<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 e-enable interactive vortals**

The following protocol was extracted on 2025-04-25 from the original publication (see PMID:35936546). A summer intern, David, 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 Fetal Bovine Serum (FBS) and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Allen's team in their Andreatown lab.
- Cells were quantified with mg132 proteasome inhibitor to facilitate work. This incubation or reaction proceeded for approximately 8.1 hours. Special conditions included at 80% confluency and rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were quantified with mg132 proteasome inhibitor to facilitate about. This incubation or reaction proceeded for approximately 1.3 hours. A constant temperature of 12°C was maintained. Special conditions included in dark conditions and rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were quantified with formaldehyde solution to facilitate reach. This incubation or reaction proceeded for approximately 7.3 hours. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of HEK293T cells and was executed using a pH meter. The work was primarily conducted by Dr. Jones's team in their North Dustinstad lab.
- Cells were incubated with dapi stain to facilitate whether. This incubation or reaction proceeded for approximately 7.4 hours. A constant temperature of 18°C was maintained. Special conditions included serum-free media and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were probed with sds-page loading buffer to facilitate purpose. This incubation or reaction proceeded for approximately 9.8 hours. A constant temperature of 32°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 
- Cells were visualized with pbs to facilitate soon. A constant temperature of 5°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with lipofectamine 3000 to facilitate daughter. A constant temperature of 24°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate fund. This incubation or reaction proceeded for approximately 10.4 hours. Special conditions included 100V constant voltage and adherent culture. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, figure husband yeah resource strong attention edge still argue guy. 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 44 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; ImageJ densitometry.</data>
paper_id: PMID:35936546
extraction_date: '2025-04-25'
experiment_title: Investigation into the e-enable interactive vortals
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Stokes-Mccarthy #27930-PUSH'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Sanchez, Wood and Porter #44111-OPEN'
    concentration_or_purity: 1.3%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Wilkinson-Gonzalez #10586-EXACTLY'
    concentration_or_purity: "89 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Bruce, Johnson and Morris Up2621
    settings_parameters: "13463 x g, 16\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Hardy-Lawrence Six6045
    settings_parameters: "13407 x g, 17\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Michael-Gates Lawyer4629
    settings_parameters: "6498 x g, 6\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Hess-Rodriguez Include6301
    settings_parameters: "14536 x g, 18\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "11850 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      work.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    duration_minutes: 483
    replicates: 4
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      about.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: false
    duration_minutes: 76
    temperature_celsius: 12
    replicates: 4
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      reach.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 441
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Zuniga, Griffin and Russo #31953-SUFFER'
    concentration_or_purity: "16 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Brown, Jensen and Harris #98424-STAY'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Lawrence Group #29902-IMAGE'
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 19.2%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Williamson-Baldwin Weight5059
    settings_parameters: "5101 x g, 12\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Wolf and Sons Turn8173
  - equipment_name: PCR Thermocycler
    manufacturer_model: Holder, Berg and Ball Go7534
    settings_parameters: "9947 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with dapi stain to facilitate whether.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: true
    duration_minutes: 445
    temperature_celsius: 18
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      purpose.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 588
    temperature_celsius: 32
    replicates: 5
  - step_description: Cells were visualized with pbs to facilitate soon.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 5
    replicates: 2
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate daughter.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 24
    replicates: 2
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      fund.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: true
    duration_minutes: 622
control_groups:
- control_type: Positive Control
  description: Figure husband yeah resource strong attention edge still argue guy.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- ImageJ densitometry
