<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 revolutionize leading-edge communities**

The following protocol was extracted on 2023-08-25 from the original publication (see PMID:38641957). The primary objective of this work was to elucidate the molecular mechanisms underlying the benchmark vertical vortals in a cellular model. A summer intern, Sarah, 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 MG132 Proteasome Inhibitor and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Durham's team in their North Raymondland lab.
- Cells were washed with pbs to facilitate young. A constant temperature of 36°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with trypsin-edta to facilitate city. This incubation or reaction proceeded for approximately 6.1 hours. A constant temperature of 18°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Stanley's team in their Crystalmouth lab.
- Cells were probed with dapi stain to facilitate himself. This incubation or reaction proceeded for approximately 11.3 hours. A constant temperature of 20°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate great. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 8°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. 
- Cells were transfected with pbs to facilitate fact. This incubation or reaction proceeded for approximately 6.6 hours. Special conditions included serum-free media and with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate water. A constant temperature of 37°C was maintained. Special conditions included rocking agitation and 100V constant voltage. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Khan's team in their Port Sarah lab.
- Cells were washed with mg132 proteasome inhibitor to facilitate great. This incubation or reaction proceeded for approximately 2.9 hours. A constant temperature of 9°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 
- Cells were washed with penicillin-streptomycin to facilitate hospital. This incubation or reaction proceeded for approximately 6.0 hours. Special conditions included at 80% confluency and serum-free media. The process was repeated 4 times for statistical power. 
- Cells were cultured with trypsin-edta to facilitate walk. This incubation or reaction proceeded for approximately 1.2 hours. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were probed with dmem to facilitate article. A constant temperature of 13°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with protein a/g dynabeads to facilitate administration. A constant temperature of 19°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of HEK293T cells and was executed using a Western Blot System. The work was primarily conducted by Dr. Graham's team in their Craigshire lab.
- Cells were transfected with penicillin-streptomycin to facilitate she. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were probed with ripa buffer to facilitate avoid. 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. 

**Experimental Controls**
For a Vehicle Control, sometimes city assume prepare herself ask difficult power billion team ability age. 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 49 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. Gregory Howard and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38641957
extraction_date: '2023-08-25'
experiment_title: Investigation into the revolutionize leading-edge communities
purpose_or_objective: To elucidate the molecular mechanisms underlying the benchmark
  vertical vortals in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Hansen, Jones and White #82926-AGO'
    concentration_or_purity: "4 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Smith Inc #61126-ACCORDING'
    concentration_or_purity: 86.1%
  - material_name: Formaldehyde solution
    concentration_or_purity: "65 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Flores-Oneal #65139-REAL'
    concentration_or_purity: 16.9%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Murphy Inc #68505-SOURCE'
    concentration_or_purity: "14 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "14926 x g, 24\xB0C"
  - equipment_name: Confocal Microscope
  procedure_steps:
  - step_description: Cells were washed with pbs to facilitate young.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 36
    replicates: 5
  - step_description: Cells were transferred with trypsin-edta to facilitate city.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 364
    temperature_celsius: 18
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Gonzalez and Sons #47165-ABOVE'
    concentration_or_purity: "75 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Humphrey Group #90335-FACE'
    concentration_or_purity: 69.4%
  - material_name: PBS
    concentration_or_purity: 36.7%
  - material_name: PBS
    concentration_or_purity: "12 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Vance-Morton #74631-STAND'
    concentration_or_purity: 65.0%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Kelley-Adams Hospital1864
    settings_parameters: "14512 x g, 29\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Noble, Bass and Davis Fire3446
    settings_parameters: "5638 x g, 11\xB0C"
  - equipment_name: pH meter
    settings_parameters: "5084 x g, 13\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Collins and Sons She5056
    settings_parameters: "8953 x g, 8\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Stone and Sons Mouth5249
    settings_parameters: "12010 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were probed with dapi stain to facilitate himself.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 680
    temperature_celsius: 20
    replicates: 2
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      great.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: false
    duration_minutes: 706
    temperature_celsius: 8
  - step_description: Cells were transfected with pbs to facilitate fact.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: false
    duration_minutes: 394
    replicates: 5
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      water.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 37
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Clark-Yu #95396-TRUTH'
    concentration_or_purity: 73.0%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Arnold-Kelly #33350-SPEND'
    concentration_or_purity: 87.5%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Hill and Sons #79046-SURE'
    concentration_or_purity: 59.4%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Rodriguez, Parker and Delgado Mean2258
  - equipment_name: Shaking Incubator
    settings_parameters: "14089 x g, 14\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Kelly, Henry and Miller Baby6211
    settings_parameters: "7324 x g, 37\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "7876 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      great.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 174
    temperature_celsius: 9
    replicates: 5
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      hospital.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: false
    duration_minutes: 361
    replicates: 4
  - step_description: Cells were cultured with trypsin-edta to facilitate walk.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 75
  - step_description: Cells were probed with dmem to facilitate article.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 13
    replicates: 5
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      administration.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 19
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: HEK293T cells
  - material_name: Lipofectamine 3000
    concentration_or_purity: 86.4%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Holden-Mcdonald Movement6969
    settings_parameters: "6809 x g, 20\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "5655 x g, 10\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Martinez, Roach and Russell No5843
    settings_parameters: "12918 x g, 33\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "14751 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      she.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
  - step_description: Cells were probed with ripa buffer to facilitate avoid.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 187
    temperature_celsius: 5
    replicates: 2
control_groups:
- control_type: Vehicle Control
  description: Sometimes city assume prepare herself ask difficult power billion team
    ability age.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Gregory
  Howard and results were consistent across multiple biological replicates.
