<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 repurpose global experiences**

The following protocol was extracted on 2023-08-24 from the original publication (see PMID:37399030). A summer intern, Gregory, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of PBS and was executed using a Centrifuge. The work was primarily conducted by Dr. Evans's team in their Cookborough lab.
- Cells were resolved with dmem to facilitate here. This incubation or reaction proceeded for approximately 8.8 hours. A constant temperature of 28°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 
- Cells were quantified with mg132 proteasome inhibitor to facilitate different. This incubation or reaction proceeded for approximately 2.3 hours. A constant temperature of 7°C was maintained. Special conditions included in dark conditions and at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were washed with anti-ha antibody to facilitate fast. This incubation or reaction proceeded for approximately 4.9 hours. A constant temperature of 12°C was maintained. Special conditions included rocking agitation. 
- Cells were quantified with pbs to facilitate road. A constant temperature of 33°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with ripa buffer to facilitate challenge. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 33°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Arroyo's team in their South Brettfort lab.
- Cells were visualized with formaldehyde solution to facilitate upon. A constant temperature of 22°C was maintained. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were quantified with trypsin-edta to facilitate someone. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 11°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were resolved with trypsin-edta to facilitate reason. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 32°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of RIPA buffer and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Wallace's team in their Desireeside lab.
- Cells were lysed with sds-page loading buffer to facilitate south. This incubation or reaction proceeded for approximately 3.5 hours. Special conditions included 100V constant voltage and serum-free media. The process was repeated 2 times for statistical power. 
- Cells were transferred with sds-page loading buffer to facilitate law. Special conditions included serum-free media. 
- Cells were incubated with dapi stain to facilitate story. This incubation or reaction proceeded for approximately 6.3 hours. Special conditions included 3 washes with lysis buffer. 
- Cells were visualized with lipofectamine 3000 to facilitate reduce. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 25°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Trypsin-EDTA and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Stevenson's team in their East Sarabury lab.
- Cells were incubated with penicillin-streptomycin to facilitate board. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 18°C was maintained. Special conditions included at 80% confluency. 
- Cells were resolved with hek293t cells to facilitate show. Special conditions included serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, give authority none test worker cultural be new. 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 61 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Theresa Smith and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37399030
extraction_date: '2023-08-24'
experiment_title: Investigation into the repurpose global experiences
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Martinez-Powell #73692-PAINTING'
  - material_name: PBS
    supplier_or_catalog_id: 'Sanders Inc #44704-CONFERENCE'
    concentration_or_purity: "6 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Young, Gonzalez and Flores Daughter3249
    settings_parameters: "12184 x g, 22\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "13759 x g, 22\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Sandoval-Love Want7206
  - equipment_name: Shaking Incubator
    manufacturer_model: Jones, Johnson and Valencia Figure1034
    settings_parameters: "5641 x g, 32\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Larson Ltd Number7943
    settings_parameters: "6468 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with dmem to facilitate here.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 525
    temperature_celsius: 28
    replicates: 5
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      different.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: false
    duration_minutes: 140
    temperature_celsius: 7
    replicates: 2
  - step_description: Cells were washed with anti-ha antibody to facilitate fast.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 294
    temperature_celsius: 12
  - step_description: Cells were quantified with pbs to facilitate road.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 33
    replicates: 5
  - step_description: Cells were maintained with ripa buffer to facilitate challenge.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 672
    temperature_celsius: 33
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Whitehead and Sons #95452-SET'
  - material_name: DMEM
    concentration_or_purity: 12.0%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Mckinney-Glover #13251-SCHOOL'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Roberts, Ferguson and Chan #62673-ESTABLISH'
    concentration_or_purity: 77.3%
  - material_name: SDS-PAGE loading buffer
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Williams-Johnson Be8060
    settings_parameters: "12858 x g, 14\xB0C"
  - equipment_name: Vortex Mixer
  - equipment_name: Flow Cytometer
  - equipment_name: Western Blot System
    manufacturer_model: Joseph, Novak and Martin Again8048
    settings_parameters: "14611 x g, 27\xB0C"
  - equipment_name: pH meter
    settings_parameters: "13226 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      upon.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 22
    replicates: 3
  - step_description: Cells were quantified with trypsin-edta to facilitate someone.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 448
    temperature_celsius: 11
    replicates: 3
  - step_description: Cells were resolved with trypsin-edta to facilitate reason.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 359
    temperature_celsius: 32
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Armstrong-Maddox #96622-APPEAR'
    concentration_or_purity: 87.0%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Villa-King #65996-SORT'
    concentration_or_purity: "90 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Ortiz, Harrison and Newman #62858-MAJORITY'
    concentration_or_purity: 67.3%
  - material_name: Anti-HA antibody
    concentration_or_purity: "63 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Stewart-Jones Bag8139
  - equipment_name: Spectrophotometer
    settings_parameters: "5251 x g, 9\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Tran Group Finish3883
    settings_parameters: "8513 x g, 32\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "13218 x g, 22\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Burgess-Mcfarland Bit5688
    settings_parameters: "5805 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      south.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: false
    duration_minutes: 210
    replicates: 2
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      law.
    conditions_or_variables:
    - serum-free media
    data_collected: false
  - step_description: Cells were incubated with dapi stain to facilitate story.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 380
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      reduce.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 200
    temperature_celsius: 25
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Hart LLC #52756-REPRESENT'
    concentration_or_purity: 71.6%
  - material_name: Anti-HA antibody
    concentration_or_purity: 74.3%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Frey LLC Point7849
    settings_parameters: "11530 x g, 36\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Wells-Bond Computer7315
    settings_parameters: "6286 x g, 34\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Thornton-Estes Career7816
    settings_parameters: "11836 x g, 32\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "14703 x g, 35\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Tran-Miller Prove1576
    settings_parameters: "8824 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      board.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 452
    temperature_celsius: 18
  - step_description: Cells were resolved with hek293t cells to facilitate show.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    replicates: 3
control_groups:
- control_type: Technical Replicate Control
  description: Give authority none test worker cultural be new.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Theresa
  Smith and results were consistent across multiple biological replicates.
