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4 protocols using 35 mm polystyrene dishes

1

Stable HEK 293 Cell Line Generation

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HEK 293 cells were seeded at 8,000 –10,000 cells/cm2 on type 1 collagen (10 μg/cm2, Sigma-Aldrich) coated 35 mm polystyrene dishes (Falcon) and were cultured overnight in MEM (Corning) with 10% FBS and 1% P/S. Transfection was accomplished using unsupplemented MEM media and Lipofectin (Life Technologies), per the manufacturer’s instructions. Cells were incubated for 24 hr at 37°C in 5% CO2/95% air. Following this incubation, the transfection mixture was replaced with growth media and cells were grown for an additional 48 hr before being replaced with growth media supplemented with 200 μg/ml G418 sulfate (Gibco). Cells were cultured for an additional 48 hours before being plated as single cells in a 96-well plate (Corning). Colonies were cultured for 4 days before transferring to T25 flasks (Corning) and grown until 70% confluent.
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2

Metabolite Extraction from P. aeruginosa

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All P. aeruginosa strains were grown until the end of exponential phase of growth in glycerol minimal medium. Bacteria was then loaded into 0.25-μm nylon membranes (Millipore) using vacuum, transferred to pre-warmed hard agar plates with the same medium composition and incubated at 37°C during 2.5 hr. The filters were then passed to 35-mm polystyrene dishes (Falcon) with 1 mL of 2:2:1 methanol:acetonitrile:H2O quenching buffer and incubated there during 15 min on dry ice. Cells were removed by scraping, and the lysate containing quenching buffer was transferred to 1.5 mL tubes and centrifuged at 16,000 rpm for 10 min at 4°C. Supernatant transferred to fresh tubes and stored at –80°C.
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3

Transient Transfection of TRPM8 in HEK-293 Cells

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Human embryonic kidney (HEK) 293 cells (ATCC CRL-1573) were cultured in growth medium comprising 90% Dulbecco’s modified Eagle’s medium, 10% fetal bovine serum, 100 U·mL−1 penicillin-streptomycin, and 2 mM l-glutamine (Gibco). Cells were cultured in 35 mm polystyrene dishes (Falcon) at 37 °C in the presence of 5% CO2. Cells were transiently transfected with human TRPM8 in a pIRES2 plasmid containing EGFP as a reporter. This plasmid expresses bicistronic mRNA with an internal ribosome entry site (IRES) positioned between the TRPM8 gene and the fluorescent protein reporter gene such that the reporter is not covalently fused to TRPM8. Transient transfection was performed using Fugene 6 transfection reagent (Promega) and 0.5 μg of plasmid in a 35 mm dish (Falcon) at a ratio of 3 μL transfection reagent per μg of plasmid according to manufacturer protocol. HEK-293 cells were authenticated by polymorphic genetic marker testing (DNA Diagnostics Center Medical).
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4

Bacterial Metabolite Extraction Protocol

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Strains were grown to exponential phase in fully synthetic minimal media with 3.0 gC/l (glycerol) 0.5 gN/l (ammonium sulfate) and 5 µM iron (iron III sulfate). Bacteria were loaded onto 0.20 µm nylon membranes (Millipore) using a vacuum apparatus. Bacteria laden filters were immediately transferred to pre-warmed hard agar plates with a media composition identical to the synthetic liquid media. Filters on hard agar plates were incubated at 37°C for 2.5 h. Filters were then transferred to 35 mm polystyrene dishes (Falcon) with 1 ml 2:2:1 acetonitrile:methanol:water quenching buffer on dry ice. Filters were incubated in quenching buffer for 15 min on ice and cells were removed from filters by scraping. Quenching buffer containing cell lysate was then transferred to 1.5 ml micro-centrifuge tubes (Eppendorf) on ice and centrifuged at 16,000 rcf for 10 min at 4°C. Supernatant was then transferred to a fresh tube and stored at −80°C. The experiment was performed with two biological replicates with three technical replicates each.
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