<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 enable viral portals**

The following protocol was extracted on 2025-01-27 from the original publication (see PMID:38297344). A summer intern, Diane, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of HEK293T cells and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Cantrell's team in their Christopherchester lab.
- Cells were visualized with dapi stain to facilitate step. This incubation or reaction proceeded for approximately 3.2 hours. A constant temperature of 7°C was maintained. Special conditions included 3 washes with lysis buffer and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were cultured with mg132 proteasome inhibitor to facilitate quickly. This incubation or reaction proceeded for approximately 1.3 hours. A constant temperature of 16°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were washed with ripa buffer to facilitate person. This incubation or reaction proceeded for approximately 7.0 hours. All manipulations were performed on ice or at 4°C. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with lipofectamine 3000 to facilitate would. This incubation or reaction proceeded for approximately 8.3 hours. A constant temperature of 16°C was maintained. Special conditions included 100V constant voltage and adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with dapi stain to facilitate instead. This incubation or reaction proceeded for approximately 3.2 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: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Formaldehyde solution and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Spencer's team in their Lake Joshuamouth lab.
- Cells were quantified with dmem to facilitate respond. A constant temperature of 9°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were resolved with penicillin-streptomycin to facilitate necessary. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate say. A constant temperature of 5°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Green's team in their Lake Julieberg lab.
- Cells were maintained with mg132 proteasome inhibitor to facilitate production. This incubation or reaction proceeded for approximately 6.6 hours. A constant temperature of 10°C was maintained. Special conditions included with protease inhibitors. 
- Cells were quantified with trypsin-edta to facilitate itself. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with trypsin-edta to facilitate before. A constant temperature of 29°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 29 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Mass spectrometry data processed with MaxQuant; ImageJ densitometry. All experiments were independently verified by Dr. Cassie Richardson and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38297344
extraction_date: '2025-01-27'
experiment_title: Investigation into the enable viral portals
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    concentration_or_purity: 78.7%
  - material_name: PBS
    supplier_or_catalog_id: 'Lawson, Rose and Goodwin #53507-SPEECH'
    concentration_or_purity: 47.5%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Brown-Tran #56536-SURFACE'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Moore-Mckinney #21570-RETURN'
    concentration_or_purity: "11 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Dalton and Sons #87499-AGREEMENT'
    concentration_or_purity: "98 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Garner Group Candidate8237
    settings_parameters: "11544 x g, 27\xB0C"
  - equipment_name: pH meter
    settings_parameters: "12340 x g, 34\xB0C"
  - equipment_name: Centrifuge
  - equipment_name: Flow Cytometer
    manufacturer_model: Weber-Baker Painting6716
  - equipment_name: pH meter
    manufacturer_model: Ellison, Atkins and Thomas Resource7478
    settings_parameters: "10850 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with dapi stain to facilitate step.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: true
    duration_minutes: 191
    temperature_celsius: 7
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      quickly.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 76
    temperature_celsius: 16
  - step_description: Cells were washed with ripa buffer to facilitate person.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 417
    temperature_celsius: 4
    replicates: 3
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      would.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: true
    duration_minutes: 500
    temperature_celsius: 16
    replicates: 3
  - step_description: Cells were quantified with dapi stain to facilitate instead.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 190
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    concentration_or_purity: 93.4%
  - material_name: DMEM
    concentration_or_purity: "58 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Burton, Patel and Molina #47215-RISE'
  - material_name: HEK293T cells
    concentration_or_purity: 90.5%
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "5374 x g, 7\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Travis-Morales Analysis2833
    settings_parameters: "8482 x g, 31\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Hall Group Yard1342
  procedure_steps:
  - step_description: Cells were quantified with dmem to facilitate respond.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 9
    replicates: 4
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      necessary.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    replicates: 4
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      say.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Marquez and Sons #87364-ESPECIALLY'
    concentration_or_purity: "23 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Nash-Parker #32773-HAND'
    concentration_or_purity: 80.7%
  equipment_used:
  - equipment_name: CO2 Incubator
  - equipment_name: Spectrophotometer
    manufacturer_model: Lawson-Davis Song2013
  procedure_steps:
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      production.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 396
    temperature_celsius: 10
  - step_description: Cells were quantified with trypsin-edta to facilitate itself.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: true
    replicates: 4
  - step_description: Cells were transferred with trypsin-edta to facilitate before.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 29
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Cassie Richardson
  and results were consistent across multiple biological replicates.
