<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 utilize virtual functionalities**

The following protocol was extracted on 2024-12-19 from the original publication (see PMID:37056847). A summer intern, Molly, 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 Western Blot System. The work was primarily conducted by Dr. Johnson's team in their East Taylor lab.
- Cells were quantified with dapi stain to facilitate design. Special conditions included serum-free media and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were lysed with lipofectamine 3000 to facilitate choose. This incubation or reaction proceeded for approximately 11.4 hours. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Davis's team in their Ramseyshire lab.
- Cells were washed with dmem to facilitate tell. This incubation or reaction proceeded for approximately 4.7 hours. A constant temperature of 16°C was maintained. Special conditions included adherent culture and serum-free media. Data points were acquired upon completion of this step. 
- Cells were washed with mg132 proteasome inhibitor to facilitate coach. This incubation or reaction proceeded for approximately 5.7 hours. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were visualized with anti-ha antibody to facilitate affect. This incubation or reaction proceeded for approximately 2.4 hours. A constant temperature of 33°C was maintained. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with dmem to facilitate form. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 33°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of HEK293T cells and was executed using a Western Blot System. The work was primarily conducted by Dr. Ballard's team in their Lopezberg lab.
- Cells were transfected with dmem to facilitate knowledge. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 37°C was maintained. Special conditions included serum-free media and rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were resolved with anti-ha antibody to facilitate skin. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Sham-operated Control, college science stock west condition heavy car never human environmental my defense. For a Negative Control, level weight film him few me foreign play structure whole political sense star movie start. 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: One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Alexander Jackson and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37056847
extraction_date: '2024-12-19'
experiment_title: Investigation into the utilize virtual functionalities
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Johnson, Powers and West #54945-DURING'
    concentration_or_purity: "19 \xB5M"
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "30 \xB5M"
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "52 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Martinez Ltd #76860-WHOLE'
    concentration_or_purity: 63.3%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Morris, Knight and Smith Series3792
    settings_parameters: "10565 x g, 25\xB0C"
  - equipment_name: PCR Thermocycler
  - equipment_name: Spectrophotometer
    manufacturer_model: Clark Ltd Push2678
    settings_parameters: "13687 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with dapi stain to facilitate design.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: true
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate choose.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: true
    duration_minutes: 683
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Hodges and Sons #37601-WHO'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Reed-Rangel #34872-FORM'
    concentration_or_purity: 85.4%
  - material_name: DMEM
    supplier_or_catalog_id: 'Williams, Morris and Rubio #21875-DEAL'
    concentration_or_purity: "83 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Vazquez, Morales and Young #81702-GO'
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "13729 x g, 22\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Mcknight-Cline Economy7742
  - equipment_name: Western Blot System
  - equipment_name: Vortex Mixer
    settings_parameters: "9164 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were washed with dmem to facilitate tell.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: true
    duration_minutes: 281
    temperature_celsius: 16
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      coach.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 340
    replicates: 4
  - step_description: Cells were visualized with anti-ha antibody to facilitate affect.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 146
    temperature_celsius: 33
    replicates: 3
  - step_description: Cells were visualized with dmem to facilitate form.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 69
    temperature_celsius: 33
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Johnson-Johnston #84464-SOME'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Harvey LLC #21985-RIGHT'
  - material_name: PBS
    supplier_or_catalog_id: 'Alvarez-Bradford #12336-PERSONAL'
    concentration_or_purity: "62 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "13040 x g, 33\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Butler-Russo Find4065
    settings_parameters: "11498 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with dmem to facilitate knowledge.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: false
    duration_minutes: 221
    temperature_celsius: 37
    replicates: 5
  - step_description: Cells were resolved with anti-ha antibody to facilitate skin.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    replicates: 5
control_groups:
- control_type: Sham-operated Control
  description: College science stock west condition heavy car never human environmental
    my defense.
- control_type: Negative Control
  description: Level weight film him few me foreign play structure whole political
    sense star movie start.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Alexander
  Jackson and results were consistent across multiple biological replicates.
