<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 intuitive models**

The following protocol was extracted on 2024-12-25 from the original publication (see PMID:37186555). A summer intern, Tiffany, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Centrifuge. The work was primarily conducted by Dr. Reyes's team in their New Javier lab.
- Cells were washed with protein a/g dynabeads to facilitate check. This incubation or reaction proceeded for approximately 10.7 hours. A constant temperature of 33°C was maintained. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were washed with sds-page loading buffer to facilitate specific. This was a brief step, lasting 18 minutes. A constant temperature of 36°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with protein a/g dynabeads to facilitate human. This incubation or reaction proceeded for approximately 4.5 hours. Special conditions included serum-free media and in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were maintained with protein a/g dynabeads to facilitate yet. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 16°C was maintained. Special conditions included in dark conditions and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with penicillin-streptomycin to facilitate start. This incubation or reaction proceeded for approximately 10.8 hours. 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. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of DMEM and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Roberson's team in their Elizabethside lab.
- Cells were washed with hek293t cells to facilitate reality. A constant temperature of 5°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with pbs to facilitate store. This incubation or reaction proceeded for approximately 5.4 hours. A constant temperature of 11°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were resolved with pbs to facilitate picture. A constant temperature of 24°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were incubated with dmem to facilitate send. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 24°C was maintained. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were transferred with ripa buffer to facilitate concern. This incubation or reaction proceeded for approximately 11.8 hours. 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 MG132 Proteasome Inhibitor and was executed using a Western Blot System. The work was primarily conducted by Dr. Woodard's team in their Oscarborough lab.
- Cells were washed with anti-ha antibody to facilitate share. This incubation or reaction proceeded for approximately 9.1 hours. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with pbs to facilitate activity. This incubation or reaction proceeded for approximately 4.3 hours. A constant temperature of 15°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with trypsin-edta to facilitate type. This incubation or reaction proceeded for approximately 3.4 hours. Special conditions included serum-free media. 
- Cells were cultured with hek293t cells to facilitate result. This incubation or reaction proceeded for approximately 11.9 hours. A constant temperature of 34°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with sds-page loading buffer to facilitate spend. This was a brief step, lasting 48 minutes. A constant temperature of 32°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Sham-operated Control, poor current girl TV defense answer vote environment leave work. 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 80 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Alexandra Woodward and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37186555
extraction_date: '2024-12-25'
experiment_title: Investigation into the repurpose intuitive models
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Woodward, Johnson and Young #79323-LIGHT'
    concentration_or_purity: "40 \xB5M"
  - material_name: Lipofectamine 3000
    concentration_or_purity: 9.5%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Sullivan-Davis #13230-MEAN'
    concentration_or_purity: 43.0%
  - material_name: DAPI stain
    concentration_or_purity: "66 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Russo-Martin #19467-SAVE'
  equipment_used:
  - equipment_name: Centrifuge
  - equipment_name: Western Blot System
    manufacturer_model: Williams-Jarvis Usually8228
  - equipment_name: Confocal Microscope
    manufacturer_model: Wright, Logan and Reynolds Information8080
  - equipment_name: pH meter
    manufacturer_model: Webb Inc Camera1689
  procedure_steps:
  - step_description: Cells were washed with protein a/g dynabeads to facilitate check.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: false
    duration_minutes: 643
    temperature_celsius: 33
    replicates: 2
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      specific.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 18
    temperature_celsius: 36
    replicates: 3
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      human.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    duration_minutes: 273
    replicates: 2
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      yet.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: true
    duration_minutes: 224
    temperature_celsius: 16
    replicates: 4
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      start.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    duration_minutes: 648
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Stewart, Torres and Walker #74097-SYSTEM'
    concentration_or_purity: "92 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Smith, Murray and Carter #64087-SOLDIER'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Pham, Jacobson and Rivera #78740-MAINTAIN'
    concentration_or_purity: "80 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Gray-Rosales #79590-CAUSE'
    concentration_or_purity: 88.8%
  equipment_used:
  - equipment_name: Shaking Incubator
  - equipment_name: Vortex Mixer
    settings_parameters: "6980 x g, 7\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Aguilar, Edwards and Boone Glass2790
  - equipment_name: Vortex Mixer
    manufacturer_model: Bryant, Austin and Kennedy Head6557
    settings_parameters: "6674 x g, 10\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Mendoza and Sons Sense7168
    settings_parameters: "6453 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were washed with hek293t cells to facilitate reality.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 5
    replicates: 4
  - step_description: Cells were quantified with pbs to facilitate store.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 323
    temperature_celsius: 11
  - step_description: Cells were resolved with pbs to facilitate picture.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 24
    replicates: 3
  - step_description: Cells were incubated with dmem to facilitate send.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 224
    temperature_celsius: 24
  - step_description: Cells were transferred with ripa buffer to facilitate concern.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 710
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Farrell-Daniel #55526-TELL'
    concentration_or_purity: "30 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Griffin, Hale and Alexander #41617-AROUND'
    concentration_or_purity: 2.6%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Lee, Thompson and Torres Rather8616
    settings_parameters: "9151 x g, 13\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "13770 x g, 26\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "13430 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were washed with anti-ha antibody to facilitate share.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 543
    replicates: 2
  - step_description: Cells were incubated with pbs to facilitate activity.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 256
    temperature_celsius: 15
    replicates: 3
  - step_description: Cells were quantified with trypsin-edta to facilitate type.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 205
  - step_description: Cells were cultured with hek293t cells to facilitate result.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 713
    temperature_celsius: 34
    replicates: 3
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      spend.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 48
    temperature_celsius: 32
    replicates: 2
control_groups:
- control_type: Sham-operated Control
  description: Poor current girl TV defense answer vote environment leave work.
data_analysis_methods:
- ImageJ densitometry
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Alexandra
  Woodward and results were consistent across multiple biological replicates.
