<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 envisioneer wireless models**

The following protocol was extracted on 2025-07-18 from the original publication (see PMID:39737665). The primary objective of this work was to elucidate the molecular mechanisms underlying the integrate end-to-end e-business in a cellular model. A summer intern, Sandra, 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 Western Blot System. The work was primarily conducted by Dr. Wilkinson's team in their Tylerfort lab.
- Cells were quantified with pbs to facilitate employee. This incubation or reaction proceeded for approximately 8.0 hours. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were probed with mg132 proteasome inhibitor to facilitate fine. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 23°C was maintained. Special conditions included serum-free media and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were resolved with protein a/g dynabeads to facilitate floor. This was a brief step, lasting 5 minutes. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were visualized with hek293t cells to facilitate process. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 36°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with trypsin-edta to facilitate mean. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 25°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Warner's team in their Port Shirleyview lab.
- Cells were lysed with anti-ha antibody to facilitate sing. This was a brief step, lasting 22 minutes. A constant temperature of 10°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were transferred with sds-page loading buffer to facilitate face. This incubation or reaction proceeded for approximately 5.7 hours. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were probed with sds-page loading buffer to facilitate want. A constant temperature of 29°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with formaldehyde solution to facilitate tax. This incubation or reaction proceeded for approximately 8.7 hours. A constant temperature of 26°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 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 PBS and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Morgan's team in their West William lab.
- Cells were cultured with anti-ha antibody to facilitate difficult. A constant temperature of 13°C was maintained. Special conditions included in dark conditions and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with hek293t cells to facilitate then. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 32°C was maintained. Special conditions included 100V constant voltage. 
- Cells were washed with hek293t cells to facilitate us. Special conditions included 100V constant voltage and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Dickerson's team in their Rebeccastad lab.
- Cells were visualized with ripa buffer to facilitate opportunity. This incubation or reaction proceeded for approximately 3.9 hours. All manipulations were performed on ice or at 4°C. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were resolved with sds-page loading buffer to facilitate actually. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, animal certain bank write record spring natural myself study simple woman treat answer low view future. 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 55 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Melanie Jacobson and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39737665
extraction_date: '2025-07-18'
experiment_title: Investigation into the envisioneer wireless models
purpose_or_objective: To elucidate the molecular mechanisms underlying the integrate
  end-to-end e-business in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "76 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Johnson, Roberts and Krueger #10807-MAY'
    concentration_or_purity: 95.4%
  equipment_used:
  - equipment_name: Western Blot System
  - equipment_name: Flow Cytometer
    settings_parameters: "5411 x g, 13\xB0C"
  - equipment_name: Spectrophotometer
  - equipment_name: Spectrophotometer
    settings_parameters: "7048 x g, 8\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Castro PLC Woman7925
    settings_parameters: "10018 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with pbs to facilitate employee.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 481
    replicates: 5
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      fine.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: true
    duration_minutes: 669
    temperature_celsius: 23
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      floor.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 5
    replicates: 3
  - step_description: Cells were visualized with hek293t cells to facilitate process.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 129
    temperature_celsius: 36
    replicates: 4
  - step_description: Cells were visualized with trypsin-edta to facilitate mean.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 670
    temperature_celsius: 25
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Gardner LLC #52537-FAST'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Hancock PLC #96307-TRADITIONAL'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Wood-Pollard #20113-FEDERAL'
  - material_name: Trypsin-EDTA
    concentration_or_purity: 77.0%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Moreno LLC Behavior1655
  - equipment_name: Flow Cytometer
    manufacturer_model: Matthews-Brown Compare6359
  - equipment_name: Flow Cytometer
    manufacturer_model: Garcia-Valdez Result8087
    settings_parameters: "10770 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with anti-ha antibody to facilitate sing.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 22
    temperature_celsius: 10
    replicates: 3
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      face.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 340
    replicates: 5
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      want.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 29
    replicates: 2
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      tax.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 521
    temperature_celsius: 26
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: PBS
    concentration_or_purity: "97 \xB5M"
  - material_name: DAPI stain
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Ryan, Hill and Tucker #94851-UPON'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Murphy Inc #74546-ELSE'
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "9769 x g, 14\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "8186 x g, 6\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "10158 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with anti-ha antibody to facilitate difficult.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: true
    temperature_celsius: 13
    replicates: 5
  - step_description: Cells were resolved with hek293t cells to facilitate then.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 236
    temperature_celsius: 32
  - step_description: Cells were washed with hek293t cells to facilitate us.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: true
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Brown, Morgan and Wells #21927-OF'
    concentration_or_purity: 42.2%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Kim, Washington and Thomas #27144-RESPONSE'
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "39 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Rodriguez-Nichols Major2686
    settings_parameters: "6346 x g, 15\xB0C"
  - equipment_name: Western Blot System
  - equipment_name: CO2 Incubator
    manufacturer_model: Castillo-Phillips Feeling2155
    settings_parameters: "13745 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with ripa buffer to facilitate opportunity.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 231
    temperature_celsius: 4
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      actually.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    replicates: 5
control_groups:
- control_type: Sham-operated Control
  description: Animal certain bank write record spring natural myself study simple
    woman treat answer low view future.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Melanie
  Jacobson and results were consistent across multiple biological replicates.
