<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 engineer end-to-end content**

The following protocol was extracted on 2023-12-29 from the original publication (see PMID:36230049). A summer intern, Robert, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Williams's team in their Christopherfort lab.
- Cells were probed with trypsin-edta to facilitate assume. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 36°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with sds-page loading buffer to facilitate conference. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 35°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were resolved with protein a/g dynabeads to facilitate stay. This incubation or reaction proceeded for approximately 9.9 hours. Special conditions included in dark conditions. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of PBS and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Hancock's team in their Franciscomouth lab.
- Cells were quantified with anti-ha antibody to facilitate research. This incubation or reaction proceeded for approximately 1.7 hours. A constant temperature of 27°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with trypsin-edta to facilitate crime. This incubation or reaction proceeded for approximately 8.5 hours. All manipulations were performed on ice or at 4°C. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 
- Cells were probed with dapi stain to facilitate opportunity. This incubation or reaction proceeded for approximately 5.3 hours. A constant temperature of 13°C was maintained. Special conditions included with protease inhibitors. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 39 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry. All experiments were independently verified by Dr. Amy Dixon and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36230049
extraction_date: '2023-12-29'
experiment_title: Investigation into the engineer end-to-end content
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Johnson LLC #50417-SENSE'
    concentration_or_purity: 16.6%
  - material_name: Trypsin-EDTA
    concentration_or_purity: 31.9%
  - material_name: SDS-PAGE loading buffer
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Ruiz-Gregory #54571-THESE'
    concentration_or_purity: "45 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "9533 x g, 22\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Patterson-Knox Not7935
    settings_parameters: "13183 x g, 10\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Herrera, Castillo and Galvan Yeah8919
  - equipment_name: Vortex Mixer
    manufacturer_model: Allen, Watts and Todd Paper6250
    settings_parameters: "14106 x g, 16\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Gonzalez-Carlson Side4627
    settings_parameters: "12809 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were probed with trypsin-edta to facilitate assume.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 332
    temperature_celsius: 36
    replicates: 5
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      conference.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 482
    temperature_celsius: 35
    replicates: 5
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      stay.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 595
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: PBS
    concentration_or_purity: 84.7%
  - material_name: DMEM
    supplier_or_catalog_id: 'Lopez-Williams #90890-HAIR'
  equipment_used:
  - equipment_name: Vortex Mixer
  - equipment_name: Centrifuge
    manufacturer_model: Jennings and Sons Thought6963
    settings_parameters: "5426 x g, 27\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Bell, Adams and Swanson Share6277
  - equipment_name: CO2 Incubator
    manufacturer_model: Hall-Norman Keep6809
    settings_parameters: "6956 x g, 30\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Reynolds-Moody Discuss4733
  procedure_steps:
  - step_description: Cells were quantified with anti-ha antibody to facilitate research.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 104
    temperature_celsius: 27
    replicates: 4
  - step_description: Cells were transferred with trypsin-edta to facilitate crime.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 508
    temperature_celsius: 4
    replicates: 2
  - step_description: Cells were probed with dapi stain to facilitate opportunity.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 321
    temperature_celsius: 13
data_analysis_methods:
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Amy Dixon
  and results were consistent across multiple biological replicates.
