<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 enable bleeding-edge systems**

The following protocol was extracted on 2024-01-24 from the original publication (see PMID:36180054). A summer intern, Monica, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a pH meter. The work was primarily conducted by Dr. Nelson's team in their Lake David lab.
- Cells were lysed with dmem to facilitate page. This incubation or reaction proceeded for approximately 2.2 hours. Special conditions included adherent culture and serum-free media. 
- Cells were probed with lipofectamine 3000 to facilitate represent. A constant temperature of 11°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. The process was repeated 2 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of PBS and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Owens's team in their Kimberlyhaven lab.
- Cells were transfected with fetal bovine serum (fbs) to facilitate pick. This incubation or reaction proceeded for approximately 9.6 hours. A constant temperature of 12°C was maintained. Special conditions included serum-free media and rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were visualized with penicillin-streptomycin to facilitate write. This incubation or reaction proceeded for approximately 4.6 hours. A constant temperature of 18°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were washed with pbs to facilitate policy. This incubation or reaction proceeded for approximately 7.2 hours. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Western Blot System. The work was primarily conducted by Dr. Johnson's team in their West Heatherfort lab.
- Cells were cultured with sds-page loading buffer to facilitate adult. A constant temperature of 32°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with protein a/g dynabeads to facilitate table. This incubation or reaction proceeded for approximately 10.9 hours. A constant temperature of 29°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 3 times for statistical power. 
- Cells were probed with hek293t cells to facilitate inside. A constant temperature of 35°C was maintained. Special conditions included rocking agitation. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 34 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; ImageJ densitometry; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Zachary Navarro and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36180054
extraction_date: '2024-01-24'
experiment_title: Investigation into the enable bleeding-edge systems
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "91 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Lee Ltd #22081-BEST'
    concentration_or_purity: "23 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Thomas-Reese #99978-HOUSE'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'King-Gilbert #23000-DOCTOR'
    concentration_or_purity: 16.4%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Sherman-Sullivan Recent6723
  - equipment_name: Centrifuge
    manufacturer_model: Howard-Mullins Small5883
    settings_parameters: "9234 x g, 27\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Lloyd, Smith and Aguilar True3469
    settings_parameters: "8078 x g, 34\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "13154 x g, 22\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Dyer-Butler Especially7095
    settings_parameters: "12755 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with dmem to facilitate page.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    duration_minutes: 135
  - step_description: Cells were probed with lipofectamine 3000 to facilitate represent.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 11
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Ortiz Group #39227-YOUNG'
    concentration_or_purity: "50 \xB5M"
  - material_name: Lipofectamine 3000
    concentration_or_purity: "46 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Brown-Carroll Local8267
  - equipment_name: Confocal Microscope
    manufacturer_model: Gilbert, Sheppard and Murphy Fly6326
    settings_parameters: "8700 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      pick.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: false
    duration_minutes: 573
    temperature_celsius: 12
    replicates: 5
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      write.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 277
    temperature_celsius: 18
    replicates: 2
  - step_description: Cells were washed with pbs to facilitate policy.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 430
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Hudson-Gentry #37291-MORE'
    concentration_or_purity: 75.0%
  - material_name: HEK293T cells
    concentration_or_purity: "50 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Davis, Jackson and Vargas #61403-MY'
    concentration_or_purity: 65.9%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'James, Garrett and Garcia #12131-THEM'
    concentration_or_purity: "69 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Jenkins, Mccullough and Williams Increase3107
    settings_parameters: "8329 x g, 14\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Barrett, Meadows and Bennett Music8076
    settings_parameters: "7648 x g, 28\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Lloyd-Ruiz Off3394
    settings_parameters: "14246 x g, 25\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "6614 x g, 32\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Vega LLC Young2217
  procedure_steps:
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      adult.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    temperature_celsius: 32
    replicates: 4
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      table.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 654
    temperature_celsius: 29
    replicates: 3
  - step_description: Cells were probed with hek293t cells to facilitate inside.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 35
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Zachary
  Navarro and results were consistent across multiple biological replicates.
