined. The collected supernatants were extracted by adding acetonitrile containing an internal standard, 1 ‘-OH midazolam 13C3. LC–MS/MS quantified the metabolites with the liquid chromatography Nexera I LC-2040C 3D (Shimadzu) and the mass spectrometer LCMS-8050 (Shimadzu), using Inertsil ODS-3, 2.1 × 33 mm, 3 µm column (GL Sciences) (Supplemental Table S2). The protein amount per well was quantified using the Bradford protein assay. Metabolite concentrations were normalized with protein amounts.
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3

Co-Culture of Hepatocytes and CD45+ Cells

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FHCs were plated into rat-tail collagen-coated 24-well plate at 2 × 105 per well in primary hepatocyte maintenance medium (PHM medium) (CM4000; Thermo Fisher Scientific), 24 h later, the unattached FHCs were washed out and autologous CD45+ cells (purified from the CD34 fraction of FLCs) were seeded (5 × 104 per well). CD45+ cells cultured in the PHM medium without human hepatocytes were used as controls. A half medium change was performed twice a week.
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4

Hepatocyte Culture and Fatty Acid Oxidation

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The hepatocytes were prepared by standard procedures at Yale Liver Center, spun down at 50g, plated on collagen-coated dishes at a density of 105/cm2, and maintained in William’s E media plus 10% FBS plus 1× supplement (Thermo Fisher Scientific, CM4000) plus 1 μM dexamethasone in a 5% CO2 incubator. For in vitro transduction experiments, the titrated AAV8 viral particles were transduced at an MOI of 60 in William’s E media plus 1 nM insulin plus 1 μM dexamethasone for 24 hours. Seventy-two hours after transduction, cells were fixed in 10% formalin for Oil Red O staining.
Seahorse experiments for determining β-oxidation of fatty acids. The β-oxidation assay was carried out with the Seahorse XF Cell Mito Stress Test Kit per the manufacturer’s instructions (Agilent, part 02720-100) in the 96-well format with hepatocyte density of 2 × 103 cells per 100 μL. The Mito Stress Test (oligomycin 2.5 μg/mL, FCCP 0.8 μg/mL, 2 μM rotenone) was performed under the following 4 conditions: BSA, BSA + 400 μM etomoxir, BSA-palmitate, and BSA-palmitate + 400 μM etomoxir. For virus transduction experiments, the cells were incubated in AAV8 in William’s E media plus 1 nM insulin plus 1 μM dexamethasone, for 24 hours before the assay.
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5

Thawing and Culturing Primary Human Hepatocytes

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Primary human hepatocytes are thawed in Cryopreserved Hepatocyte Recovery Medium (CHRM, CM7000, ThermoFisher) and plated using Primary Hepatocyte Thawing/Plating supplements (CM3000, ThermoFisher), with a 1:40 dilution of Matrigel (354277, Corning) and at least 3% fetal bovine serum (FBS). 24 h post-plating, media is changed and Primary Hepatocyte Maintenence Supplements (CM4000, ThermoFisher), plus 1% FBS are added. All supplements are added to Williams E Media, with no phenol red (A1217601, ThermoFisher).
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6

Investigating Hepatocyte Signaling Pathways

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Primary human, mouse, or rat hepatocytes were thawed in cryopreserved hepatocyte recovery medium (CM7000, Thermo Fisher Scientific) and plated in Williams E Media, with no phenol red (A1217601, Thermo Fisher Scientific) with primary hepatocyte thawing/plating supplements (CM3000, Thermo Fisher Scientific). Twenty-four hours postplating, the medium is changed and primary hepatocyte maintenance supplements (CM4000, Thermo Fisher Scientific) and 1% fetal bovine serum (FBS) are added. Hepatocytes were treated with recombinant hIL-6 (ab119444), mIL-6 (ab238300), rIL-6 (Cell Applications, RP3009), human HGF (R&D Systems, 294-HG-025), or mouse HGF (R&D Systems, 2207-HG-025) for 15 min at 50 ng/ml. Cells were lysed using radioimmunoprecipitation assay buffer (Thermo Fisher Scientific, 89900), containing protease and phosphatase inhibitors (Thermo Fisher Scientific, A32965 and 88667), run by SDS–polyacrylamide gel electrophoresis and probed using antibodies against pSTAT3 (Cell Signaling Technology, 9145, RRID:AB_2491009), total STAT3 (Cell Signaling Technology, 4904, RRID:AB_331269), pMET (Cell Signaling Technology, 3077, RRID:AB_2143884), and β-actin (Sigma-Aldrich, A5316, RRID:AB_476743).
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7

