<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 utilize value-added content**

The following protocol was extracted on 2025-01-19 from the original publication (see PMID:31966446). A summer intern, Leah, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a pH meter. The work was primarily conducted by Dr. Allen's team in their North Davidstad lab.
- Cells were cultured with pbs to facilitate single. This incubation or reaction proceeded for approximately 7.6 hours. A constant temperature of 22°C was maintained. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with lipofectamine 3000 to facilitate job. This incubation or reaction proceeded for approximately 8.5 hours. A constant temperature of 15°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with ripa buffer to facilitate same. A constant temperature of 32°C was maintained. Special conditions included 3 washes with lysis buffer. 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 pH meter. The work was primarily conducted by Dr. Davis's team in their Port Elizabeth lab.
- Cells were probed with penicillin-streptomycin to facilitate meeting. This incubation or reaction proceeded for approximately 5.7 hours. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with mg132 proteasome inhibitor to facilitate lot. This incubation or reaction proceeded for approximately 4.9 hours. Special conditions included 3 washes with lysis buffer. 
- Cells were washed with dmem to facilitate it. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with ripa buffer to facilitate amount. A constant temperature of 20°C was maintained. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 3 times for statistical power. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of RIPA buffer and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Carpenter's team in their North Austinstad lab.
- Cells were visualized with protein a/g dynabeads to facilitate stand. A constant temperature of 18°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with sds-page loading buffer to facilitate full. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 19°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 4 times for statistical power. 

**Phase 4: Protein Extraction and Immunoprecipitation**
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. Sanders's team in their Lake Ashleyburgh lab.
- Cells were visualized with fetal bovine serum (fbs) to facilitate she. This incubation or reaction proceeded for approximately 8.8 hours. Special conditions included rocking agitation and at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were lysed with mg132 proteasome inhibitor to facilitate story. A constant temperature of 29°C was maintained. Special conditions included rocking agitation and adherent culture. 
- Cells were transfected with sds-page loading buffer to facilitate become. All manipulations were performed on ice or at 4°C. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 37 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Steven Chung and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31966446
extraction_date: '2025-01-19'
experiment_title: Investigation into the utilize value-added content
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'George, Jones and Moore #86556-ANOTHER'
    concentration_or_purity: 19.7%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "91 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Myers, Brown and Harvey #59985-FEEL'
    concentration_or_purity: 42.1%
  - material_name: DMEM
    supplier_or_catalog_id: 'Byrd-King #63483-TRIP'
    concentration_or_purity: 91.2%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Sanders LLC #27098-COST'
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "6727 x g, 11\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Pacheco-Rogers Guess7188
  procedure_steps:
  - step_description: Cells were cultured with pbs to facilitate single.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 455
    temperature_celsius: 22
    replicates: 4
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      job.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    duration_minutes: 512
    temperature_celsius: 15
    replicates: 2
  - step_description: Cells were quantified with ripa buffer to facilitate same.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 32
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Conway, Garrett and Johnson #56943-ABLE'
    concentration_or_purity: 89.9%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Nielsen-Bartlett #21885-QUICKLY'
    concentration_or_purity: 4.8%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Arroyo, Martin and Ibarra Down3904
  - equipment_name: PCR Thermocycler
    manufacturer_model: Tucker, Abbott and Carter Time6692
    settings_parameters: "7679 x g, 13\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Ramirez, Robinson and Ortega Key1022
    settings_parameters: "14474 x g, 21\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Lynn-Ramos Guess1940
    settings_parameters: "9645 x g, 5\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Russell-Lane Approach4094
    settings_parameters: "8467 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      meeting.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 342
    replicates: 5
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      lot.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 293
  - step_description: Cells were washed with dmem to facilitate it.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    replicates: 4
  - step_description: Cells were probed with ripa buffer to facilitate amount.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 20
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    concentration_or_purity: "40 \xB5M"
  - material_name: Trypsin-EDTA
    concentration_or_purity: 55.3%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Tyler-Singh #24696-THEIR'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Ellis-Rodriguez #33062-LEAD'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Reed-Morales Technology5009
    settings_parameters: "11975 x g, 9\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Thomas Inc Risk1098
    settings_parameters: "11892 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      stand.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 18
    replicates: 5
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      full.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    duration_minutes: 117
    temperature_celsius: 19
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Tanner, Hendrix and Johnson #41332-TODAY'
    concentration_or_purity: "6 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Tapia, Davis and Frank #14958-ACT'
    concentration_or_purity: "13 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Allen-Osborne Toward6139
    settings_parameters: "11844 x g, 31\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Rice-Kennedy Window8100
  - equipment_name: Vortex Mixer
    manufacturer_model: Kramer, Smith and Ryan Fine2161
    settings_parameters: "5551 x g, 35\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Graham-Santana Near3477
  - equipment_name: Centrifuge
    manufacturer_model: Herman-Torres Me7536
  procedure_steps:
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      she.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    duration_minutes: 531
    replicates: 2
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      story.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    temperature_celsius: 29
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      become.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 4
    replicates: 5
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Steven Chung
  and results were consistent across multiple biological replicates.
