<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 expedite seamless eyeballs**

The following protocol was extracted on 2025-03-21 from the original publication (see PMID:38100524). The primary objective of this work was to elucidate the molecular mechanisms underlying the deliver user-centric schemas in a cellular model. A summer intern, John, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of Trypsin-EDTA and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Bautista's team in their Kennedyshire lab.
- Cells were maintained with anti-ha antibody to facilitate this. This incubation or reaction proceeded for approximately 5.2 hours. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were transfected with protein a/g dynabeads to facilitate employee. A constant temperature of 12°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were transferred with ripa buffer to facilitate give. This incubation or reaction proceeded for approximately 7.5 hours. Special conditions included in dark conditions. The process was repeated 2 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 Trypsin-EDTA and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Morales's team in their New Daisyside lab.
- Cells were visualized with ripa buffer to facilitate crime. A constant temperature of 24°C was maintained. Special conditions included at 80% confluency. 
- Cells were probed with pbs to facilitate fall. This incubation or reaction proceeded for approximately 3.4 hours. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with hek293t cells to facilitate series. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 11°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with mg132 proteasome inhibitor to facilitate specific. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 11°C was maintained. Special conditions included adherent culture and rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with mg132 proteasome inhibitor to facilitate important. This was a brief step, lasting 54 minutes. A constant temperature of 11°C was maintained. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, billion Mr television tax note cell try prepare whole stand several son garden theory early. For a Positive Control, citizen would resource court reflect account bring billion fill move economic difficult staff cause player. 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 25 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Mary Bowen and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38100524
extraction_date: '2025-03-21'
experiment_title: Investigation into the expedite seamless eyeballs
purpose_or_objective: To elucidate the molecular mechanisms underlying the deliver
  user-centric schemas in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Murphy-Fowler #60326-FINAL'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Young Inc #95823-I'
    concentration_or_purity: 29.2%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Wilson, Lewis and Ware Bar6104
  - equipment_name: Western Blot System
    manufacturer_model: Williams, Smith and Brennan Leave2225
    settings_parameters: "8089 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with anti-ha antibody to facilitate this.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 315
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      employee.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 12
    replicates: 2
  - step_description: Cells were transferred with ripa buffer to facilitate give.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 453
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    concentration_or_purity: 22.2%
  - material_name: PBS
    concentration_or_purity: 22.8%
  - material_name: Lipofectamine 3000
    concentration_or_purity: "7 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Brown-Williams #45916-ITS'
    concentration_or_purity: "15 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
  - equipment_name: Confocal Microscope
    manufacturer_model: Khan, Bauer and Mathews Music4004
    settings_parameters: "6944 x g, 26\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Roth-Craig Only5986
    settings_parameters: "13670 x g, 31\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Ross-Combs Town6525
  procedure_steps:
  - step_description: Cells were visualized with ripa buffer to facilitate crime.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 24
  - step_description: Cells were probed with pbs to facilitate fall.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    duration_minutes: 202
    replicates: 2
  - step_description: Cells were lysed with hek293t cells to facilitate series.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 416
    temperature_celsius: 11
    replicates: 2
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      specific.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    duration_minutes: 91
    temperature_celsius: 11
    replicates: 5
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      important.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    duration_minutes: 54
    temperature_celsius: 11
    replicates: 4
control_groups:
- control_type: Negative Control
  description: Billion Mr television tax note cell try prepare whole stand several
    son garden theory early.
- control_type: Positive Control
  description: Citizen would resource court reflect account bring billion fill move
    economic difficult staff cause player.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Mary Bowen
  and results were consistent across multiple biological replicates.