Isolation and Culture of Mouse Hepatocytes

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Primary hepatocytes were isolated C57BL/6J mouse (4-week-old or 1-year-old, Charles River Japan) and prepared using the two-step collagenase perfusion method [15 (link)]. The primary culture of mouse hepatocyte from C57BL/6J was maintained with CM4000 (Thermo Fisher) changing every two days. The medium was contained with 0.1 μM dexamethasone, 6.25 μg/mL insulin, 6.25 μg/mL transferrin, 6.25 ng/mL selenous acid, 1,25 ng/mL BSA, 5.35 μg/mL linoleic acid, 2mM GlutaMAX and 15 mM HEPES 7.4 [13 (link)].
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8

Standardized Cell Culture and Hepatocyte Protocols

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HepG2 and HeLa cells were obtained from the Cell Culture Facility, University of California, Berkeley and maintained in EMEM (ATCC, 30-2003), supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Gibco, 10082) at 37°C under 5% CO2. Cells were cultured no >20 passages. To minimize effects of unknown factors, growth medium was replaced with serum-free medium and incubated 18 h prior to experiments. Cryopreserved pooled plateable human hepatocytes (ThermoFisher, HMCPP5) were purchased and seeded on a 12-well plate in William’s E medium (ThermoFisher, A1217601) and primary hepatocyte thawing and plating supplements (ThermoFisher, CM3000), following manufacturer’s instructions, and then incubated 12 h at 37°C under 5% CO2. The medium was replaced with William’s E medium and primary hepatocyte maintenance supplements (ThermoFisher, CM4000) and incubated 2 h, followed by the experimental protocol.
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9

Cryopreserved Hepatocyte Culturing Protocol

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Primary human hepatocytes (PHH) were purchased from Thermofisher scientific (HMCPMS; Thermofisher Scientific, MA, USA), and were cultured and maintained according to the supplemented protocol. In brief, the hepatocytes were thawed in Cryopreserved hepatocytes recovery medium (CM7000; Thermofisher Scientific), centrifuged at 100 x g for 10 min, and seeded at 2 × 106 cells/well on a collagen-coated plate in cryopreserved hepatocyte plating medium (CM9000; Thermofisher Scientific). After incubating the plate at 37 °C for 6 h, the culture medium was replaced by William’s medium (Gibco) supplemented with hepatocytes maintenance supplement pack (CM4000; Thermofisher Scientific).
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10

Cryopreserved PHH Lipid Loading Experiment

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Cryopreserved PHH from single donors (BD Gentest, Tewksbury, MA; Lonza, Walkersville, MD; and Thermo Fisher Scientific) were used for all in vitro experiments. PHH were thawed according to the supplier’s instructions using Cryopreserved Hepatocyte Recovery Medium (CM7000; Thermo Fisher Scientific), resuspended in Williams’ Medium E (MilliporeSigma, Burlington, MA) with plating supplements (CM3000; Thermo Fisher Scientific), and plated at a density of 50,000 cells/cm2. One day after seeding, PHH were serum starved overnight in serum-free Williams’ Medium E with maintenance supplements (CM4000; Thermo Fisher Scientific). Cells were then incubated for 48 h in DMEM supplemented with 0.5% BSA (free fatty acid free; MilliporeSigma) and 1% penicillin–streptomycin with or without the addition of 400 μM sodium oleate (68 (link), 69 (link)).
For albumin measurements, media were collected at the end of 48 h of lipid loading, and albumin concentration was measured with a commercially available human albumin ELISA kit (Invitrogen, Waltham, MA).
After 48-h lipid loading, media were changed to DMEM with 1% penicillin–streptomycin with or without the addition of cytoskeletal drugs: 5 µM blebbistatin (MilliporeSigma), 5 µM latrunculin (MilliporeSigma), or 10 µM nocodazole (Cayman Chemicals, Ann Arbor, MI). Cells were treated for 4 h before fixation.
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