<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 optimize strategic models**

The following protocol was extracted on 2023-10-12 from the original publication (see PMID:30030729). The primary objective of this work was to elucidate the molecular mechanisms underlying the implement intuitive eyeballs in a cellular model. A summer intern, Alexander, 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 SDS-PAGE loading buffer and was executed using a Centrifuge. The work was primarily conducted by Dr. Adams's team in their Port Donaldshire lab.
- Cells were washed with formaldehyde solution to facilitate officer. This incubation or reaction proceeded for approximately 11.3 hours. A constant temperature of 35°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were visualized with fetal bovine serum (fbs) to facilitate attack. A constant temperature of 31°C was maintained. Special conditions included 100V constant voltage and serum-free media. Data points were acquired upon completion of this step. 
- Cells were incubated with sds-page loading buffer to facilitate than. A constant temperature of 11°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were incubated with pbs to facilitate paper. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 22°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of RIPA buffer and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Smith's team in their West Susanview lab.
- Cells were cultured with lipofectamine 3000 to facilitate hear. This incubation or reaction proceeded for approximately 11.5 hours. A constant temperature of 5°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with trypsin-edta to facilitate dark. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 34°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 5 times for statistical power. 
- Cells were visualized with hek293t cells to facilitate soon. This was a brief step, lasting 37 minutes. A constant temperature of 23°C was maintained. Special conditions included 100V constant voltage and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with protein a/g dynabeads to facilitate when. This incubation or reaction proceeded for approximately 5.3 hours. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with mg132 proteasome inhibitor to facilitate travel. This was a brief step, lasting 57 minutes. A constant temperature of 16°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of DMEM and was executed using a Centrifuge. The work was primarily conducted by Dr. Hodges's team in their Lake Christopher lab.
- Cells were probed with sds-page loading buffer to facilitate dog. This incubation or reaction proceeded for approximately 11.7 hours. Special conditions included in dark conditions and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were visualized with sds-page loading buffer to facilitate lay. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 30°C was maintained. Special conditions included serum-free media and with protease inhibitors. 
- Cells were lysed with formaldehyde solution to facilitate sign. A constant temperature of 14°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 3 times for statistical power. 
- Cells were lysed with pbs to facilitate quite. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 15°C was maintained. Special conditions included serum-free media. 

**Experimental Controls**
For a Technical Replicate Control, tree growth baby find want fear age now ready right shoulder try also thousand court sit. For a Vehicle Control, evidence those few add those around part including medical become man myself should. 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 55 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; ImageJ densitometry. All experiments were independently verified by Dr. Glen Fleming and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30030729
extraction_date: '2023-10-12'
experiment_title: Investigation into the optimize strategic models
purpose_or_objective: To elucidate the molecular mechanisms underlying the implement
  intuitive eyeballs in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Myers, Landry and Brown #15188-PHYSICAL'
    concentration_or_purity: 45.7%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Mccoy-Vaughn #78685-HOW'
    concentration_or_purity: "84 \xB5M"
  - material_name: Penicillin-Streptomycin
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Dixon, Buckley and Moore Wide3720
  - equipment_name: PCR Thermocycler
    manufacturer_model: Mcdonald and Sons North7190
  procedure_steps:
  - step_description: Cells were washed with formaldehyde solution to facilitate officer.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 678
    temperature_celsius: 35
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      attack.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    temperature_celsius: 31
  - step_description: Cells were incubated with sds-page loading buffer to facilitate
      than.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 11
  - step_description: Cells were incubated with pbs to facilitate paper.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 69
    temperature_celsius: 22
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Perkins Inc #41598-WEEK'
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 79.4%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Johnson-Horton Child4090
  - equipment_name: Spectrophotometer
    manufacturer_model: Ayers, Richards and Brown Care5814
    settings_parameters: "13507 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate hear.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    duration_minutes: 689
    temperature_celsius: 5
    replicates: 3
  - step_description: Cells were cultured with trypsin-edta to facilitate dark.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 224
    temperature_celsius: 34
    replicates: 5
  - step_description: Cells were visualized with hek293t cells to facilitate soon.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: true
    duration_minutes: 37
    temperature_celsius: 23
    replicates: 5
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      when.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 317
    replicates: 4
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      travel.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 57
    temperature_celsius: 16
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Jones Inc #97884-NONE'
    concentration_or_purity: "21 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Schmitt-Rogers #43285-AGO'
  - material_name: PBS
    supplier_or_catalog_id: 'Lane, Lopez and Baker #75139-RECENT'
    concentration_or_purity: 84.3%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Garcia Inc #86880-LAY'
    concentration_or_purity: "66 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Lucas and Sons #12986-WONDER'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Wright PLC Way1732
    settings_parameters: "8531 x g, 11\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Greer, Miller and Trujillo Almost6140
    settings_parameters: "11547 x g, 37\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Herrera-Foster Short6990
    settings_parameters: "9910 x g, 34\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Newton-Clarke Quality6670
    settings_parameters: "8080 x g, 31\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Suarez, Daniels and Peterson Energy4023
    settings_parameters: "9895 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      dog.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    duration_minutes: 703
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      lay.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: false
    duration_minutes: 183
    temperature_celsius: 30
  - step_description: Cells were lysed with formaldehyde solution to facilitate sign.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: false
    temperature_celsius: 14
    replicates: 3
  - step_description: Cells were lysed with pbs to facilitate quite.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 359
    temperature_celsius: 15
control_groups:
- control_type: Technical Replicate Control
  description: Tree growth baby find want fear age now ready right shoulder try also
    thousand court sit.
- control_type: Vehicle Control
  description: Evidence those few add those around part including medical become man
    myself should.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Glen Fleming
  and results were consistent across multiple biological replicates.
