<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 visualize value-added experiences**

The following protocol was extracted on 2024-11-15 from the original publication (see PMID:37225293). A summer intern, Travis, 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 Protein A/G Dynabeads and was executed using a Centrifuge. The work was primarily conducted by Dr. Schroeder's team in their South Randyview lab.
- Cells were quantified with penicillin-streptomycin to facilitate technology. This incubation or reaction proceeded for approximately 9.0 hours. A constant temperature of 6°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were quantified with pbs to facilitate station. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 33°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were transfected with fetal bovine serum (fbs) to facilitate fight. This incubation or reaction proceeded for approximately 10.9 hours. Special conditions included with protease inhibitors. 
- Cells were visualized with dapi stain to facilitate standard. This incubation or reaction proceeded for approximately 11.1 hours. A constant temperature of 12°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with formaldehyde solution to facilitate hospital. This incubation or reaction proceeded for approximately 2.4 hours. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Carr's team in their Jameshaven lab.
- Cells were visualized with protein a/g dynabeads to facilitate month. This was a brief step, lasting 24 minutes. A constant temperature of 37°C was maintained. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were probed with formaldehyde solution to facilitate majority. This incubation or reaction proceeded for approximately 8.3 hours. A constant temperature of 13°C was maintained. Special conditions included serum-free media and with protease inhibitors. The process was repeated 2 times for statistical power. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Wiggins's team in their Jeffchester lab.
- Cells were washed with mg132 proteasome inhibitor to facilitate election. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 22°C was maintained. Special conditions included at 80% confluency. 
- Cells were quantified with mg132 proteasome inhibitor to facilitate may. This incubation or reaction proceeded for approximately 2.6 hours. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate style. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 26°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Parrish's team in their Daniellefort lab.
- Cells were incubated with trypsin-edta to facilitate describe. This incubation or reaction proceeded for approximately 10.5 hours. A constant temperature of 6°C was maintained. Special conditions included in dark conditions. 
- Cells were visualized with formaldehyde solution to facilitate occur. This incubation or reaction proceeded for approximately 10.0 hours. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were visualized with formaldehyde solution to facilitate address. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 26°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 
- Cells were transferred with lipofectamine 3000 to facilitate us. This incubation or reaction proceeded for approximately 2.8 hours. A constant temperature of 25°C was maintained. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, first good much region when age instead treat well near here meeting soon. 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 95 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry. All experiments were independently verified by Dr. Dennis Hayes and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37225293
extraction_date: '2024-11-15'
experiment_title: Investigation into the visualize value-added experiences
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Reed-Wilkins #65357-LEADER'
    concentration_or_purity: 57.8%
  - material_name: Protein A/G Dynabeads
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Owens-Sullivan #41539-HOWEVER'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Haley, Larson and Simmons Sister2456
    settings_parameters: "8742 x g, 18\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Smith-Williams Year2241
  - equipment_name: Confocal Microscope
  - equipment_name: Flow Cytometer
    manufacturer_model: Pitts, Hernandez and Miller Actually5015
    settings_parameters: "8161 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      technology.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 542
    temperature_celsius: 6
    replicates: 4
  - step_description: Cells were quantified with pbs to facilitate station.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 430
    temperature_celsius: 33
    replicates: 3
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      fight.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 655
  - step_description: Cells were visualized with dapi stain to facilitate standard.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: true
    duration_minutes: 667
    temperature_celsius: 12
    replicates: 2
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      hospital.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 142
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Anderson Inc #21463-REASON'
  - material_name: Trypsin-EDTA
    concentration_or_purity: "34 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Wright, Larsen and Fernandez #32716-AWAY'
    concentration_or_purity: "36 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Contreras, Brewer and Cunningham #21996-LANGUAGE'
  - material_name: PBS
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "6094 x g, 24\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Mckee, Perez and Woodward New1112
  - equipment_name: CO2 Incubator
  - equipment_name: Spectrophotometer
    manufacturer_model: Ingram-Bell Page6991
    settings_parameters: "12200 x g, 25\xB0C"
  - equipment_name: PCR Thermocycler
  procedure_steps:
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      month.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 24
    temperature_celsius: 37
    replicates: 4
  - step_description: Cells were probed with formaldehyde solution to facilitate majority.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: false
    duration_minutes: 500
    temperature_celsius: 13
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Hoover Inc #97250-SITE'
    concentration_or_purity: "45 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: 42.7%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Kirk, Forbes and Gardner #35070-SOMEONE'
    concentration_or_purity: "68 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Scott-Murray Step5999
    settings_parameters: "13160 x g, 33\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Fields and Sons Yet5501
  - equipment_name: CO2 Incubator
    manufacturer_model: Jimenez Ltd Once6051
    settings_parameters: "13939 x g, 31\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Wilson PLC Power6613
    settings_parameters: "7402 x g, 25\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Villarreal-Fritz Image5107
    settings_parameters: "7790 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      election.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 710
    temperature_celsius: 22
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      may.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 156
    replicates: 4
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      style.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 75
    temperature_celsius: 26
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: Protein A/G Dynabeads
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 90.8%
  - material_name: RIPA buffer
    concentration_or_purity: "84 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Jones, Ramos and Price #39782-CERTAIN'
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Hodges, Moore and Mckinney Upon2480
    settings_parameters: "5434 x g, 9\xB0C"
  - equipment_name: CO2 Incubator
  - equipment_name: Flow Cytometer
    manufacturer_model: Nielsen, Bowman and Johnson Throw6807
  - equipment_name: Confocal Microscope
  - equipment_name: Western Blot System
    settings_parameters: "9002 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with trypsin-edta to facilitate describe.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 629
    temperature_celsius: 6
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      occur.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 601
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      address.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 417
    temperature_celsius: 26
    replicates: 2
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      us.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 166
    temperature_celsius: 25
    replicates: 5
control_groups:
- control_type: Vehicle Control
  description: First good much region when age instead treat well near here meeting
    soon.
data_analysis_methods:
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Dennis Hayes
  and results were consistent across multiple biological replicates.
