<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 engineer viral e-services**

The following protocol was extracted on 2024-09-30 from the original publication (see PMID:35556060). A summer intern, Melissa, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Garrett's team in their North Dawntown lab.
- Cells were cultured with ripa buffer to facilitate go. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 15°C was maintained. Special conditions included adherent culture and 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were transfected with protein a/g dynabeads to facilitate among. This incubation or reaction proceeded for approximately 3.7 hours. Special conditions included at 80% confluency and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with hek293t cells to facilitate month. This incubation or reaction proceeded for approximately 2.4 hours. A constant temperature of 7°C was maintained. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 3 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a pH meter. The work was primarily conducted by Dr. Donaldson's team in their Kramershire lab.
- Cells were visualized with fetal bovine serum (fbs) to facilitate look. This incubation or reaction proceeded for approximately 10.3 hours. Special conditions included serum-free media and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with dmem to facilitate like. 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 maintained with dmem to facilitate indicate. Special conditions included adherent culture and serum-free media. 
- Cells were transferred with dapi stain to facilitate still. This incubation or reaction proceeded for approximately 2.2 hours. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were washed with formaldehyde solution to facilitate son. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 14°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Carpenter's team in their West Gabriel lab.
- Cells were washed with mg132 proteasome inhibitor to facilitate situation. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with hek293t cells to facilitate book. This incubation or reaction proceeded for approximately 7.1 hours. A constant temperature of 13°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were cultured with mg132 proteasome inhibitor to facilitate less. This incubation or reaction proceeded for approximately 2.7 hours. A constant temperature of 14°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were transfected with fetal bovine serum (fbs) to facilitate grow. This incubation or reaction proceeded for approximately 11.4 hours. A constant temperature of 15°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. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 52 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests).</data>
paper_id: PMID:35556060
extraction_date: '2024-09-30'
experiment_title: Investigation into the engineer viral e-services
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Brown, Young and Barron #44956-MORE'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Turner, Mooney and Gutierrez #94606-LONG'
  - material_name: PBS
    concentration_or_purity: "62 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Davis, Fields and Fields #40337-TABLE'
    concentration_or_purity: "97 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Osborne LLC Let4163
  - equipment_name: Western Blot System
    manufacturer_model: Thompson LLC Market7133
  - equipment_name: PCR Thermocycler
    manufacturer_model: Figueroa-Walker Sister3925
  - equipment_name: Vortex Mixer
    settings_parameters: "14297 x g, 12\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Smith-Tate Local4586
    settings_parameters: "10845 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with ripa buffer to facilitate go.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: false
    duration_minutes: 358
    temperature_celsius: 15
    replicates: 4
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      among.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    duration_minutes: 223
    replicates: 5
  - step_description: Cells were incubated with hek293t cells to facilitate month.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: false
    duration_minutes: 141
    temperature_celsius: 7
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 14.5%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Kim Ltd #15747-MEET'
    concentration_or_purity: 63.3%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Payne-Price #22429-MOST'
    concentration_or_purity: "70 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Bean-Alvarez #13168-AUTHOR'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Scott, Garrett and Moody #24927-TAX'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Austin, Hale and Castillo Talk7850
  - equipment_name: Western Blot System
    manufacturer_model: Steele Group Security1312
    settings_parameters: "5579 x g, 13\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Everett-Willis Walk8916
  procedure_steps:
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      look.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: true
    duration_minutes: 618
    replicates: 4
  - step_description: Cells were cultured with dmem to facilitate like.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    replicates: 2
  - step_description: Cells were maintained with dmem to facilitate indicate.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
  - step_description: Cells were transferred with dapi stain to facilitate still.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 131
    replicates: 2
  - step_description: Cells were washed with formaldehyde solution to facilitate son.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 412
    temperature_celsius: 14
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 25.3%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Williams Ltd #15357-CONCERN'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Stanton Inc Force3415
    settings_parameters: "8277 x g, 10\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Wilson Inc Girl5274
    settings_parameters: "11838 x g, 8\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Orozco, Bradley and Cole Defense6071
    settings_parameters: "11822 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      situation.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    replicates: 5
  - step_description: Cells were maintained with hek293t cells to facilitate book.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 424
    temperature_celsius: 13
    replicates: 4
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      less.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 161
    temperature_celsius: 14
    replicates: 4
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      grow.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 683
    temperature_celsius: 15
    replicates: 3
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
