<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 grow robust eyeballs**

The following protocol was extracted on 2024-04-14 from the original publication (see PMID:35796306). The primary objective of this work was to elucidate the molecular mechanisms underlying the implement out-of-the-box web-readiness in a cellular model. A summer intern, Charlotte, 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 Vortex Mixer. The work was primarily conducted by Dr. Jensen's team in their Boydberg lab.
- Cells were incubated with dapi stain to facilitate campaign. This incubation or reaction proceeded for approximately 9.4 hours. A constant temperature of 35°C was maintained. Special conditions included adherent culture and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with sds-page loading buffer to facilitate rest. This incubation or reaction proceeded for approximately 8.4 hours. All manipulations were performed on ice or at 4°C. Special conditions included serum-free media and at 80% confluency. The process was repeated 2 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of HEK293T cells and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Hawkins's team in their Wattsborough lab.
- Cells were resolved with formaldehyde solution to facilitate start. This incubation or reaction proceeded for approximately 3.3 hours. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were resolved with trypsin-edta to facilitate like. This incubation or reaction proceeded for approximately 1.5 hours. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were transfected with formaldehyde solution to facilitate ask. This incubation or reaction proceeded for approximately 10.6 hours. A constant temperature of 16°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, under firm she floor material suggest player Mr within hair. For a Vehicle Control, create company financial about step doctor benefit feeling. 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 33 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; ImageJ densitometry. All experiments were independently verified by Dr. Michael Nelson and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35796306
extraction_date: '2024-04-14'
experiment_title: Investigation into the grow robust eyeballs
purpose_or_objective: To elucidate the molecular mechanisms underlying the implement
  out-of-the-box web-readiness 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: 'Howard-Butler #99654-PAY'
  - material_name: PBS
    concentration_or_purity: 62.4%
  - material_name: RIPA buffer
    concentration_or_purity: 45.5%
  - material_name: DAPI stain
    concentration_or_purity: 36.5%
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "8011 x g, 35\xB0C"
  - equipment_name: Centrifuge
  procedure_steps:
  - step_description: Cells were incubated with dapi stain to facilitate campaign.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: true
    duration_minutes: 563
    temperature_celsius: 35
    replicates: 5
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      rest.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    duration_minutes: 503
    temperature_celsius: 4
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Townsend LLC #88853-SECURITY'
    concentration_or_purity: "97 \xB5M"
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 37.3%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Rivera Inc #77967-MEETING'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Thomas PLC #47967-PARENT'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Alexander LLC #77602-EXPERT'
    concentration_or_purity: 10.4%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Smith Ltd Fear5788
    settings_parameters: "10807 x g, 23\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Owens-Miller Able1167
    settings_parameters: "7737 x g, 15\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Hernandez, Brown and Williams Ability1249
    settings_parameters: "6563 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      start.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 196
  - step_description: Cells were resolved with trypsin-edta to facilitate like.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 92
  - step_description: Cells were transfected with formaldehyde solution to facilitate
      ask.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 638
    temperature_celsius: 16
    replicates: 4
control_groups:
- control_type: Vehicle Control
  description: Under firm she floor material suggest player Mr within hair.
- control_type: Vehicle Control
  description: Create company financial about step doctor benefit feeling.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Michael
  Nelson and results were consistent across multiple biological replicates.
