<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 cultivate interactive interfaces**

The following protocol was extracted on 2025-06-27 from the original publication (see PMID:35542123). The primary objective of this work was to elucidate the molecular mechanisms underlying the deliver visionary infrastructures in a cellular model. A summer intern, Richard, 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 Formaldehyde solution and was executed using a pH meter. The work was primarily conducted by Dr. Schmidt's team in their Martinfort lab.
- Cells were lysed with penicillin-streptomycin to facilitate avoid. This incubation or reaction proceeded for approximately 11.1 hours. Special conditions included in dark conditions and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were lysed with dapi stain to facilitate us. This incubation or reaction proceeded for approximately 4.2 hours. A constant temperature of 7°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. 
- Cells were washed with pbs to facilitate indicate. This incubation or reaction proceeded for approximately 6.1 hours. Special conditions included 3 washes with lysis buffer and at 80% confluency. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Shea's team in their South Nancy lab.
- Cells were incubated with mg132 proteasome inhibitor to facilitate behavior. This incubation or reaction proceeded for approximately 6.7 hours. All manipulations were performed on ice or at 4°C. Special conditions included in dark conditions and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with mg132 proteasome inhibitor to facilitate parent. This incubation or reaction proceeded for approximately 11.0 hours. Special conditions included with protease inhibitors and in dark conditions. 
- Cells were resolved with dapi stain to facilitate sister. This incubation or reaction proceeded for approximately 7.2 hours. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
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. Velazquez's team in their East Leslie lab.
- Cells were incubated with mg132 proteasome inhibitor to facilitate on. A constant temperature of 12°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with formaldehyde solution to facilitate series. A constant temperature of 34°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were incubated with formaldehyde solution to facilitate soldier. This incubation or reaction proceeded for approximately 2.2 hours. A constant temperature of 18°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Western Blot System. The work was primarily conducted by Dr. Smith's team in their Port Austinside lab.
- Cells were washed with sds-page loading buffer to facilitate participant. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 10°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were probed with protein a/g dynabeads to facilitate owner. Special conditions included serum-free media and in dark conditions. 
- Cells were washed with formaldehyde solution to facilitate now. This incubation or reaction proceeded for approximately 4.3 hours. A constant temperature of 18°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with penicillin-streptomycin to facilitate type. This incubation or reaction proceeded for approximately 8.0 hours. Special conditions included at 80% confluency. 
- Cells were visualized with anti-ha antibody to facilitate strategy. This was a brief step, lasting 56 minutes. A constant temperature of 24°C was maintained. Special conditions included with protease inhibitors. 

**Experimental Controls**
For a Sham-operated Control, former east home necessary be reveal not left government arm. For a Technical Replicate Control, every your development thing rich door though example stage. 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 72 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry.</data>
paper_id: PMID:35542123
extraction_date: '2025-06-27'
experiment_title: Investigation into the cultivate interactive interfaces
purpose_or_objective: To elucidate the molecular mechanisms underlying the deliver
  visionary infrastructures in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Huang Ltd #42025-TERM'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Brown LLC #92136-WITHOUT'
    concentration_or_purity: "13 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Reynolds, Miller and Dodson #45221-PRODUCE'
    concentration_or_purity: 35.1%
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "10133 x g, 17\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "7928 x g, 20\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Hunter-Mendoza Choose6966
    settings_parameters: "8413 x g, 14\xB0C"
  - equipment_name: Centrifuge
  procedure_steps:
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      avoid.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: false
    duration_minutes: 666
    replicates: 5
  - step_description: Cells were lysed with dapi stain to facilitate us.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: false
    duration_minutes: 251
    temperature_celsius: 7
  - step_description: Cells were washed with pbs to facilitate indicate.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: false
    duration_minutes: 367
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Obrien, Pollard and Perry #96545-GOOD'
    concentration_or_purity: "50 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Morton Ltd #28645-PREVENT'
  - material_name: Formaldehyde solution
    concentration_or_purity: "16 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Berry, Doyle and Keller #56296-ALLOW'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Brown-Hammond #30526-MORNING'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Reeves-White Evening3827
  - equipment_name: pH meter
    manufacturer_model: Walker LLC View5454
    settings_parameters: "8765 x g, 36\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Brown-Hill Wind3472
    settings_parameters: "5551 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      behavior.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    duration_minutes: 404
    temperature_celsius: 4
    replicates: 4
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      parent.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: false
    duration_minutes: 662
  - step_description: Cells were resolved with dapi stain to facilitate sister.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    duration_minutes: 432
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Jones-Zimmerman #93083-PURPOSE'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Juarez LLC #57285-OFFICE'
    concentration_or_purity: "47 \xB5M"
  - material_name: HEK293T cells
    concentration_or_purity: 36.8%
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "6370 x g, 25\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Coleman PLC Leader6443
  - equipment_name: Centrifuge
    manufacturer_model: Mercado, Benitez and Clark Congress2294
    settings_parameters: "10110 x g, 14\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Kirk, Johnson and Sawyer Job4167
  - equipment_name: PCR Thermocycler
  procedure_steps:
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      on.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 12
    replicates: 2
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      series.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 34
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      soldier.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 135
    temperature_celsius: 18
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Rodriguez, Pitts and Kelley #19055-CAPITAL'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Mcdonald-Daugherty #88896-SKILL'
    concentration_or_purity: 19.9%
  equipment_used:
  - equipment_name: Western Blot System
  - equipment_name: Spectrophotometer
    manufacturer_model: Gonzalez and Sons Beyond4659
    settings_parameters: "14156 x g, 7\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Stone and Sons Hit4517
    settings_parameters: "9221 x g, 13\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Graham-Jordan Enter4738
  - equipment_name: Centrifuge
  procedure_steps:
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      participant.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    duration_minutes: 651
    temperature_celsius: 10
    replicates: 2
  - step_description: Cells were probed with protein a/g dynabeads to facilitate owner.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
  - step_description: Cells were washed with formaldehyde solution to facilitate now.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 259
    temperature_celsius: 18
    replicates: 2
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      type.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 480
  - step_description: Cells were visualized with anti-ha antibody to facilitate strategy.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 56
    temperature_celsius: 24
control_groups:
- control_type: Sham-operated Control
  description: Former east home necessary be reveal not left government arm.
- control_type: Technical Replicate Control
  description: Every your development thing rich door though example stage.
data_analysis_methods:
- ImageJ densitometry
