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160 protocols using rpmi 1640 media

1

Cell Culture Protocols for Diverse Cell Lines

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K562 cells were obtained from the American Type Tissue Collection (ATCC, catalog number CCL-243) and maintained in RPMI 1640 media (Corning) with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin, and 1% L-glutamine. Normal primary human peripheral blood mononuclear cells (PBMCs) were obtained from ATCC (catalog number PCS-800-011) and maintained in RPMI 1640 media (Corning) with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin, and 1% L-glutamine. HEK293FT cells were obtained from ATCC (catalog number CRL-3216) and maintained in DMEM (Corning) with 10% FBS, 1% penicillin/streptomycin, and 1% L-glutamine. All mammalian cell lines were maintained at 37°C with 5% CO2. Primary Zebrafish Kidney Stromal (ZKS) cells were maintained and cultured as previously described [39 (link)]. All cell lines were monitored visually to confirm their morphology and tested for mycoplasma contamination via PCR analysis before use.
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Stable Cell Line Generation for Protein Induction

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The Flp-In T-REx-293 (T-REx-293) cell line was purchased from Invitrogen (#R78007). HEK293, HEK293T, Hela, NCI-H1299, and NCI-H460 cell lines were obtained from American Type Culture Collection (ATCC). The stable cell lines used in this study were generated from T-REx-293, H1299, or H460 cells (Supplementary Table 10). All cells were maintained in 5% CO2 at 37 °C. H1299 and the derived stable cell lines were cultured in RPMI-1640 media (Corning) supplemented with 10% fetal bovine serum (FBS, MilliporeSigma #F0926) and 0.8% penicillin-streptomycin unless otherwise indicated. Other cell lines were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Corning) supplemented with 10% FBS and 0.8% penicillin-streptomycin. To induce expression or knockdown of protein target in the stable cell lines, cells were treated with doxycycline ranging from 2.5–60 ng/mL for the indicated time.
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Colon and Stomach Cell Line Treatments

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All cell lines were maintained in a humidified atmosphere with 5% CO2. Our study included five colon cell lines (HT29, SW480, HCT116, LoVo and RKO) and one stomach cell line (AGS). HT29, SW480, HCT116 and LoVo cells were cultured in McCoys 5A media (Corning), RKO and AGS were cultured in RPMI 1640 media (Corning) supplemented with 10% FBS (Gibco). All cell lines were purchased from the ATCC and authenticated and tested for Mycoplasma by IDEXX on 6/20/2019. All cells used in experiments were passaged fewer than 15 times with most being passaged fewer than 10 times. For H2O2 treatments, 30% H2O2 (Sigma) was diluted in PBS immediately prior to treatment at 250 μM for 1H at 37°C. For EGF treatments, cells were starved in media lacking serum for 48H prior to treatment. Cells were then treated with 100 ng/ml recombinant EGF (R&D Systems: 236-EG) for 48H. GSK-LSD1 (Sigma, SML1072), GSK690693 (Sigma, SML0428) and corin (generously provided by Dr. Philip Cole and Dr. Jay Kalin) were solubilized in DMSO (Sigma) prior to treatment. Treatment dosages and durations are defined in the figure legends.
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Culturing Pancreatic Cancer Cell Lines

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BxPC3, MIA PaCa2 and PANC1 cell lines were provided by the Cell Bank, Type Culture Collection, Chinese Academy of Sciences (Shanghai, China). BxPC3 was maintained in RPMI 1640 media (Corning, NY, USA) with 10% foetal bovine serum (Gibco, Grand Island, NY, USA). And, MIA PaCa2 was cultured in DMEM containing 10% FBS (Gibco, Grand Island, NY, USA). All medium were supplemented with 100 μg/mL streptomycin and 100 U/mL penicillin. All pancreatic cancer cell lines were cultured in a humidified atmosphere containing 5% CO2 at the temperature of 37°C.
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Culturing RS4;11 Leukemia Cells

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The human acute leukemia RS4;11 cell line was purchased from American Type Culture Collection (ATCC, CRL-1873), and cultured in RPMI-1640 media (Corning) supplemented with 10% fetal bovine serum (FBS), 1% Sodium Pyruvate, 1% Penicillin/Streptomycin, and 10 mM HEPES at 37°C under a humidified 5% CO2 atmosphere. The experiments were performed by using cells within 20 passages after purchasing.
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Isolation and Culture of Alveolar Macrophages from Lung Lavages

