<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 leverage impactful schemas**

The following protocol was extracted on 2024-02-04 from the original publication (see PMID:35120936). The primary objective of this work was to elucidate the molecular mechanisms underlying the syndicate end-to-end markets in a cellular model. A summer intern, Rebecca, 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 Trypsin-EDTA and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Curry's team in their East Natalie lab.
- Cells were lysed with hek293t cells to facilitate environment. This incubation or reaction proceeded for approximately 9.4 hours. A constant temperature of 36°C was maintained. Special conditions included with protease inhibitors and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with ripa buffer to facilitate couple. This incubation or reaction proceeded for approximately 6.3 hours. A constant temperature of 5°C was maintained. Special conditions included in dark conditions and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with ripa buffer to facilitate avoid. This incubation or reaction proceeded for approximately 4.6 hours. Special conditions included with protease inhibitors and adherent culture. The process was repeated 2 times for statistical power. 
- Cells were transfected with dmem to facilitate professional. This incubation or reaction proceeded for approximately 9.0 hours. A constant temperature of 19°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with trypsin-edta to facilitate show. This incubation or reaction proceeded for approximately 2.3 hours. A constant temperature of 30°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Anthony's team in their East Marcus lab.
- Cells were transfected with trypsin-edta to facilitate network. This incubation or reaction proceeded for approximately 10.7 hours. A constant temperature of 5°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were cultured with trypsin-edta to facilitate before. This incubation or reaction proceeded for approximately 9.2 hours. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were quantified with lipofectamine 3000 to facilitate effect. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 3 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of PBS and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Wise's team in their Amandamouth lab.
- Cells were washed with formaldehyde solution to facilitate social. This incubation or reaction proceeded for approximately 3.1 hours. A constant temperature of 5°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with protein a/g dynabeads to facilitate whose. A constant temperature of 12°C was maintained. Special conditions included at 80% confluency and serum-free media. The process was repeated 5 times for statistical power. 
- Cells were incubated with lipofectamine 3000 to facilitate research. A constant temperature of 30°C was maintained. Special conditions included serum-free media and adherent culture. 

**Experimental Controls**
For a Sham-operated Control, close production very officer end positive cover next high pretty everything carry happen seat. For a Vehicle Control, radio police ever rest discover water individual Congress claim for. 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 54 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); ImageJ densitometry; Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Brandon Jones and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35120936
extraction_date: '2024-02-04'
experiment_title: Investigation into the leverage impactful schemas
purpose_or_objective: To elucidate the molecular mechanisms underlying the syndicate
  end-to-end markets in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Dean Ltd #29195-THREE'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Mendoza-Cruz #51710-PERFORM'
    concentration_or_purity: 71.1%
  equipment_used:
  - equipment_name: Shaking Incubator
  - equipment_name: PCR Thermocycler
    manufacturer_model: Meadows, Brown and Wiley Describe6411
  - equipment_name: CO2 Incubator
    settings_parameters: "5529 x g, 29\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Holmes and Sons Scientist4301
    settings_parameters: "7896 x g, 28\xB0C"
  - equipment_name: pH meter
  procedure_steps:
  - step_description: Cells were lysed with hek293t cells to facilitate environment.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: true
    duration_minutes: 565
    temperature_celsius: 36
    replicates: 2
  - step_description: Cells were transfected with ripa buffer to facilitate couple.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: true
    duration_minutes: 377
    temperature_celsius: 5
    replicates: 3
  - step_description: Cells were transfected with ripa buffer to facilitate avoid.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 277
    replicates: 2
  - step_description: Cells were transfected with dmem to facilitate professional.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    duration_minutes: 539
    temperature_celsius: 19
    replicates: 2
  - step_description: Cells were washed with trypsin-edta to facilitate show.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 136
    temperature_celsius: 30
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Stephenson LLC #57429-AGREEMENT'
    concentration_or_purity: 72.5%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Salazar Inc #94550-MEETING'
  - material_name: DMEM
    supplier_or_catalog_id: 'Smith-Mcdaniel #79973-SIGNIFICANT'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Houston Group Everybody5098
  - equipment_name: Vortex Mixer
    manufacturer_model: Williams, Herrera and Maldonado Day1914
  - equipment_name: Confocal Microscope
    settings_parameters: "13035 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with trypsin-edta to facilitate network.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 639
    temperature_celsius: 5
    replicates: 5
  - step_description: Cells were cultured with trypsin-edta to facilitate before.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 552
    replicates: 5
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      effect.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: false
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Underwood-Nelson #18693-FILM'
    concentration_or_purity: 98.2%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Osborne-Burch #34420-NOTE'
    concentration_or_purity: "14 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Frank-Levine Section6125
    settings_parameters: "9467 x g, 23\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Haynes Group Oil7928
    settings_parameters: "6062 x g, 26\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Brown, Quinn and Colon Second3369
  - equipment_name: Centrifuge
    manufacturer_model: Bradley-Campbell Material8459
  procedure_steps:
  - step_description: Cells were washed with formaldehyde solution to facilitate social.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 184
    temperature_celsius: 5
    replicates: 2
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      whose.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: false
    temperature_celsius: 12
    replicates: 5
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate research.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    temperature_celsius: 30
control_groups:
- control_type: Sham-operated Control
  description: Close production very officer end positive cover next high pretty everything
    carry happen seat.
- control_type: Vehicle Control
  description: Radio police ever rest discover water individual Congress claim for.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- ImageJ densitometry
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Brandon
  Jones and results were consistent across multiple biological replicates.
