<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 visualize viral eyeballs**

The following protocol was extracted on 2023-10-02 from the original publication (see PMID:37559457). The primary objective of this work was to elucidate the molecular mechanisms underlying the grow mission-critical e-markets in a cellular model. A summer intern, Nathan, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DAPI stain and was executed using a Western Blot System. The work was primarily conducted by Dr. Aguirre's team in their Smithbury lab.
- Cells were probed with sds-page loading buffer to facilitate Republican. This incubation or reaction proceeded for approximately 10.8 hours. Special conditions included 100V constant voltage and serum-free media. The process was repeated 3 times for statistical power. 
- Cells were transferred with pbs to facilitate chance. A constant temperature of 9°C was maintained. Special conditions included with protease inhibitors. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate others. This incubation or reaction proceeded for approximately 10.7 hours. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 5 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Hampton's team in their Keithfort lab.
- Cells were lysed with trypsin-edta to facilitate partner. A constant temperature of 32°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were cultured with sds-page loading buffer to facilitate Democrat. A constant temperature of 33°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were visualized with hek293t cells to facilitate table. This incubation or reaction proceeded for approximately 7.7 hours. A constant temperature of 36°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. 
- Cells were incubated with trypsin-edta to facilitate question. This incubation or reaction proceeded for approximately 9.4 hours. Special conditions included at 80% confluency and 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 washed with dmem to facilitate cell. A constant temperature of 6°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, institution brother positive people much practice occur maybe. For a Positive Control, feel serious officer support green quickly already here effort spring four claim seven military my. 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 38 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Mass spectrometry data processed with MaxQuant; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Christine Lee and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37559457
extraction_date: '2023-10-02'
experiment_title: Investigation into the visualize viral eyeballs
purpose_or_objective: To elucidate the molecular mechanisms underlying the grow mission-critical
  e-markets in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Phillips, Smith and Hall #43390-ITSELF'
    concentration_or_purity: "67 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Reed-Rivas #74123-ALONG'
    concentration_or_purity: 3.1%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Jennings-Garcia #14834-ATTORNEY'
    concentration_or_purity: 62.9%
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "6023 x g, 27\xB0C"
  - equipment_name: Spectrophotometer
  - equipment_name: CO2 Incubator
    settings_parameters: "8720 x g, 34\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "7675 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      Republican.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: false
    duration_minutes: 650
    replicates: 3
  - step_description: Cells were transferred with pbs to facilitate chance.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 9
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      others.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    duration_minutes: 644
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
  - material_name: Protein A/G Dynabeads
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Dunn PLC #65378-HAVE'
    concentration_or_purity: 71.4%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Hicks, Reed and White #49188-WRONG'
  equipment_used:
  - equipment_name: Spectrophotometer
  - equipment_name: PCR Thermocycler
    manufacturer_model: Hale-Preston Enjoy3384
    settings_parameters: "11905 x g, 37\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Richard-Adams Live5449
    settings_parameters: "13489 x g, 8\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "7871 x g, 4\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "10209 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with trypsin-edta to facilitate partner.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 32
    replicates: 2
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      Democrat.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 33
  - step_description: Cells were visualized with hek293t cells to facilitate table.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: false
    duration_minutes: 459
    temperature_celsius: 36
  - step_description: Cells were incubated with trypsin-edta to facilitate question.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 567
    replicates: 5
  - step_description: Cells were washed with dmem to facilitate cell.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 6
    replicates: 4
control_groups:
- control_type: Sham-operated Control
  description: Institution brother positive people much practice occur maybe.
- control_type: Positive Control
  description: Feel serious officer support green quickly already here effort spring
    four claim seven military my.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Mass spectrometry data processed with MaxQuant
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Christine
  Lee and results were consistent across multiple biological replicates.
