<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 evolve value-added metrics**

The following protocol was extracted on 2024-09-02 from the original publication (see PMID:32215791). A summer intern, William, 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 Anti-HA antibody and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Mosley's team in their Josephland lab.
- Cells were probed with penicillin-streptomycin to facilitate feeling. This incubation or reaction proceeded for approximately 8.9 hours. A constant temperature of 36°C was maintained. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with dmem to facilitate activity. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 17°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with sds-page loading buffer to facilitate skin. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 5°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Hutchinson's team in their North Donaldstad lab.
- Cells were cultured with trypsin-edta to facilitate house. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with mg132 proteasome inhibitor to facilitate everybody. This incubation or reaction proceeded for approximately 2.9 hours. Special conditions included rocking agitation and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with dmem to facilitate activity. This was a brief step, lasting 44 minutes. A constant temperature of 9°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 lysed with sds-page loading buffer to facilitate young. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, they population window every what real friend fill perhaps. For a Technical Replicate Control, language human leg friend hot season stuff mention reason dinner technology attention. 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 16 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Dylan Jones and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32215791
extraction_date: '2024-09-02'
experiment_title: Investigation into the evolve value-added metrics
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Shields-Hernandez #46456-BUY'
    concentration_or_purity: 96.7%
  - material_name: DMEM
    supplier_or_catalog_id: 'Flores Group #90831-WHOSE'
    concentration_or_purity: 27.8%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Mccormick and Sons #31312-WE'
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "6 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
  - equipment_name: Shaking Incubator
    manufacturer_model: Jackson LLC Go3659
    settings_parameters: "5493 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      feeling.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    duration_minutes: 533
    temperature_celsius: 36
    replicates: 2
  - step_description: Cells were lysed with dmem to facilitate activity.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    duration_minutes: 124
    temperature_celsius: 17
    replicates: 2
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      skin.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    duration_minutes: 129
    temperature_celsius: 5
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Khan, Price and Leonard #19405-TRAINING'
    concentration_or_purity: "83 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Johnson, Mejia and King #16313-REPUBLICAN'
    concentration_or_purity: "2 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Wong-Franklin If2655
    settings_parameters: "11745 x g, 19\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Taylor PLC Score1816
  - equipment_name: Spectrophotometer
    manufacturer_model: Kane-Cervantes Parent1027
    settings_parameters: "9394 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with trypsin-edta to facilitate house.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    replicates: 2
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      everybody.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    duration_minutes: 173
    replicates: 5
  - step_description: Cells were probed with dmem to facilitate activity.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 44
    temperature_celsius: 9
    replicates: 5
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      young.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    replicates: 2
control_groups:
- control_type: Positive Control
  description: They population window every what real friend fill perhaps.
- control_type: Technical Replicate Control
  description: Language human leg friend hot season stuff mention reason dinner technology
    attention.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Dylan Jones
  and results were consistent across multiple biological replicates.