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Cells within the lungs were isolated by performing lung lavages and assessed as previously described [19 (link), 20 (link)]. Briefly, the lungs were removed from the body and lavaged with ice-cold PBS to obtain optimal cell yields. The first pull (instillation of 0.5 mL of ice-cold PBS, withdrawn, then the same fluid repeated twice more) consisted of the most concentrated lung lavage fluid (LLF). Lung lavaged cells were isolated by centrifugation (400 x g, 5 min, 4°C) and cell counts were obtained via Coulter Z2 particle counter (Beckman Coulter; Brea, CA, USA). Cells were stained for differential analysis via Wright-Geimsa stain in a Hematek 2000 autostainer (Miles-Bayer-Siemens Diagnostics; Deerfield, IL, USA). Alveolar macrophages (AM) within the LLF were isolated and cultured ex vivo in RPMI-1640 media (Corning; Corning, NY, USA) supplemented with 10% heat-inactivated fetal bovine serum (VWR; Radnor, PA, USA), 1% penicillin-streptomycin (Corning) and 1% sodium pyruvate (Corning) for 24 hours at 37°C with LPS for priming (20 ng/mL) to assess IL-1β levels within the supernatant.
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Extraction and Stimulation of Peritoneal Macrophages

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Peritoneal macrophages were extracted from C57BL/6 mice. Mice were sacrificed with CO2 and 5 mL of RPMI 1640 media (Corning), supplemented with 10% Fetal Bovine Serum (Sigma-Aldrich) and 1% Penicillin-Streptomycin (Gibco), was injected into the peritoneal cavity. The abdomen was gently massaged for 5 minutes to dislodge attached macrophages. Then, peritoneal fluid was recovered using a Pasteur pipette.
5×105 macrophages per well were seeded on 96-well plates and let rest for 2 hours at 37°C 5% CO2. CS NCs were added at 20 µg/mL (or free media) and incubated overnight. Conditions were tested in biological duplicates. Media was replaced every two days. At day 7, macrophages were incubated with 0.1 µg/mL LPS (Sigma-Aldrich) (or free media) for 3 hours. Then, cells were incubated with new media overnight. At day 8, cells were centrifuged and supernatants recovered.
Tumor necrosis factor α (TNF-α) levels were measured using Mouse TNF alpha Uncoated ELISA kit (Invitrogen), following manufacturer’s instructions. TNF-α standard control was used to determine cytokine levels. OD was measured at 450 nm using an Envision Multilabel Plate Reader (Perkin Elmer).
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Murine Mast Cell Generation and Reconstitution

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Bone marrow was obtained by flushing from mouse femurs and tibias using RPMI 1640 media (Corning) containing 10% FBS (Atlanta Biologicals), 2.5% HEPES (Sigma), 1% sodium pyruvate (Sigma), 1% non-essential amino acids (Sigma), 1% penicillin/streptomycin (Corning), and 0.05 mM β-mercaptoethanol (Sigma) (BMMC media). Cells were then cultured in BMMC media with 30 ng/mL recombinant mIL-3 (Miltenyi Biotec) for 4–5 weeks. Mast cell phenotype was determined by flow cytometry as cells staining double-positive for APC–anti-mCD117 (2B8, BD Biosciences) and PE–anti-mFcεRI (MAR-1, eBioscience). BMMCs with a >95% pure were used. For mast cell reconstitution, BMMCs were injected intradermally for 8 weeks in the experiments to determine necessity and for 1 week in the experiments to determine sufficiency.
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9

Isolation and Culture of Alveolar Macrophages

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Cells within the lungs were isolated by performing lung lavages and assessed as previously described (Burmeister et al., 2019 (link); Jessop and Holian, 2015 (link)). Briefly, lungs were extracted and lavaged with ice-cold PBS to obtain optimal cell yields. The first pull (instillation of 0.5 ml ice-cold PBS, withdrawn, then the same fluid repeated twice more) consisted of the most concentrated lung lavage fluid (LLF). Lung lavaged cells were isolated by centrifugation (400 x g, 5 min, 4°C) and cell counts obtained via Coulter Z2 particle counter (Beckman Coulter; Brea, CA, USA). Cells were stained for differential analysis via Wright-Geimsa stain in a Hematek 2000 autostainer (Miles-Bayer-Siemens Diagnostics; Deerfield, IL, USA). Alveolar macrophages (AM) within the LLF were isolated and cultured ex vivo in RPMI-1640 media (Corning; Corning, NY, USA) supplemented with 10% heat-inactivated FBS (VWR; Radnor, PA, USA), 1% penicillin-streptomycin (Corning) and 1% sodium pyruvate (Corning) for 24-hr at 37°C with LPS for priming (20 ng/ml) to assess IL-1β levels within the supernatant.
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10

Transwell Migration and Invasion Assay

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The transwell (Corning) experiment was performed to assess the migration capacity of cells after manipulating 14-3-3ζ. Briefly, cells were serum starved for 12 h and resuspended at a final concentration of 2 × 104 cells/ml with serum-free RPMI-1640 media (Corning). Cells were seeded into the upper chamber and RPMI-1640 media with 10% FBS was added in the lower chamber. After incubation for 24 h, migrated cells which penetrated the membrane were fixed with 10% methanol for 30 min and stained with Giemsa (Sigma), whereas cells on the upper surface of the membrane were carefully removed by cotton swabs. Migrated cells were counted under a light microscope at 100× magnification. For the cell invasion assay, the polycarbonate membrane was coated with 100 μl Matrigel (BD BioCoat Matrigel). The following assay was similar to that described in the transwell migration assay. All experiments were repeated three times.
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