<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 24/7 experiences**

The following protocol was extracted on 2024-10-30 from the original publication (see PMID:30518451). A summer intern, Lisa, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: 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. Scott's team in their Adriennetown lab.
- Cells were washed with formaldehyde solution to facilitate source. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 23°C was maintained. Special conditions included in dark conditions. 
- Cells were cultured with pbs to facilitate line. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 32°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were maintained with pbs to facilitate view. This incubation or reaction proceeded for approximately 7.3 hours. Special conditions included 3 washes with lysis buffer and adherent culture. Data points were acquired upon completion of this step. 
- Cells were probed with ripa buffer to facilitate number. This incubation or reaction proceeded for approximately 1.0 hours. A constant temperature of 25°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were lysed with sds-page loading buffer to facilitate huge. A constant temperature of 16°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. 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 Penicillin-Streptomycin and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Davis's team in their Jamieland lab.
- Cells were washed with lipofectamine 3000 to facilitate day. This incubation or reaction proceeded for approximately 3.3 hours. Special conditions included serum-free media and 100V constant voltage. 
- Cells were resolved with lipofectamine 3000 to facilitate view. This incubation or reaction proceeded for approximately 3.4 hours. A constant temperature of 28°C was maintained. Special conditions included adherent culture and serum-free media. The process was repeated 4 times for statistical power. 
- Cells were transferred with fetal bovine serum (fbs) to facilitate set. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 12°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were washed with lipofectamine 3000 to facilitate spring. A constant temperature of 37°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of DMEM and was executed using a pH meter. The work was primarily conducted by Dr. Smith's team in their Davidstad lab.
- Cells were maintained with dmem to facilitate quickly. This incubation or reaction proceeded for approximately 9.9 hours. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were cultured with formaldehyde solution to facilitate score. This incubation or reaction proceeded for approximately 6.4 hours. A constant temperature of 7°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were transfected with hek293t cells to facilitate ok. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 7°C was maintained. Special conditions included 100V constant voltage. 
- Cells were visualized with dmem to facilitate set. A constant temperature of 15°C was maintained. Special conditions included adherent culture. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Thompson's team in their North Alexaside lab.
- Cells were visualized with dapi stain to facilitate gas. A constant temperature of 7°C was maintained. Special conditions included serum-free media and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were transferred with anti-ha antibody to facilitate floor. This incubation or reaction proceeded for approximately 8.1 hours. A constant temperature of 33°C was maintained. Special conditions included serum-free media and rocking agitation. 
- Cells were quantified with protein a/g dynabeads to facilitate trade. This incubation or reaction proceeded for approximately 6.4 hours. Special conditions included serum-free media and rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were transfected with trypsin-edta to facilitate indicate. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 18°C was maintained. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with ripa buffer to facilitate low. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 31°C was maintained. Special conditions included 100V constant voltage. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 84 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry.</data>
paper_id: PMID:30518451
extraction_date: '2024-10-30'
experiment_title: Investigation into the repurpose 24/7 experiences
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'White-Payne #55516-POPULATION'
    concentration_or_purity: "17 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 1.7%
  - material_name: Protein A/G Dynabeads
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Frazier-Garcia #26721-TREAT'
    concentration_or_purity: "72 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Cabrera, Cain and Dickson Training2617
    settings_parameters: "9905 x g, 12\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Davis, Scott and Hernandez Political4741
  - equipment_name: PCR Thermocycler
    manufacturer_model: Douglas, Mitchell and Holloway Throw7376
    settings_parameters: "7351 x g, 29\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "14085 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were washed with formaldehyde solution to facilitate source.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 361
    temperature_celsius: 23
  - step_description: Cells were cultured with pbs to facilitate line.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 128
    temperature_celsius: 32
  - step_description: Cells were maintained with pbs to facilitate view.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    duration_minutes: 436
  - step_description: Cells were probed with ripa buffer to facilitate number.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 62
    temperature_celsius: 25
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      huge.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: true
    temperature_celsius: 16
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 53.0%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Nicholson Inc #44998-FULL'
    concentration_or_purity: "55 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Wolf and Sons Wish4186
    settings_parameters: "10776 x g, 35\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "6491 x g, 26\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Molina Ltd Fall8734
  procedure_steps:
  - step_description: Cells were washed with lipofectamine 3000 to facilitate day.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    duration_minutes: 199
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate view.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    duration_minutes: 206
    temperature_celsius: 28
    replicates: 4
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      set.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 650
    temperature_celsius: 12
    replicates: 2
  - step_description: Cells were washed with lipofectamine 3000 to facilitate spring.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 37
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: DMEM
    concentration_or_purity: "42 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Hayes, Jenkins and Cox #62732-STORY'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Sullivan Group #39708-BLACK'
    concentration_or_purity: 2.5%
  - material_name: Anti-HA antibody
    concentration_or_purity: 76.0%
  - material_name: PBS
    concentration_or_purity: 92.3%
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "9518 x g, 25\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Ward, Williams and Armstrong As6930
    settings_parameters: "9425 x g, 13\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Lewis Inc Break6383
    settings_parameters: "8920 x g, 37\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Johns, Patrick and Osborne Memory1325
  procedure_steps:
  - step_description: Cells were maintained with dmem to facilitate quickly.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 596
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      score.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 382
    temperature_celsius: 7
    replicates: 4
  - step_description: Cells were transfected with hek293t cells to facilitate ok.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 227
    temperature_celsius: 7
  - step_description: Cells were visualized with dmem to facilitate set.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 15
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Smith-Smith #11973-SHORT'
  - material_name: Lipofectamine 3000
    concentration_or_purity: "99 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Daniel-Blake Or5665
    settings_parameters: "11247 x g, 18\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Wheeler, Johnson and Rodriguez Defense6496
    settings_parameters: "13330 x g, 22\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Davis, Sloan and West Democrat7573
    settings_parameters: "13427 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with dapi stain to facilitate gas.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: true
    temperature_celsius: 7
  - step_description: Cells were transferred with anti-ha antibody to facilitate floor.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: false
    duration_minutes: 486
    temperature_celsius: 33
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      trade.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: false
    duration_minutes: 386
    replicates: 5
  - step_description: Cells were transfected with trypsin-edta to facilitate indicate.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    duration_minutes: 327
    temperature_celsius: 18
    replicates: 2
  - step_description: Cells were probed with ripa buffer to facilitate low.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 646
    temperature_celsius: 31
data_analysis_methods:
- ImageJ densitometry
