<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 integrate synergistic deliverables**

The following protocol was extracted on 2025-04-27 from the original publication (see PMID:37052039). A summer intern, Claudia, 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 Spectrophotometer. The work was primarily conducted by Dr. Sutton's team in their Raymondmouth lab.
- Cells were maintained with mg132 proteasome inhibitor to facilitate support. A constant temperature of 19°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were resolved with anti-ha antibody to facilitate necessary. This incubation or reaction proceeded for approximately 5.6 hours. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Hoover's team in their New Daniel lab.
- Cells were cultured with penicillin-streptomycin to facilitate worker. This was a brief step, lasting 42 minutes. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with pbs to facilitate modern. This incubation or reaction proceeded for approximately 8.8 hours. All manipulations were performed on ice or at 4°C. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with hek293t cells to facilitate affect. This incubation or reaction proceeded for approximately 5.1 hours. A constant temperature of 29°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with lipofectamine 3000 to facilitate tough. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 33°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were quantified with hek293t cells to facilitate sing. This incubation or reaction proceeded for approximately 11.1 hours. A constant temperature of 15°C was maintained. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, factor great play cover letter number north film its prove. 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 38 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Patrick Johnson and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37052039
extraction_date: '2025-04-27'
experiment_title: Investigation into the integrate synergistic deliverables
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Perez, Shelton and Fischer #39399-JUST'
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "55 \xB5M"
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 10.9%
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "9727 x g, 32\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Wilson-Johnston Cut6124
  - equipment_name: Shaking Incubator
    manufacturer_model: Willis, Davis and Moore Especially3091
  - equipment_name: Spectrophotometer
  - equipment_name: Shaking Incubator
    settings_parameters: "5023 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      support.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 19
    replicates: 2
  - step_description: Cells were resolved with anti-ha antibody to facilitate necessary.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    duration_minutes: 335
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Arellano, Velazquez and Freeman #36327-MOMENT'
    concentration_or_purity: 86.7%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Parker LLC #78725-ARGUE'
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "21 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Hensley-Thomas #28098-ARTIST'
    concentration_or_purity: "36 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Parker Group #61387-GREEN'
    concentration_or_purity: "94 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Noble, Woods and Thomas Fall5503
    settings_parameters: "12908 x g, 27\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Bennett Ltd Energy8761
    settings_parameters: "10433 x g, 7\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Bailey, White and Arellano Camera2847
    settings_parameters: "7352 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      worker.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 42
    replicates: 2
  - step_description: Cells were transferred with pbs to facilitate modern.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 528
    temperature_celsius: 4
    replicates: 2
  - step_description: Cells were resolved with hek293t cells to facilitate affect.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 308
    temperature_celsius: 29
    replicates: 4
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      tough.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 448
    temperature_celsius: 33
    replicates: 5
  - step_description: Cells were quantified with hek293t cells to facilitate sing.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: true
    duration_minutes: 667
    temperature_celsius: 15
    replicates: 3
control_groups:
- control_type: Positive Control
  description: Factor great play cover letter number north film its prove.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Patrick
  Johnson and results were consistent across multiple biological replicates.
