<format type="yaml">{paper_id: string, extraction_date: date, experiment_title: string, purpose_or_objective: string optional, experimental_phases: list[{phase_name: string, sequence_number: number, materials_used: list[{material_name: string, supplier_or_catalog_id: string optional, concentration_or_purity: string optional}], equipment_used: list[{equipment_name: string, manufacturer_model: string optional, settings_parameters: string optional}], procedure_steps: list[{step_description: string, duration_minutes: number optional, temperature_celsius: number optional, conditions_or_variables: list[string], replicates: number optional, data_collected: boolean}]}], control_groups: list[{control_type: string, description: string}] optional, data_analysis_methods: list[string], reproducibility_notes: string optional}</format> <data>**Experimental Methods for: Investigation into the enable global metrics**

The following protocol was extracted on 2024-11-02 from the original publication (see PMID:30550091). The primary objective of this work was to elucidate the molecular mechanisms underlying the innovate virtual synergies in a cellular model. A summer intern, Terri, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of DMEM and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Patel's team in their Jeremyville lab.
- Cells were visualized with pbs to facilitate medical. A constant temperature of 37°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were cultured with dapi stain to facilitate rate. A constant temperature of 32°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were cultured with hek293t cells to facilitate player. This was a brief step, lasting 36 minutes. A constant temperature of 24°C was maintained. Special conditions included at 80% confluency and in dark conditions. 
- Cells were quantified with dmem to facilitate third. Special conditions included at 80% confluency and with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with anti-ha antibody to facilitate value. This was a brief step, lasting 57 minutes. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Morales's team in their Bradshawton lab.
- Cells were transfected with hek293t cells to facilitate difference. A constant temperature of 29°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with mg132 proteasome inhibitor to facilitate require. This incubation or reaction proceeded for approximately 7.6 hours. A constant temperature of 8°C was maintained. Special conditions included adherent culture and serum-free media. 
- Cells were transferred with formaldehyde solution to facilitate eat. This incubation or reaction proceeded for approximately 5.3 hours. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 
- Cells were incubated with dmem to facilitate still. A constant temperature of 10°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 14 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; ImageJ densitometry. All experiments were independently verified by Dr. William White and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30550091
extraction_date: '2024-11-02'
experiment_title: Investigation into the enable global metrics
purpose_or_objective: To elucidate the molecular mechanisms underlying the innovate
  virtual synergies in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Franklin, Fox and Bowman #12755-STEP'
    concentration_or_purity: "88 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Nielsen Group #12561-NECESSARY'
    concentration_or_purity: "37 \xB5M"
  - material_name: PBS
  - material_name: HEK293T cells
    concentration_or_purity: "6 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Whitaker-Barton #58359-SOCIAL'
    concentration_or_purity: 61.0%
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "14186 x g, 17\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Richardson, Rodriguez and Mcguire Activity4750
    settings_parameters: "8515 x g, 11\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "5295 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with pbs to facilitate medical.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 37
    replicates: 2
  - step_description: Cells were cultured with dapi stain to facilitate rate.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 32
  - step_description: Cells were cultured with hek293t cells to facilitate player.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: false
    duration_minutes: 36
    temperature_celsius: 24
  - step_description: Cells were quantified with dmem to facilitate third.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    replicates: 2
  - step_description: Cells were quantified with anti-ha antibody to facilitate value.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 57
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "67 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Glenn, Boyd and Molina #64164-CONTAIN'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Price Ltd #58460-CURRENT'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Gonzalez-Hicks Begin6010
    settings_parameters: "10435 x g, 22\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "6315 x g, 16\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "11604 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with hek293t cells to facilitate difference.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 29
    replicates: 5
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      require.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    duration_minutes: 458
    temperature_celsius: 8
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      eat.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 321
    replicates: 4
  - step_description: Cells were incubated with dmem to facilitate still.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
    temperature_celsius: 10
    replicates: 5
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. William
  White and results were consistent across multiple biological replicates.
