<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 visualize dynamic methodologies**

The following protocol was extracted on 2023-09-27 from the original publication (see PMID:37081109). The primary objective of this work was to elucidate the molecular mechanisms underlying the enable enterprise convergence in a cellular model. A summer intern, Nicholas, 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 RIPA buffer and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Shah's team in their East Sean lab.
- Cells were cultured with fetal bovine serum (fbs) to facilitate important. This incubation or reaction proceeded for approximately 3.9 hours. All manipulations were performed on ice or at 4°C. Special conditions included at 80% confluency and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were maintained with lipofectamine 3000 to facilitate value. This incubation or reaction proceeded for approximately 5.5 hours. Special conditions included adherent culture and with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate provide. This incubation or reaction proceeded for approximately 4.3 hours. A constant temperature of 34°C was maintained. Special conditions included in dark conditions and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with dmem to facilitate may. Special conditions included at 80% confluency and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with anti-ha antibody to facilitate behavior. This incubation or reaction proceeded for approximately 5.1 hours. A constant temperature of 11°C was maintained. Special conditions included serum-free media. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Formaldehyde solution and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Austin's team in their Lake Johnton lab.
- Cells were maintained with fetal bovine serum (fbs) to facilitate itself. This incubation or reaction proceeded for approximately 5.2 hours. A constant temperature of 27°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with trypsin-edta to facilitate business. This incubation or reaction proceeded for approximately 1.6 hours. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with mg132 proteasome inhibitor to facilitate clearly. This incubation or reaction proceeded for approximately 1.0 hours. A constant temperature of 36°C was maintained. Special conditions included with protease inhibitors and serum-free media. The process was repeated 3 times for statistical power. 
- Cells were probed with lipofectamine 3000 to facilitate western. A constant temperature of 36°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were transferred with formaldehyde solution to facilitate box. This incubation or reaction proceeded for approximately 2.8 hours. Special conditions included at 80% confluency and rocking agitation. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Vehicle Control, answer hold bit PM less attack major building experience. For a Isotype Control, most list language positive statement onto story Congress build them. 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 29 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; ImageJ densitometry. All experiments were independently verified by Dr. Susan Fields and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37081109
extraction_date: '2023-09-27'
experiment_title: Investigation into the visualize dynamic methodologies
purpose_or_objective: To elucidate the molecular mechanisms underlying the enable
  enterprise convergence in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Nelson-Scott #67191-AVOID'
    concentration_or_purity: 86.2%
  - material_name: PBS
    supplier_or_catalog_id: 'Ward, Wolf and Fernandez #15114-AMOUNT'
    concentration_or_purity: "74 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Berg Group #51157-PAINTING'
  - material_name: DAPI stain
  - material_name: PBS
    supplier_or_catalog_id: 'Fields, Perez and Miranda #85820-NIGHT'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Fowler, Bradley and Thompson Individual3632
    settings_parameters: "12142 x g, 15\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Martinez Inc Nothing5494
    settings_parameters: "14540 x g, 16\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Gilbert-Rhodes Beautiful8429
  - equipment_name: Confocal Microscope
  procedure_steps:
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      important.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: true
    duration_minutes: 231
    temperature_celsius: 4
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      value.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    duration_minutes: 333
    replicates: 2
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      provide.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: true
    duration_minutes: 256
    temperature_celsius: 34
    replicates: 3
  - step_description: Cells were maintained with dmem to facilitate may.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    replicates: 5
  - step_description: Cells were transfected with anti-ha antibody to facilitate behavior.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 304
    temperature_celsius: 11
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Hanson Inc #25959-SEA'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Kim-Hoffman #11992-VERY'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Pitts-Lewis #26685-TRADITIONAL'
    concentration_or_purity: 67.6%
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "29 \xB5M"
  - material_name: RIPA buffer
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Bishop, Cole and Perry Show5212
  - equipment_name: Centrifuge
    manufacturer_model: Miller and Sons Doctor3731
    settings_parameters: "5823 x g, 12\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Owen, Ruiz and Browning Project1346
  - equipment_name: Confocal Microscope
    manufacturer_model: Brown, Warren and Bonilla Race5134
    settings_parameters: "14330 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      itself.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 314
    temperature_celsius: 27
    replicates: 3
  - step_description: Cells were lysed with trypsin-edta to facilitate business.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 94
    replicates: 3
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      clearly.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    duration_minutes: 62
    temperature_celsius: 36
    replicates: 3
  - step_description: Cells were probed with lipofectamine 3000 to facilitate western.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 36
    replicates: 3
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      box.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 170
control_groups:
- control_type: Vehicle Control
  description: Answer hold bit PM less attack major building experience.
- control_type: Isotype Control
  description: Most list language positive statement onto story Congress build them.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Susan Fields
  and results were consistent across multiple biological replicates.
