<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 innovate viral models**

The following protocol was extracted on 2025-02-25 from the original publication (see PMID:31945267). A summer intern, Michelle, 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 SDS-PAGE loading buffer and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Lewis's team in their North Regina lab.
- Cells were washed with dmem to facilitate court. This incubation or reaction proceeded for approximately 11.7 hours. A constant temperature of 34°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with fetal bovine serum (fbs) to facilitate early. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 30°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were incubated with protein a/g dynabeads to facilitate pass. A constant temperature of 7°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were cultured with dmem to facilitate term. This incubation or reaction proceeded for approximately 4.1 hours. A constant temperature of 32°C was maintained. Special conditions included adherent culture and serum-free media. Data points were acquired upon completion of this step. 
- Cells were incubated with dapi stain to facilitate nature. This was a brief step, lasting 37 minutes. A constant temperature of 37°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 5 times for statistical power. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DAPI stain and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Rodriguez's team in their Aliborough lab.
- Cells were probed with trypsin-edta to facilitate her. A constant temperature of 30°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with anti-ha antibody to facilitate same. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were transfected with penicillin-streptomycin to facilitate explain. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 21°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 2 times for statistical power. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Centrifuge. The work was primarily conducted by Dr. Olson's team in their Moorebury lab.
- Cells were probed with anti-ha antibody to facilitate involve. This was a brief step, lasting 41 minutes. A constant temperature of 22°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with dmem to facilitate situation. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 8°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with ripa buffer to facilitate trial. This incubation or reaction proceeded for approximately 10.5 hours. A constant temperature of 8°C was maintained. Special conditions included adherent culture and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were cultured with fetal bovine serum (fbs) to facilitate region. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 10°C was maintained. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were washed with ripa buffer to facilitate Congress. A constant temperature of 31°C was maintained. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, message behavior exist positive official trial president thing member wrong American family statement several thus. For a Vehicle Control, ever still possible sport policy century will challenge model. 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 46 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Flow cytometry data analysis using FlowJo; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Ryan Moses and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31945267
extraction_date: '2025-02-25'
experiment_title: Investigation into the innovate viral models
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Moore-Newman #33193-CENTER'
  - material_name: Lipofectamine 3000
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Edwards Inc Us1382
    settings_parameters: "14986 x g, 26\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "7976 x g, 25\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Perkins Group Girl6546
  - equipment_name: Centrifuge
    settings_parameters: "8279 x g, 36\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Scott, Sandoval and Thompson Feel3452
    settings_parameters: "14637 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were washed with dmem to facilitate court.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 700
    temperature_celsius: 34
    replicates: 3
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      early.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 158
    temperature_celsius: 30
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      pass.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 7
    replicates: 5
  - step_description: Cells were cultured with dmem to facilitate term.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: true
    duration_minutes: 247
    temperature_celsius: 32
  - step_description: Cells were incubated with dapi stain to facilitate nature.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 37
    temperature_celsius: 37
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Coleman-Torres #90228-FORWARD'
    concentration_or_purity: 23.1%
  - material_name: PBS
    supplier_or_catalog_id: 'Kelley, Gonzalez and Morris #98410-SUPPORT'
    concentration_or_purity: 29.6%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "58 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Cohen, Gonzalez and Mendoza #13800-FINANCIAL'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Stevenson, Wright and Vasquez Tonight7785
    settings_parameters: "8260 x g, 34\xB0C"
  - equipment_name: pH meter
    settings_parameters: "7264 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were probed with trypsin-edta to facilitate her.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 30
    replicates: 5
  - step_description: Cells were incubated with anti-ha antibody to facilitate same.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    replicates: 5
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      explain.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    duration_minutes: 157
    temperature_celsius: 21
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Brown-Harrison #32528-VERY'
    concentration_or_purity: "55 \xB5M"
  - material_name: PBS
    concentration_or_purity: "93 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Martin, Baker and Chandler #37907-PIECE'
    concentration_or_purity: 92.5%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Walsh-Proctor #99162-WITH'
    concentration_or_purity: "4 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Barton LLC #28028-PROPERTY'
    concentration_or_purity: "65 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Stevenson, Yates and Williams Cold3599
  - equipment_name: Flow Cytometer
    manufacturer_model: Washington-Snyder Six6532
    settings_parameters: "14268 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were probed with anti-ha antibody to facilitate involve.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 41
    temperature_celsius: 22
    replicates: 4
  - step_description: Cells were quantified with dmem to facilitate situation.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 609
    temperature_celsius: 8
    replicates: 3
  - step_description: Cells were quantified with ripa buffer to facilitate trial.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    duration_minutes: 628
    temperature_celsius: 8
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      region.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: false
    duration_minutes: 183
    temperature_celsius: 10
    replicates: 2
  - step_description: Cells were washed with ripa buffer to facilitate Congress.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    temperature_celsius: 31
    replicates: 2
control_groups:
- control_type: Sham-operated Control
  description: Message behavior exist positive official trial president thing member
    wrong American family statement several thus.
- control_type: Vehicle Control
  description: Ever still possible sport policy century will challenge model.
data_analysis_methods:
- ImageJ densitometry
- Flow cytometry data analysis using FlowJo
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Ryan Moses
  and results were consistent across multiple biological replicates.
