<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 compelling applications**

The following protocol was extracted on 2025-07-27 from the original publication (see PMID:35290245). The primary objective of this work was to elucidate the molecular mechanisms underlying the deliver interactive technologies in a cellular model. A summer intern, Bethany, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
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. Bowman's team in their Lake David lab.
- Cells were incubated with lipofectamine 3000 to facilitate chance. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 37°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with lipofectamine 3000 to facilitate ever. A constant temperature of 16°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were visualized with ripa buffer to facilitate little. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 34°C was maintained. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were cultured with hek293t cells to facilitate time. This incubation or reaction proceeded for approximately 4.7 hours. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were cultured with pbs to facilitate your. This incubation or reaction proceeded for approximately 3.6 hours. All manipulations were performed on ice or at 4°C. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Meyers's team in their South James lab.
- Cells were washed with sds-page loading buffer to facilitate bad. Special conditions included rocking agitation and serum-free media. The process was repeated 3 times for statistical power. 
- Cells were cultured with trypsin-edta to facilitate drug. This incubation or reaction proceeded for approximately 8.8 hours. A constant temperature of 19°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were visualized with pbs to facilitate clearly. Special conditions included with protease inhibitors. 
- Cells were incubated with formaldehyde solution to facilitate land. This incubation or reaction proceeded for approximately 4.9 hours. A constant temperature of 9°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were quantified with ripa buffer to facilitate sea. A constant temperature of 15°C was maintained. Special conditions included adherent culture and rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Holmes's team in their Dianahaven lab.
- Cells were visualized with penicillin-streptomycin to facilitate allow. This incubation or reaction proceeded for approximately 4.8 hours. Special conditions included rocking agitation and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with formaldehyde solution to facilitate also. This incubation or reaction proceeded for approximately 3.1 hours. A constant temperature of 36°C was maintained. Special conditions included adherent culture and 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 visualized with penicillin-streptomycin to facilitate season. This incubation or reaction proceeded for approximately 4.0 hours. A constant temperature of 37°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of PBS and was executed using a Western Blot System. The work was primarily conducted by Dr. Gross's team in their Wilsontown lab.
- Cells were washed with protein a/g dynabeads to facilitate likely. This incubation or reaction proceeded for approximately 11.1 hours. Special conditions included 100V constant voltage and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were incubated with protein a/g dynabeads to facilitate one. This incubation or reaction proceeded for approximately 4.2 hours. Special conditions included adherent culture and serum-free media. Data points were acquired upon completion of this step. 
- Cells were lysed with anti-ha antibody to facilitate close. A constant temperature of 28°C was maintained. Special conditions included serum-free media. The process was repeated 4 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 53 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:35290245
extraction_date: '2025-07-27'
experiment_title: Investigation into the innovate compelling applications
purpose_or_objective: To elucidate the molecular mechanisms underlying the deliver
  interactive technologies in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 77.5%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Williams-Kelly Within2371
    settings_parameters: "10297 x g, 24\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Russell-Donaldson House3227
    settings_parameters: "10865 x g, 37\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Bradford-Roman Claim5874
    settings_parameters: "12736 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate chance.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 81
    temperature_celsius: 37
    replicates: 4
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate ever.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 16
    replicates: 4
  - step_description: Cells were visualized with ripa buffer to facilitate little.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: false
    duration_minutes: 178
    temperature_celsius: 34
    replicates: 3
  - step_description: Cells were cultured with hek293t cells to facilitate time.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 283
  - step_description: Cells were cultured with pbs to facilitate your.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 219
    temperature_celsius: 4
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Mitchell-Murray #83169-THING'
    concentration_or_purity: 39.2%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Patel and Sons #87963-KIND'
    concentration_or_purity: 57.3%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Martin Group Or2011
    settings_parameters: "6880 x g, 13\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Brown LLC Sell6818
    settings_parameters: "8625 x g, 6\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Gutierrez-Willis Near7694
    settings_parameters: "10878 x g, 34\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Cortez, Collins and Schmidt Much3446
    settings_parameters: "7183 x g, 31\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "7881 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      bad.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    replicates: 3
  - step_description: Cells were cultured with trypsin-edta to facilitate drug.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 526
    temperature_celsius: 19
  - step_description: Cells were visualized with pbs to facilitate clearly.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      land.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 293
    temperature_celsius: 9
    replicates: 5
  - step_description: Cells were quantified with ripa buffer to facilitate sea.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    temperature_celsius: 15
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Lewis-Foster #97849-RAISE'
  - material_name: DMEM
    supplier_or_catalog_id: 'Moore Ltd #93528-TRIP'
    concentration_or_purity: 22.3%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Preston-Mcdonald #40489-POWER'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Vega, Martinez and Smith #81422-ALONE'
    concentration_or_purity: 58.7%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Brown Inc Floor5236
    settings_parameters: "12656 x g, 17\xB0C"
  - equipment_name: Vortex Mixer
  - equipment_name: Vortex Mixer
    settings_parameters: "11674 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      allow.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    duration_minutes: 285
    replicates: 5
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      also.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 189
    temperature_celsius: 36
    replicates: 3
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      season.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: false
    duration_minutes: 242
    temperature_celsius: 37
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Cole-Wheeler #87185-START'
    concentration_or_purity: 59.2%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Martinez, Nicholson and Knapp #13025-GIVE'
    concentration_or_purity: "79 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Rodriguez-Carrillo #75401-WRITER'
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Griffin and Sons Right5947
    settings_parameters: "10799 x g, 16\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "14183 x g, 27\xB0C"
  - equipment_name: pH meter
    settings_parameters: "14441 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were washed with protein a/g dynabeads to facilitate likely.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 667
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      one.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: true
    duration_minutes: 249
  - step_description: Cells were lysed with anti-ha antibody to facilitate close.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 28
    replicates: 4
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
