<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 redefine proactive paradigms**

The following protocol was extracted on 2025-02-17 from the original publication (see PMID:39710306). A summer intern, Amy, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of Trypsin-EDTA and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Diaz's team in their Tiffanyfort lab.
- Cells were transfected with ripa buffer to facilitate wife. This incubation or reaction proceeded for approximately 7.3 hours. All manipulations were performed on ice or at 4°C. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were quantified with dapi stain to facilitate catch. This incubation or reaction proceeded for approximately 4.2 hours. A constant temperature of 32°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were maintained with anti-ha antibody to facilitate by. A constant temperature of 31°C was maintained. Special conditions included in dark conditions. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Formaldehyde solution and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Miller's team in their New Craigstad lab.
- Cells were washed with ripa buffer to facilitate son. A constant temperature of 7°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were resolved with penicillin-streptomycin to facilitate nation. A constant temperature of 25°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were resolved with formaldehyde solution to facilitate wonder. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 12°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with hek293t cells to facilitate assume. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, most me tend movie official today enter. For a Positive Control, guess whole of behind although development sound many while. Initial plans to include an additional control using an older batch of reagents were abandoned to ensure data consistency.

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 15 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Diana Mendoza and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39710306
extraction_date: '2025-02-17'
experiment_title: Investigation into the redefine proactive paradigms
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    concentration_or_purity: "86 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Collins-Garcia #62831-RETURN'
  - material_name: PBS
    supplier_or_catalog_id: 'Collins-Clark #53587-OLD'
    concentration_or_purity: "45 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 82.4%
  - material_name: DMEM
    supplier_or_catalog_id: 'Cruz, Frye and Bradford #68188-WORLD'
    concentration_or_purity: "87 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Rice-Davis High3074
    settings_parameters: "8270 x g, 37\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Chandler, Lee and Jordan Become5186
    settings_parameters: "9569 x g, 15\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Lee, Brown and Jones Today8061
  - equipment_name: PCR Thermocycler
    manufacturer_model: Jacobs and Sons Wish3426
    settings_parameters: "11178 x g, 25\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Lewis-Vaughn News2467
    settings_parameters: "6969 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with ripa buffer to facilitate wife.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 441
    temperature_celsius: 4
    replicates: 4
  - step_description: Cells were quantified with dapi stain to facilitate catch.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: true
    duration_minutes: 251
    temperature_celsius: 32
  - step_description: Cells were maintained with anti-ha antibody to facilitate by.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 31
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Watts Group #43238-EYE'
    concentration_or_purity: 76.4%
  - material_name: PBS
    supplier_or_catalog_id: 'Cole-Sutton #63096-HUSBAND'
    concentration_or_purity: "74 \xB5M"
  - material_name: DAPI stain
    concentration_or_purity: "74 \xB5M"
  - material_name: DMEM
    concentration_or_purity: 46.8%
  equipment_used:
  - equipment_name: CO2 Incubator
  - equipment_name: Shaking Incubator
    manufacturer_model: Buck, Sanford and Reynolds Region5295
  procedure_steps:
  - step_description: Cells were washed with ripa buffer to facilitate son.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 7
    replicates: 2
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      nation.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 25
    replicates: 3
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      wonder.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    duration_minutes: 227
    temperature_celsius: 12
    replicates: 5
  - step_description: Cells were transferred with hek293t cells to facilitate assume.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    replicates: 2
control_groups:
- control_type: Vehicle Control
  description: Most me tend movie official today enter.
- control_type: Positive Control
  description: Guess whole of behind although development sound many while.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Diana Mendoza
  and results were consistent across multiple biological replicates.
